Contacts of the helix formed by residues 72 - 93 (chain A) in PDB entry 1CD9
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 LEU 72 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 4.7 3.6 - - - +
9A SER* 3.2 26.0 - - - +
10A LEU* 3.4 36.6 - - + -
68A GLN* 3.3 12.3 - - + +
69A ALA 3.4 17.5 - - - +
70A LEU 4.1 0.2 + - - -
71A GLN* 1.3 74.7 - - - +
73A ALA* 1.3 66.3 + - - +
74A GLY 3.1 2.7 - - - -
75A CYS* 3.0 23.0 + - + -
76A LEU* 3.1 14.9 + - + +
127A MET* 3.7 26.7 - - + -
172A LEU* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 4.3 0.2 + - - -
71A GLN 3.9 0.8 - - - -
72A LEU* 1.3 78.7 - - - +
74A GLY* 1.3 59.1 + - - +
76A LEU* 3.8 1.2 + - - +
77A SER* 3.0 27.9 + - - -
122A MET* 4.6 3.3 - - - +
127A MET* 3.7 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 4.4 11.4 - - - -
68A GLN* 4.1 6.8 + - - -
72A LEU 3.1 1.2 - - - -
73A ALA* 1.3 80.4 - - - +
75A CYS* 1.3 56.2 + - - +
77A SER* 3.2 7.8 - - - -
78A GLN* 3.0 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 3.5 14.2 + - - +
65A CYS* 2.1 53.1 - - - -
68A GLN* 3.9 6.9 + - + +
72A LEU* 3.0 19.3 + - + +
74A GLY* 1.3 71.8 - - - +
76A LEU* 1.3 70.6 + - + +
78A GLN* 3.2 4.8 + - - +
79A LEU* 3.0 24.1 + - - +
168A VAL* 3.8 14.4 - - - -
169A LEU* 6.4 0.4 - - - -
172A LEU* 5.0 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.8 41.7 - - + -
14A PHE* 4.3 20.0 - - + -
72A LEU* 3.1 16.9 + - + +
73A ALA* 4.3 2.5 - - - +
75A CYS* 1.3 80.8 - - - +
77A SER* 1.3 57.8 + - - +
79A LEU* 3.1 23.1 + - + +
80A HIS* 2.8 31.4 + - - +
118A ILE* 4.0 11.1 - - + +
121A GLN* 5.3 0.9 - - + -
122A MET* 3.8 31.9 - - + +
127A MET* 4.5 8.1 - - + -
169A LEU* 5.1 6.7 - - + -
172A LEU* 5.4 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA 3.0 22.3 + - - -
74A GLY* 3.2 9.9 - - - -
75A CYS 3.2 0.2 - - - -
76A LEU* 1.3 77.3 - - - +
78A GLN* 1.3 56.9 + - - +
80A HIS* 3.5 4.0 + - - +
81A SER* 3.0 30.4 + - - -
122A MET* 3.7 15.6 - - - -
129A PRO* 4.6 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO* 3.5 44.6 + - + +
62A LEU* 3.2 9.5 - - + -
63A SER* 3.1 12.2 + - - +
64A SER* 2.8 42.6 + - - +
65A CYS* 4.9 0.7 - - - -
74A GLY 3.0 17.8 + - - +
75A CYS* 3.7 6.3 - - - +
77A SER* 1.3 70.9 - - - +
79A LEU* 1.3 66.6 + - - +
80A HIS 3.0 1.1 - - - -
81A SER* 3.1 6.6 + - - +
82A GLY* 2.8 23.0 + - - -
161A PHE* 4.4 1.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A CYS* 5.8 0.4 - - - -
62A LEU* 4.4 8.8 - - + +
75A CYS* 3.0 17.2 + - - +
76A LEU* 3.4 20.2 - - + +
78A GLN* 1.3 76.9 - - - +
