Contacts of the helix formed by residues 88 - 109 (chain A) in PDB entry 4IXU
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 ASN 88 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN* 3.2 58.5 + - + +
37A GLN 4.9 2.3 - - - +
79A ASP* 3.1 28.5 + - - +
81A LEU* 4.8 0.6 - - - +
87A VAL* 1.3 91.3 - - - +
89A PRO* 1.4 70.8 - - - +
91A SER* 4.1 0.4 + - - -
92A VAL* 2.9 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ASP* 3.3 11.4 - - - +
80A ASP 3.6 6.5 - - - +
82A TYR* 3.8 24.9 - - + -
86A ILE* 3.5 13.0 - - + +
87A VAL 2.9 10.0 - - - +
88A ASN* 1.4 90.6 - - - +
90A ARG* 1.3 68.5 + - - +
93A GLY* 2.8 25.1 + - - -
159A LEU* 3.8 13.9 - - + -
178A LEU* 4.5 9.0 - - + -
179A PRO* 3.5 22.6 - - + +
181A PHE* 3.2 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.6 31.1 - - + +
77A PRO 5.2 0.7 - - - -
78A LYS 4.4 6.1 + - - -
79A ASP* 2.9 29.8 + - - +
80A ASP* 2.9 35.6 + - - +
81A LEU 4.6 5.3 + - - -
82A TYR* 5.7 1.0 - - - +
89A PRO* 1.3 81.5 - - - +
91A SER* 1.3 58.1 + - - +
94A LEU* 2.9 32.4 + - - +
179A PRO* 3.6 45.7 - - + +
180A GLY* 4.3 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN* 3.2 33.5 + - - -
74A THR 5.1 4.0 - - - +
75A PRO* 5.5 1.7 - - - +
76A VAL* 4.0 21.0 + - - +
79A ASP* 2.6 35.1 + - - +
88A ASN* 3.9 2.9 + - - -
90A ARG* 1.3 74.5 - - - +
92A VAL* 1.3 57.9 + - - +
94A LEU* 4.2 0.9 - - - +
95A ALA* 3.0 32.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
33A PHE* 4.5 4.7 - - + -
35A GLN* 3.5 38.1 - - + +
36A GLY* 3.8 4.7 - - - +
88A ASN 2.9 20.8 + - - +
91A SER* 1.3 73.8 - - - +
93A GLY* 1.3 66.6 + - - +
95A ALA* 4.0 4.5 - - - +
96A ASN* 3.0 47.8 + - - +
121A SER* 3.6 19.1 - - - +
124A ILE* 4.8 1.1 - - + -
159A LEU* 3.7 24.2 - - + -
181A PHE* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO 2.8 21.2 + - - -
90A ARG 3.8 0.4 - - - -
91A SER 3.3 0.2 - - - -
92A VAL* 1.3 76.3 - - - +
94A LEU* 1.3 56.6 + - - +
96A ASN* 3.4 3.1 + - - +
97A GLN 3.0 22.2 + - - -
180A GLY 3.4 22.0 - - - -
181A PHE* 3.6 13.2 - - - -
183A TRP* 3.1 14.8 + - - -
184A ILE* 5.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A THR* 3.5 40.8 - - + +
75A PRO 4.5 0.7 - - - +
76A VAL* 3.8 15.9 - - + -
90A ARG 2.9 18.9 + - - +
91A SER 4.2 1.8 - - - +
93A GLY* 1.3 73.2 - - - +
95A ALA* 1.3 67.2 + - - +
97A GLN* 3.1 22.8 + - + +
98A GLU* 2.9 44.9 + - + +
180A GLY* 4.1 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.4 26.0 - - + -
73A PHE* 3.5 39.5 - - + -
74A THR 5.2 0.8 + - - +
91A SER 3.0 19.9 + - - +
92A VAL* 4.0 0.4 - - - +
94A LEU* 1.3 76.3 - - - +
96A ASN* 1.3 59.2 + - - +
98A GLU* 3.3 1.9 + - - -
99A LEU* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 3.4 9.8 - - - -
92A VAL* 3.0 39.3 + - - +
93A GLY* 3.7 2.0 - - - +
95A ALA* 1.3 74.7 - - - +
97A GLN* 1.3 59.4 + - - +
99A LEU* 4.2 1.6 - - - +
100A ALA* 2.8 32.1 + - - +
121A SER 2.9 18.2 + - - -
122A LEU* 3.2 19.2 - - - +
124A ILE* 3.7 10.5 - - + +
125A GLY* 2.8 31.6 + - - +
181A PHE* 5.5 0.2 - - - -
183A TRP* 3.5 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY 3.0 10.1 + - - +
94A LEU* 3.1 27.9 + - + +
96A ASN* 1.3 76.8 - - - +
98A GLU* 1.3 63.5 + - + +
100A ALA* 3.4 3.3 + - - +
101A GLU* 3.2 23.4 + - - +
132A ARG* 5.0 2.4 + - - +
180A GLY 5.3 0.2 - - - +
183A TRP* 3.3 58.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 5.4 0.7 - - - -
72A SER 4.4 1.9 - - - +
73A PHE* 3.4 20.3 - - + +
74A THR* 2.4 49.4 + - - -
94A LEU* 2.9 32.9 + - + +
95A ALA* 3.7 3.2 - - - +
97A GLN* 1.3 74.2 - - + +
