Contacts of the helix formed by residues 85 - 103 (chain A) in PDB entry 3O2Q
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 SER 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ASP* 2.7 31.3 + - - -
51A LYS* 5.6 0.9 - - - -
83A ASP* 3.0 15.7 + - - +
84A LYS* 1.3 79.3 - - - +
86A ILE* 1.3 63.1 + - - +
87A GLU 3.2 3.6 + - - -
88A VAL* 3.1 21.3 + - - +
89A ARG* 3.1 26.5 + - - +
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS 4.3 5.4 - - - +
85A SER* 1.3 68.9 + - - +
87A GLU* 1.3 78.0 + - + +
89A ARG* 3.2 34.0 + - - +
90A LYS* 2.9 40.4 + - + +
122A ASN* 3.5 39.3 - - + +
124A ASN* 4.3 8.7 - - + +
125A VAL* 3.8 7.1 - - + +
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Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP* 3.5 21.5 - - + +
52A ILE* 3.3 23.5 - - + +
85A SER* 3.2 0.8 + - - -
86A ILE* 1.3 96.9 - - + +
88A VAL* 1.3 61.2 + - - +
90A LYS* 3.2 30.9 + - - +
91A PHE* 2.8 29.5 + - - +
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Residues in contact with VAL 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASP* 4.0 7.2 - - - +
51A LYS* 3.8 24.9 - - + -
52A ILE* 4.1 9.9 - - + -
55A LEU* 4.7 8.1 - - + -
80A PHE* 3.7 26.2 - - + +
83A ASP* 3.4 32.5 - - + +
85A SER* 3.1 28.9 + - - +
87A GLU* 1.3 77.3 - - - +
89A ARG* 1.3 62.5 + - - +
91A PHE* 3.1 6.9 + - - +
92A VAL* 3.0 21.7 + - + +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A PHE 4.4 2.0 - - - +
81A GLN 3.1 29.8 - - - +
82A ALA* 5.0 0.4 - - - +
83A ASP 2.8 36.7 + - - +
84A LYS* 3.5 20.0 + - - +
85A SER 3.1 5.7 + - - +
86A ILE* 3.2 33.1 - - - +
87A GLU 3.3 0.2 - - - -
88A VAL* 1.3 76.4 - - - +
90A LYS* 1.3 61.2 + - - +
92A VAL* 3.1 17.9 + - - +
93A ILE* 3.2 20.4 + - - +
117A LEU* 4.3 11.6 - - + +
120A ASP* 2.8 41.6 + - - -
121A GLU* 4.4 13.7 + - - +
122A ASN* 4.0 3.4 - - - +
125A VAL* 4.0 8.1 - - + +
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Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ILE* 2.9 33.0 + - + +
87A GLU* 3.3 31.8 + - - +
89A ARG* 1.3 71.5 - - - +
91A PHE* 1.3 65.9 + - - +
93A ILE* 3.2 3.7 + - - +
94A GLY* 3.1 17.3 + - - -
124A ASN* 4.2 23.0 - - + +
125A VAL* 4.3 7.6 - - - -
128A LYS* 3.5 46.8 - - + -
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Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ILE* 3.9 22.7 - - + -
55A LEU* 3.4 46.9 - - + -
56A LYS* 3.7 33.4 - - + -
59A GLN* 3.3 30.7 - - + -
77A ILE* 3.9 25.8 - - + -
87A GLU 2.8 17.4 + - - +
88A VAL* 3.1 10.7 + - - +
90A LYS* 1.3 72.7 - - - +
92A VAL* 1.3 69.8 + - + +
94A GLY* 3.2 3.1 + - - +
95A PHE* 3.0 24.4 + + + +
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ILE* 3.9 13.0 - - + +
78A ILE* 4.3 17.0 - - + -
80A PHE* 3.8 12.8 - - + +
81A GLN* 3.8 41.3 - - + +
88A VAL 3.0 17.5 + - - +
89A ARG 3.1 8.4 + - - +
91A PHE* 1.3 86.6 - - + +
93A ILE* 1.3 56.6 + - - +
95A PHE* 3.1 7.1 + - + +
96A ILE* 2.9 42.3 + - + +
117A LEU* 4.4 4.7 - - + -
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ARG 3.2 11.6 + - - +
90A LYS* 3.2 6.0 + - - +
92A VAL* 1.3 74.6 - - - +
94A GLY* 1.3 62.4 + - - +
96A ILE* 3.1 11.1 + - - +
97A GLU* 3.0 21.0 + - - +
114A LEU* 3.9 6.7 - - + -
117A LEU* 3.8 21.8 - - + -
125A VAL* 3.4 43.1 - - + +
128A LYS* 3.8 13.7 - - + -
129A ALA* 3.7 23.3 - - + +
132A THR* 3.3 33.5 + - + +
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Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLN* 4.6 2.9 - - - -
90A LYS 3.1 13.4 + - - -
91A PHE* 3.6 3.8 - - - -
93A ILE* 1.3 77.5 - - - +
