Contacts of the helix formed by residues 80 - 108 (chain A) in PDB entry 3SPJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 1.3 113.2 - - + +
81A TYR* 1.3 60.5 + - + +
82A MET 3.0 6.1 - - - -
83A LEU* 2.8 40.5 + - + +
84A LEU* 3.2 15.5 + - + +
183A LYS* 6.0 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 3.4 21.0 - - + +
79A TRP* 3.6 2.3 - - + +
80A ARG* 1.3 78.9 - - + +
82A MET* 1.3 57.3 + - - +
83A LEU 3.3 0.2 - - - -
84A LEU* 3.6 20.4 + - + +
85A LEU* 2.9 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A CYS* 3.3 32.1 - - + +
77A ILE* 3.8 12.6 - - + -
78A ARG* 3.8 18.2 - - + +
79A TRP 5.0 3.4 - - - +
80A ARG 3.0 1.3 - - - -
81A TYR* 1.3 78.9 - - - +
83A LEU* 1.3 63.1 + - + +
85A LEU* 3.0 19.1 + - + +
86A PHE* 2.8 46.1 + - + -
179A ALA* 3.5 39.7 - - + +
180A ILE* 5.7 2.9 - - + -
183A LYS* 4.6 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP 5.3 1.8 - - - +
80A ARG* 2.8 31.1 + - + +
82A MET* 1.3 85.6 - - + +
84A LEU* 1.3 58.4 + - + +
86A PHE* 3.6 8.1 + - + +
87A SER* 3.0 28.2 + - - -
176A MET* 5.7 5.2 - - + -
180A ILE* 4.7 21.8 - - + -
183A LYS* 6.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 3.2 10.7 + - + +
81A TYR* 4.0 22.9 - - + +
83A LEU* 1.3 75.3 - - + +
85A LEU* 1.3 63.1 + - - +
87A SER* 2.7 23.8 + - - +
88A LEU* 3.1 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 6.5 0.4 - - + -
81A TYR 2.9 16.9 + - - +
82A MET* 3.0 30.9 + - + +
84A LEU* 1.3 78.4 - - - +
86A PHE* 1.3 61.4 + - + +
88A LEU* 3.0 13.9 + - + +
89A ALA* 2.8 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MET* 2.8 41.5 + - + +
83A LEU* 4.1 9.6 - - + +
85A LEU* 1.3 76.0 - - + +
87A SER* 1.3 63.1 + - - +
88A LEU 2.9 1.8 - - - -
89A ALA* 2.8 29.1 + - + +
90A PHE* 2.9 20.6 + + + +
172A ILE* 4.1 12.6 - - + -
175A PHE* 3.8 8.5 - - + -
176A MET* 3.3 62.6 - - + -
179A ALA* 3.4 28.9 - - + -
180A ILE* 5.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU 3.0 12.1 + - - -
84A LEU* 2.7 40.5 + - - +
86A PHE* 1.3 76.0 - - - +
88A LEU* 1.3 61.0 + - - +
90A PHE* 3.7 11.3 + - - +
91A LEU* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU 3.3 11.2 - - - +
85A LEU* 3.0 17.4 + - + +
86A PHE 2.9 0.8 - - - -
87A SER* 1.3 81.9 + - - +
89A ALA* 1.3 63.5 + - - +
91A LEU* 3.3 18.5 + - + +
92A VAL* 2.9 41.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU 2.8 12.7 + - - +
86A PHE* 2.8 24.3 + - + +
88A LEU* 1.3 77.6 - - - +
90A PHE* 1.3 63.8 + - - +
92A VAL* 3.5 6.4 + - - +
93A SER* 3.2 20.6 + - - -
172A ILE* 4.8 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 2.9 17.9 + + + -
87A SER* 3.8 12.8 - - - +
89A ALA* 1.3 74.2 - - - +
91A LEU* 1.3 68.2 + - - +
93A SER* 2.6 21.6 + - - -
94A TRP* 2.8 44.1 + + + -
141A GLN* 4.5 11.2 - - - -
169A GLY 5.3 1.6 - - - -
172A ILE* 3.5 30.7 - - + -
173A ASP* 4.3 14.8 - - + -
176A MET* 3.8 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER 3.2 15.6 + - - +
88A LEU* 3.3 20.4 + - + +
90A PHE* 1.3 77.3 - - - +
92A VAL* 1.3 59.6 + - + +
94A TRP* 3.8 13.2 - - + +
95A LEU* 2.9 55.9 + - + +
134A PHE* 4.5 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 2.9 35.9 + - + +
89A ALA* 3.8 6.5 - - - +
91A LEU* 1.3 79.3 - - + +
93A SER* 1.3 57.9 + - - +
95A LEU* 4.0 5.4 - - - +
96A LEU* 3.0 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ALA 3.2 10.7 + - - -
90A PHE* 2.6 21.4 + - - -
92A VAL* 1.3 78.5 - - - +
94A TRP* 1.3 64.3 + - - +
96A LEU* 3.5 5.1 + - - +
97A PHE* 3.1 34.7 + - - +
141A GLN* 2.7 33.2 + - - -
168A VAL* 4.7 6.3 - - - -
172A ILE* 3.8 15.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE* 2.8 45.6 + + + +
91A LEU* 3.8 15.7 - - + +
93A SER* 1.3 77.8 + - - +
95A LEU* 1.3 61.4 + - - +
98A GLY* 3.1 9.2 + - - -
134A PHE* 4.2 20.8 - + + -
137A SER* 2.9 25.0 + - - +
138A ILE* 3.9 34.3 - - + -
141A GLN* 3.3 47.5 - - + +
142A THR* 3.3 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 2.9 39.2 + - + +