99A LEU* 1.3 66.7 + - - +
101A GLU* 3.2 20.4 + - - +
102A VAL* 3.3 13.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
29A ILE* 4.0 14.1 - - + -
31A ALA* 4.1 10.1 - - + -
33A PHE* 3.9 10.8 - - + -
71A LEU* 3.9 23.6 - - + -
73A PHE* 4.1 8.6 - - + -
95A ALA 2.9 16.8 + - - +
96A ASN* 3.7 7.0 - - - +
97A GLN 3.3 0.2 - - - -
98A GLU* 1.3 74.4 - - - +
100A ALA* 1.3 65.1 + - - +
102A VAL* 3.1 2.8 + - - -
103A VAL* 2.9 35.3 + - + +
115A THR* 4.3 6.5 - - + -
122A LEU* 3.6 38.8 - - + +
125A GLY* 4.6 0.2 - - - -
126A THR* 3.7 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ASN 2.8 20.3 + - - +
97A GLN 3.7 6.1 - - - +
99A LEU* 1.3 74.2 - - - +
101A GLU* 1.3 57.5 + - - +
103A VAL* 4.5 0.4 - - - -
104A SER* 2.9 33.4 + - - -
125A GLY 3.2 22.9 + - - +
129A GLY* 3.3 14.0 - - - +
132A ARG* 3.8 20.8 + - - +
183A TRP* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLN* 3.2 11.4 + - - +
98A GLU* 3.2 13.2 + - - +
99A LEU 3.1 0.2 - - - -
100A ALA* 1.3 79.1 - - - +
102A VAL* 1.3 62.7 + - + +
104A SER* 3.8 4.0 - - - -
105A ARG* 3.1 24.6 + - - +
132A ARG* 3.6 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.6 22.7 - - + -
68A PHE* 3.7 30.6 - - + -
71A LEU* 3.9 28.9 - - + -
98A GLU 3.6 13.0 - - - +
99A LEU 3.1 6.8 + - - +
101A GLU* 1.3 75.4 - - + +
103A VAL* 1.3 60.0 + - - +
105A ARG* 3.3 6.4 + - - +
106A ALA* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.9 16.4 - - + -
99A LEU* 2.9 29.7 + - + +
100A ALA* 3.9 3.8 - - - +
102A VAL* 1.3 77.0 - - - +
104A SER* 1.3 63.6 + - - +
106A ALA* 3.2 1.9 + - - +
107A VAL* 2.9 29.2 + - + +
113A CYS* 4.1 21.3 - - + -
115A THR* 4.1 5.8 - - - +
126A THR* 3.5 24.9 - - + +
129A GLY* 4.2 3.6 - - - -
130A HIS* 3.5 29.2 - - + +
291A ALA* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ALA 2.9 19.1 + - - -
101A GLU* 3.8 5.4 - - - -
103A VAL* 1.3 76.9 - - - +
105A ARG* 1.3 57.5 + - - +
107A VAL* 3.5 2.8 + - - +
108A SER* 2.9 34.1 + - - -
129A GLY 3.3 17.6 + - - -
132A ARG* 3.4 35.2 - - - +
133A HIS* 4.4 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 5.5 9.6 - - + -
101A GLU* 3.1 16.9 + - + +
102A VAL* 3.6 6.7 - - - +
103A VAL 3.2 0.2 - - - -
104A SER* 1.3 80.6 - - - +
106A ALA* 1.3 60.7 + - - +
108A SER* 2.7 23.4 + - - -
109A ASP* 3.0 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 3.8 28.5 - - + -
29A ILE* 5.0 0.7 - - + -
68A PHE* 4.0 17.0 - - + -
102A VAL 3.0 16.9 + - - +
103A VAL 3.2 3.6 + - - +
105A ARG* 1.3 76.5 - - - +
107A VAL* 1.3 63.1 + - - +
109A ASP* 3.2 8.3 + - - -
110A GLY 3.3 0.2 + - - -
111A TYR* 3.0 32.1 + - + +
113A CYS* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 2.9 26.0 + - + +
104A SER* 4.0 3.6 - - - +
106A ALA* 1.3 75.7 - - - +
108A SER* 1.3 60.2 + - - +
110A GLY* 3.0 20.4 + - - -
111A TYR 3.5 17.0 - - - +
113A CYS* 4.0 17.5 - - + -
130A HIS* 4.1 22.0 - - + +
133A HIS* 3.7 17.9 + - + -
134A CYS* 3.7 30.5 - - - -
290A SER* 4.5 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER* 2.9 17.5 + - - -
105A ARG* 2.7 28.1 + - - -
107A VAL* 1.3 79.3 - - - +
109A ASP* 1.3 63.5 + - - +
110A GLY* 3.2 1.7 + - - -
133A HIS* 3.5 35.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LYS* 5.5 5.7 - - - -
68A PHE* 5.9 1.0 - - - -
105A ARG* 3.0 47.8 + - - +
106A ALA* 3.2 6.6 + - - +
107A VAL 3.2 0.4 - - - -
108A SER* 1.3 80.6 + - - +
110A GLY* 1.3 58.7 + - - +
111A TYR* 3.5 25.2 + - + -
----------------------------------------------------------
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