95A PHE* 1.3 60.4 + - - +
97A GLU* 3.3 10.5 + - - +
98A GLU* 3.1 28.5 + - - +
128A LYS* 4.0 16.9 - - - +
132A THR* 4.8 0.7 - - - -
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Residues in contact with PHE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLN* 3.6 36.9 - - + +
62A ILE* 4.0 23.8 - - + -
63A ILE* 3.8 18.2 - - + -
70A LEU* 4.1 13.7 - - + -
74A LEU* 3.8 23.1 - - + -
77A ILE* 3.9 39.3 - - + -
78A ILE* 4.2 13.5 - - + -
91A PHE* 3.0 18.7 + + + +
92A VAL* 3.1 10.7 + - - +
94A GLY* 1.3 72.9 - - - +
96A ILE* 1.3 64.8 + - - +
98A GLU* 3.2 1.4 + - - +
99A ALA* 2.8 33.7 + - + +
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 4.0 19.7 - - + -
92A VAL* 2.9 31.0 + - + +
93A ILE* 3.4 10.3 - - - +
95A PHE* 1.3 78.7 - - - +
97A GLU* 1.3 63.9 + - - +
99A ALA* 3.7 3.8 - - - +
100A CYS* 3.0 38.8 + - - -
107A LEU* 5.7 0.7 - - + -
110A LEU* 4.3 18.6 - - + +
113A ASN* 4.3 19.1 - - + -
114A LEU* 4.1 28.7 - - + +
117A LEU* 4.3 16.8 - - + -
136A LEU* 4.6 4.7 - - + -
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE 3.0 11.3 + - - +
94A GLY* 3.4 11.4 - - - +
95A PHE 3.3 0.2 - - - -
96A ILE* 1.3 76.5 - - - +
98A GLU* 1.3 75.4 + - - +
100A CYS* 3.3 1.6 + - - +
101A LYS* 2.9 49.3 + - - +
128A LYS* 5.0 6.1 + - - -
131A LEU 4.6 1.0 - - - +
132A THR* 2.8 38.3 + - + +
135A GLN* 3.4 30.3 - - + +
136A LEU* 4.0 15.1 - - + +
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLN* 3.6 18.2 - - - +
63A ILE* 3.7 24.8 - - + +
94A GLY 3.1 17.1 + - - +
95A PHE 3.2 0.9 + - - +
97A GLU* 1.3 98.1 - - - +
99A ALA* 1.3 63.5 + - - +
101A LYS* 3.3 20.0 + - - +
102A ARG* 2.9 23.2 + - - +
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 3.6 15.6 - - + +
70A LEU* 4.0 16.3 - - + +
74A LEU* 4.8 0.4 - - + -
95A PHE* 2.8 36.5 + - + +
96A ILE* 3.7 5.6 - - - +
98A GLU* 1.3 73.2 - - - +
100A CYS* 1.3 55.7 + - - +
102A ARG* 3.2 4.9 + - - +
103A ASP* 2.9 26.9 + - - +
106A LEU* 3.8 14.9 - - + +
110A LEU* 4.6 7.9 - - + -
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Residues in contact with CYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ILE* 3.0 31.3 + - - +
99A ALA* 1.3 73.0 - - - +
101A LYS* 1.3 65.8 + - - +
103A ASP 3.8 7.2 - - - -
104A ILE* 3.0 40.7 + - + +
106A LEU* 4.3 4.5 - - - -
107A LEU* 3.9 42.2 - - + -
110A LEU* 4.5 7.9 - - - -
136A LEU* 3.8 21.3 - - + -
139A VAL* 4.5 1.8 - - - +
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Residues in contact with LYS 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 2.9 49.0 + - + +
98A GLU* 3.3 22.2 + - - +
100A CYS* 1.3 78.8 - - - +
102A ARG* 1.3 62.7 + - - +
104A ILE 4.9 0.3 + - - -
135A GLN* 4.3 22.0 + - - -
136A LEU* 4.6 7.9 - - + -
139A VAL* 4.9 21.7 - - + +
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Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 2.7 32.0 + - + +
64A ASN* 2.7 32.3 + - - +
67A PRO* 3.7 24.3 - - + +
70A LEU* 4.0 18.8 - - + -
98A GLU 2.9 12.7 + - - +
99A ALA 3.2 7.4 + - - +
101A LYS* 1.3 80.4 + - - +
103A ASP* 1.3 59.6 + - + +
104A ILE 4.2 0.4 - - - -
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Residues in contact with ASP 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 4.7 2.5 - - + -
71A ASP* 4.6 7.3 - - - +
99A ALA 2.9 8.5 + - - +
100A CYS* 3.3 3.9 - - - +
102A ARG* 1.3 85.7 - - + +
104A ILE* 1.3 64.0 + - - +
105A GLU* 3.1 29.6 - - - +
106A LEU* 3.0 45.6 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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