92A VAL* 4.0 4.7 - - - +
94A TRP* 1.3 73.8 - - - +
96A LEU* 1.3 64.8 + - - +
98A GLY* 3.5 0.7 + - - -
99A LEU* 3.1 24.4 + - - +
130A PHE* 4.4 23.9 - - + -
134A PHE* 3.2 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 3.0 26.4 + - + +
93A SER* 3.8 6.3 - - - +
95A LEU* 1.3 78.6 - - - +
97A PHE* 1.3 77.0 + - + +
99A LEU* 3.2 11.1 + - + +
100A ILE* 3.1 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A SER* 3.1 23.8 + - - +
96A LEU* 1.3 88.1 - - + +
98A GLY* 1.3 60.1 + - - +
100A ILE* 3.3 8.9 + - + +
101A PHE* 2.9 36.5 + + + -
137A SER* 3.3 3.4 - - - +
141A GLN* 4.0 2.9 - - - -
161A MET* 3.9 29.2 - - + -
164A VAL* 3.7 23.6 - - + -
165A GLN* 3.1 65.3 - - + +
168A VAL* 4.1 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TRP 3.1 14.1 + - - -
95A LEU* 3.9 1.8 - - - -
96A LEU 3.3 0.2 - - - -
97A PHE* 1.3 76.6 - - - +
99A LEU* 1.3 57.0 + - - +
101A PHE* 3.5 1.2 + - - -
102A TRP* 2.8 30.0 + - - +
130A PHE* 4.1 6.5 - - - -
133A ALA* 3.4 20.0 - - - +
134A PHE* 4.4 3.6 - - - -
137A SER* 3.4 17.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU 3.1 14.3 + - - +
96A LEU* 3.2 13.0 + - + +
98A GLY* 1.3 73.0 - - - +
100A ILE* 1.3 58.4 + - + +
102A TRP* 3.6 16.6 - - + +
103A LEU* 2.7 45.2 + - + +
130A PHE* 3.3 30.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 3.1 23.9 + - + +
97A PHE* 3.5 13.0 - - + +
98A GLY 3.3 0.2 - - - -
99A LEU* 1.3 76.8 - - + +
101A PHE* 1.3 60.1 + - - +
103A LEU* 3.1 18.7 + - + +
104A ILE* 2.9 44.2 + - + +
161A MET* 3.6 40.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PHE* 2.9 29.2 + + + +
98A GLY* 3.8 5.2 - - - +
100A ILE* 1.3 76.8 - - - +
102A TRP* 1.3 57.4 + - - +
104A ILE* 3.4 14.4 + - + +
105A ALA* 2.9 29.5 + - - +
124A VAL* 4.2 16.1 - - + +
127A VAL* 5.0 6.3 - - + +
133A ALA* 4.8 7.9 - - + +
136A PHE* 3.5 39.9 - + + -
137A SER* 4.5 6.3 - - - -
158A ALA* 3.9 11.9 - - + -
161A MET* 3.9 23.8 - - + -
162A VAL* 3.8 24.7 - - + -
165A GLN* 3.3 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLY 2.8 18.5 + - - +
99A LEU* 3.6 20.2 - - + +
100A ILE 3.1 0.2 - - - -
101A PHE* 1.3 75.0 - - - +
103A LEU* 1.3 86.1 + - + +
105A ALA* 3.9 3.9 - - - +
106A LEU* 2.9 56.6 + - + +
111A LEU* 4.0 21.3 - - + +
127A VAL* 5.1 0.2 - - + -
129A GLY* 3.4 30.2 - - - -
130A PHE* 3.4 25.6 - + + +
133A ALA* 3.5 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 2.7 32.1 + - + +
100A ILE* 3.4 20.9 - - + +
102A TRP* 1.3 95.3 - - + +
104A ILE* 1.3 57.5 + - + +
106A LEU* 3.4 4.8 + - + +
107A ILE* 2.9 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ILE* 2.9 39.2 + - + +
101A PHE* 3.7 14.6 - - + +
102A TRP 3.2 0.2 - - - -
103A LEU* 1.3 75.7 - - + +
105A ALA* 1.3 61.1 + - - +
107A ILE* 3.3 5.6 + - - +
108A HIS* 2.9 29.4 + - + +
123A CYS* 3.8 28.5 - - + -
155A CYS* 4.8 3.8 - - + -
157A LEU* 4.1 33.9 - - + -
158A ALA* 4.3 20.6 - - + +
161A MET* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE 2.9 17.9 + - - +
102A TRP 4.0 2.9 - - - +
104A ILE* 1.3 76.0 - - - +
106A LEU* 1.3 60.8 + - - +
109A GLY 3.2 1.7 + - - -
110A ASP* 2.8 52.9 + - + +
111A LEU* 3.7 19.2 + - + -
123A CYS* 5.4 0.9 - - + -
124A VAL* 5.6 3.1 - - + +
127A VAL* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TRP* 2.9 50.0 + - + +
103A LEU* 3.5 7.6 - - + +
105A ALA* 1.3 77.9 - - - +
107A ILE* 1.3 76.6 + - + +
109A GLY* 3.2 13.2 + - - -
111A LEU* 3.5 30.1 - - + +
112A GLU* 5.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 2.9 40.5 + - + +
104A ILE* 3.9 5.2 - - - +
106A LEU* 1.3 90.8 - - + +
108A HIS* 1.3 64.7 + - + +
109A GLY* 3.0 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 2.9 17.7 + - + +
107A ILE* 1.3 79.3 - - + +
109A GLY* 1.3 60.0 + - - +
110A ASP* 2.8 24.9 + - - +
120A PHE* 3.3 26.8 - + - -
121A LYS 3.2 27.1 - - - -
123A CYS* 3.4 18.1 - - - -
154A GLU* 4.0 17.1 + - + +
155A CYS* 3.8 14.8 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il