80A HIS* 1.3 64.2 + - - +
82A GLY* 3.7 1.0 - - - -
83A LEU* 3.0 45.1 + - + +
114A PHE* 4.7 6.5 - - + -
118A ILE* 3.8 19.1 - - + -
161A PHE* 3.7 12.3 - - + -
162A LEU* 5.8 0.2 - - + -
165A SER* 3.5 31.4 - - - +
168A VAL* 6.0 2.5 - - + -
169A LEU* 4.0 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU 2.8 13.5 + - - +
77A SER 3.6 9.0 + - - +
79A LEU* 1.3 78.8 - - - +
81A SER* 1.3 60.0 + - - +
83A LEU* 3.3 4.9 + - - +
84A PHE* 2.8 46.0 + + + +
115A ALA* 3.2 35.2 + - + +
116A THR* 5.6 0.2 - - - -
118A ILE* 4.1 16.0 - - + +
119A TRP* 3.9 33.3 - + + +
122A MET* 4.2 6.5 - - + -
133A PRO* 3.3 38.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER* 3.0 19.7 + - - -
78A GLN* 3.1 8.9 + - - -
80A HIS* 1.3 80.1 + - - +
82A GLY* 1.3 58.2 + - - +
84A PHE* 3.2 7.7 + - - +
85A LEU* 2.9 28.8 + - - +
133A PRO* 4.2 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA* 3.6 28.0 - - - -
78A GLN 2.8 11.8 + - - -
81A SER* 1.3 74.2 - - - +
83A LEU* 1.3 59.7 + - - +
85A LEU* 2.8 20.6 + - - +
86A TYR* 3.0 21.8 + - - -
161A PHE* 3.7 11.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
25A ILE* 4.9 2.2 - - + -
79A LEU* 3.0 29.3 + - + +
80A HIS* 3.9 0.9 - - - +
82A GLY* 1.3 74.6 - - - +
84A PHE* 1.3 57.5 + - - +
86A TYR* 3.5 2.4 + - - -
87A GLN* 3.0 28.6 + - - +
111A VAL* 3.4 24.8 - - + +
114A PHE* 3.4 46.0 - - + -
115A ALA* 3.8 20.6 - - + +
118A ILE* 4.0 10.8 - - + -
158A LEU* 4.7 5.6 - - + -
161A PHE* 3.9 18.5 - - + -
162A LEU* 4.0 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A HIS* 2.8 34.4 + + + +
81A SER 3.3 5.8 - - - +
83A LEU* 1.3 79.1 - - - +
85A LEU* 1.3 61.5 + - - +
87A GLN* 3.2 31.3 - - - +
88A GLY 3.2 15.6 + - - -
115A ALA* 4.2 2.4 - - + +
133A PRO* 3.3 48.2 - - + -
135A GLN* 3.6 48.0 + - + -
136A GLY 5.3 0.9 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
58A PRO* 3.7 33.9 - - + +
59A TRP 3.9 18.2 - - - +
60A ALA* 4.0 15.3 - - + +
81A SER 2.9 12.7 + - - +
82A GLY* 2.8 9.1 + - - +
84A PHE* 1.3 72.9 - - - +
86A TYR* 1.3 64.3 + - + +
87A GLN 3.0 1.3 - - - -
88A GLY* 2.8 17.2 + - - -
89A LEU* 2.9 21.4 + - + +
135A GLN* 4.2 5.2 - - - +
136A GLY* 4.1 16.6 - - - +
138A MET* 3.5 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO 4.7 4.9 - - - -
59A TRP* 4.5 2.4 - - - -
60A ALA* 3.7 33.4 + - + +
82A GLY 3.0 24.2 + - - +
83A LEU* 4.1 3.8 - - - +
85A LEU* 1.3 77.5 - - + +
87A GLN* 1.3 65.5 + - - +
89A LEU* 3.9 25.1 - - + +
90A LEU* 3.1 33.7 + - + +
111A VAL* 4.6 4.0 - - + -
154A VAL* 4.2 12.1 - - + -
157A HIS* 3.5 41.9 + - + +
