Contacts of the helix formed by residues 84 - 101 (chain A) in PDB entry 2COD
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 GLU 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ASN* 4.5 17.1 + - - +
83A LYS* 1.3 69.2 - - + +
85A GLU* 1.3 77.1 + - + +
86A GLU 3.0 1.6 - - - -
87A ARG* 2.9 17.4 + - - +
88A ASN* 2.6 28.1 + - - +
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Residues in contact with GLU 85 (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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10A LYS* 5.7 1.2 + - - -
83A LYS* 4.2 30.1 + - + +
84A GLU* 1.3 85.3 - - + +
86A GLU* 1.3 61.8 + - + +
88A ASN* 3.7 7.9 + - - +
89A ASP* 2.6 50.1 + - - +
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Residues in contact with GLU 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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10A LYS* 3.6 33.7 + - - +
11A SER 5.0 2.3 - - - +
12A GLY* 4.9 12.1 - - - -
13A TRP 5.5 2.6 - - - +
14A LEU* 5.8 2.2 - - - +
81A VAL* 3.9 10.1 - - + +
82A GLU* 4.0 19.9 + - - +
83A LYS* 3.4 26.9 + - + +
84A GLU 3.0 0.8 - - - -
85A GLU* 1.3 85.5 - - + +
87A ARG* 1.3 67.7 + - - +
89A ASP* 2.9 1.3 + - - +
90A TRP* 2.8 38.8 + - - -
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Residues in contact with ARG 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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62A VAL* 3.3 36.1 - - - +
63A GLN 4.2 2.8 + - - -
64A GLY 4.2 4.9 + - - -
65A ASP* 5.7 0.2 - - - +
66A ASN* 3.9 26.9 + - - +
67A LYS 3.0 36.4 + - - +
68A PHE* 4.2 10.0 - - + -
81A VAL* 3.4 23.0 - - + +
83A LYS 3.3 3.3 + - - +
84A GLU* 2.9 11.4 + - - +
86A GLU* 1.3 80.3 - - - +
88A ASN* 1.3 79.3 + - - +
90A TRP* 3.9 2.4 - - - +
91A ILE* 3.3 29.8 + - - +
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Residues in contact with ASN 88 (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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62A VAL* 5.6 0.5 - - - +
84A GLU* 2.6 35.0 + - - +
85A GLU* 3.8 6.9 - - - +
86A GLU 3.2 0.2 - - - -
87A ARG* 1.3 94.2 + - - +
89A ASP* 1.3 68.6 + - - +
91A ILE* 3.5 8.1 + - - +
92A SER* 3.0 23.7 + - - -
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Residues in contact with ASP 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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10A LYS* 3.5 26.8 + - + +
85A GLU* 2.6 39.7 + - - +
86A GLU 2.9 5.1 + - - +
88A ASN* 1.3 76.9 - - - +
90A TRP* 1.3 65.0 + - - +
92A SER* 3.0 8.9 + - - -
93A ILE* 2.9 29.7 + - + +
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Residues in contact with TRP 90 (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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10A LYS* 3.0 64.7 - - + +
11A SER* 4.0 6.7 - - - -
12A GLY* 4.3 6.0 - - - -
14A LEU* 3.8 23.4 - - + +
30A VAL* 3.7 24.9 - - + -
32A PHE* 4.0 17.5 - + + -
37A ILE* 5.3 5.2 - - + -
68A PHE* 4.4 19.7 - + + -
81A VAL* 3.7 22.2 - - + +
86A GLU* 2.8 36.7 + - + +
87A ARG 3.9 4.3 - - - +
89A ASP* 1.3 70.6 - - - +
91A ILE* 1.3 65.3 + - - +
93A ILE* 2.9 23.1 + - + +
94A LEU* 3.0 32.7 + - + +
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Residues in contact with ILE 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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60A VAL* 4.1 22.6 - - + +
61A ARG* 4.3 9.4 - - - +
62A VAL* 3.5 32.3 - - + -
68A PHE* 4.2 18.6 - - + -
87A ARG* 3.3 19.0 + - - +
88A ASN* 3.6 9.0 - - - +
89A ASP 3.3 0.8 - - - -
90A TRP* 1.3 75.7 - - - +
92A SER* 1.3 65.4 + - - +
94A LEU* 3.0 14.4 + - - +
95A LEU* 2.9 41.2 + - + +
108A GLN* 6.1 0.9 - - + +
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Residues in contact with SER 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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88A ASN 3.0 9.9 + - - -
89A ASP* 3.0 11.9 + - - -
91A ILE* 1.3 79.5 - - - +
93A ILE* 1.3 55.5 + - - +
95A LEU* 3.1 9.6 + - - +
96A ASN* 2.7 42.4 + - - +
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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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7A GLY 3.5 16.8 - - - +
8A LYS* 3.4 18.7 - - - +
9A VAL 3.9 6.3 - - - +
10A LYS* 3.1 46.9 - - + -
32A PHE* 3.2 35.0 - - + -
89A ASP* 2.9 23.7 + - + +
90A TRP* 3.2 9.2 - - + +
92A SER* 1.3 75.0 - - - +
94A LEU* 1.3 62.8 + - + +
96A ASN* 3.4 6.5 + - - +
97A ALA* 3.1 21.8 + - - +
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Residues in contact with LEU 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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32A PHE* 4.9 15.3 - - + -
37A ILE* 3.9 30.5 - - + -
54A LEU* 4.4 1.7 - - + +
57A ILE* 4.2 12.8 - - + -
60A VAL* 4.2 28.5 - - + -
68A PHE* 5.0 6.7 - - + -
70A VAL* 4.4 14.6 - - + -
90A TRP* 3.0 30.0 + - + +
91A ILE* 3.0 14.5 + - - +
93A ILE* 1.3 73.9 - - + +
95A LEU* 1.3 60.9 + - - +
97A ALA* 2.9 8.6 + - - +
98A LEU* 2.8 36.9 + - + +
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Residues in contact with LEU 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 THR* 6.3 0.4 - - - -
60A VAL* 4.8 16.8 - - + +
91A ILE* 2.9 38.3 + - + +
92A SER* 3.6 9.9 - - - +
94A LEU* 1.3 73.2 - - - +
96A ASN* 1.3 62.4 + - - +
98A LEU* 3.5 19.9 - - + +
99A LYS* 3.1 27.4 + - - +
106A GLN 5.2 8.5 - - - +
108A GLN* 3.7 42.2 - - + +
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Residues in contact with ASN 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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3A SER 5.1 5.8 + - - +
4A GLY* 5.0 5.2 - - - -
5A SER 5.0 11.3 + - - +
7A GLY 5.8 1.2 + - - -
8A LYS* 4.4 30.6 - - + +
92A SER* 2.7 25.4 + - - +
93A ILE* 3.6 7.2 - - - +
95A LEU* 1.3 74.5 - - - +
97A ALA* 1.3 59.4 + - - +
99A LYS* 3.3 38.9 + - - +
100A SER* 3.6 6.9 + - - -
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Residues in contact with ALA 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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8A LYS* 6.2 3.1 - - + +
32A PHE* 3.8 25.6 - - + -
34A GLY* 4.2 9.9 - - - +
54A LEU* 3.3 27.9 - - + +
93A ILE 3.1 13.0 + - - +
94A LEU 2.9 8.5 + - - +
96A ASN* 1.3 74.8 - - - +
98A LEU* 1.3 61.7 - - - +
99A LYS 3.5 0.2 - - - -
100A SER* 4.0 8.0 + - - -
101A GLN* 3.5 10.0 + - - +
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Residues in contact with LEU 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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54A LEU* 3.6 18.8 - - + +
57A ILE* 3.5 42.6 - - + +
58A SER 5.2 5.4 - - - +
59A THR* 5.5 0.9 - - - -
60A VAL* 4.3 9.9 - - + -
94A LEU 2.8 22.9 + - - +
95A LEU* 3.5 18.6 - - + +
96A ASN 3.2 0.2 - - - -
97A ALA* 1.3 79.0 - - - +
99A LYS* 1.3 60.8 + - - +
100A SER 3.2 0.2 - - - -
101A GLN* 3.0 30.4 + - - +
102A SER* 2.9 29.6 + - - -
105A SER* 5.5 3.1 - - - +
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Residues in contact with LYS 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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3A SER* 5.5 14.7 + - - +
95A LEU 3.1 10.6 + - - +
96A ASN* 3.3 36.5 + - - +
98A LEU* 1.3 74.4 - - - +
100A SER* 1.3 70.6 + - - +
102A SER 2.7 26.8 - - - +
103A LEU* 3.5 6.9 + - - +
105A SER* 4.8 8.3 - - - +
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Residues in contact with SER 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 ASN 3.6 12.0 + - - -
97A ALA* 4.0 8.1 - - - -
98A LEU 3.2 0.4 - - - -
99A LYS* 1.3 87.3 - - - +
101A GLN* 1.3 59.6 + - - +
103A LEU* 3.9 14.8 - - - +
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Residues in contact with GLN 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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54A LEU* 3.1 32.9 + - + +
55A SER* 3.7 24.9 + - - +
57A ILE 4.9 0.6 + - - -
97A ALA 3.5 11.8 + - - +
98A LEU* 3.0 44.3 + - - +
100A SER* 1.3 80.4 - - - +
102A SER* 1.3 63.2 - - - +
103A LEU* 4.1 4.2 + - - +
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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