158A LEU* 3.7 35.9 - - + -
161A PHE* 3.8 27.9 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU 3.0 12.6 + - - +
84A PHE* 3.2 35.6 - - - +
85A LEU 3.0 0.2 - - - -
86A TYR* 1.3 79.6 - - - +
88A GLY* 1.3 60.0 + - - +
90A LEU* 4.8 1.3 - - - -
91A GLN* 3.3 28.5 + - - +
108A GLN* 3.1 37.6 + - - +
111A VAL* 4.2 10.0 - - + +
112A ALA* 3.6 36.1 + - + +
115A ALA* 4.2 7.5 - - - +
116A THR* 5.5 1.0 + - - -
135A GLN* 5.3 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE 3.2 4.0 + - - -
85A LEU 2.8 8.7 + - - -
87A GLN* 1.3 79.5 - - - +
89A LEU* 1.3 63.4 + - - -
91A GLN* 3.0 11.6 + - - +
92A ALA* 2.9 22.7 + - - +
135A GLN* 4.0 16.4 - - - +
138A MET* 3.4 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 4.5 4.5 - - + -
58A PRO* 3.5 26.7 - - + +
85A LEU* 2.9 25.5 + - + +
86A TYR* 3.9 29.8 - - + +
88A GLY* 1.3 71.2 - - - +
90A LEU* 1.3 63.8 + - - +
92A ALA* 3.0 15.8 + - - +
93A LEU* 3.3 15.8 + - - +
138A MET* 3.5 9.6 - - + -
139A PRO* 3.3 41.5 - - + -
141A PHE* 4.1 6.6 - - + -
154A VAL* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.8 3.4 - - + -
86A TYR 3.1 27.8 + - - +
87A GLN* 4.1 1.6 - - - +
89A LEU* 1.3 75.7 - - - +
91A GLN* 1.3 62.1 + - - +
93A LEU* 3.5 22.4 + - + +
94A GLU 4.4 0.9 + - - -
95A GLY 4.9 1.0 + - - -
104A LEU* 3.8 31.9 - - + +
107A LEU* 3.9 32.3 - - + -
108A GLN* 4.0 30.1 - - + +
111A VAL* 4.1 14.4 - - + -
151A GLY 6.0 0.2 - - - +
154A VAL* 3.6 25.4 - - + -
155A ALA 5.3 2.0 - - - +
158A LEU* 4.6 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLN* 3.3 38.8 + - - +
88A GLY* 3.0 13.8 + - - +
90A LEU* 1.3 78.8 - - - +
92A ALA* 1.3 64.2 + - - +
94A GLU* 3.1 19.4 + - - +
95A GLY 4.9 0.3 + - - -
108A GLN* 3.5 25.8 + - + +
135A GLN* 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLY 2.9 11.9 + - - +
89A LEU* 3.3 13.0 - - - +
91A GLN* 1.3 72.4 - - - +
93A LEU* 1.3 55.9 + - - +
94A GLU* 2.9 31.7 + - - +
138A MET* 4.8 12.3 - - + -
139A PRO 4.2 11.0 - - - +
140A ALA 4.7 1.2 - - - +
141A PHE* 3.5 30.3 - - + +
147A ARG* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 5.8 0.2 - - + -
89A LEU 3.3 10.0 + - - +
90A LEU* 3.6 23.3 - - + +
91A GLN 3.1 1.6 - - - -
92A ALA* 1.3 75.5 - - - +
94A GLU* 1.3 55.6 + - - +
95A GLY 3.1 0.7 - - - -
96A ILE* 2.6 48.5 + - + -
104A LEU* 4.2 15.5 - - + -
141A PHE* 3.9 26.9 - - + -
147A ARG* 3.4 36.7 - - - +
150A GLY 3.9 6.7 - - - +
151A GLY* 3.6 29.4 - - - +
154A VAL* 4.8 4.9 - - + -
----------------------------------------------------------
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