Contacts of the helix formed by residues 84 - 104 (chain B) in PDB entry 5GOW
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 THR 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LYS* 3.1 13.3 + - - -
81B ASN* 3.2 2.8 + - - -
82B GLU 4.8 0.2 - - - -
83B SER* 1.3 87.5 - - - +
85B ALA* 1.3 55.2 + - - +
86B VAL 3.2 2.9 - - - -
87B LYS* 2.9 30.1 + - + +
88B GLU* 2.6 64.5 + - - +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.5 16.6 - - + +
79B PHE* 3.5 36.9 - - + +
81B ASN* 2.7 27.3 + - - +
82B GLU* 4.2 5.2 + - - +
83B SER 3.8 0.6 - - - -
84B THR* 1.3 70.0 - - - +
86B VAL* 1.3 53.8 + - - +
88B GLU* 3.1 10.4 + - - +
89B ARG* 2.7 35.9 + - - +
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 3.3 27.8 - - + +
63B ILE* 3.3 30.0 - - + +
82B GLU 5.6 0.2 + - - -
84B THR 3.1 1.0 + - - -
85B ALA* 1.3 77.6 - - - +
87B LYS* 1.3 72.2 + - + +
89B ARG* 3.3 16.3 + - - +
90B ASP* 3.0 35.0 + - - +
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Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B SER 2.7 25.3 + - - -
84B THR* 2.9 31.6 + - + +
86B VAL* 1.3 83.7 - - + +
88B GLU* 1.3 55.7 + - + +
90B ASP* 3.3 9.2 + - - +
91B ALA* 2.7 35.9 + - - +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 6.3 0.7 - - + -
11B ILE 5.2 2.5 - - - +
12B VAL* 3.0 15.7 - - + +
13B LYS* 2.6 49.0 + - - +
79B PHE* 3.4 17.9 - - + -
81B ASN* 3.5 8.8 - - - +
84B THR* 2.6 52.4 + - - +
85B ALA* 3.1 8.0 + - - +
87B LYS* 1.3 70.5 - - - +
89B ARG* 1.3 55.9 + - - +
91B ALA* 3.1 5.5 + - - +
92B VAL* 2.8 39.1 + - - +
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 3.3 28.7 - - + +
56B SER 3.2 17.9 + - - -
57B PRO* 3.9 3.6 - - - +
58B GLU* 2.7 36.7 + - - -
63B ILE* 3.3 21.5 - - + +
64B GLN 3.3 28.7 - - - +
65B LEU* 3.3 17.2 - - + +
79B PHE* 3.5 14.7 - - + -
85B ALA 2.7 20.9 + - - +
86B VAL* 3.3 17.2 - - - +
88B GLU* 1.3 72.0 - - - +
90B ASP* 1.3 82.8 + - - +
92B VAL* 3.8 0.2 - - - +
93B LYS* 2.8 30.7 + - - +
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ILE* 4.7 2.9 - - - +
86B VAL* 3.0 11.1 + - - +
87B LYS* 3.4 11.9 - - - +
89B ARG* 1.3 114.1 + - - +
91B ALA* 1.3 52.4 + - - +
93B LYS* 2.7 31.8 + - - +
94B ASP* 2.6 43.2 + - - +
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.7 26.3 - - + +
87B LYS 2.7 19.9 + - - +
88B GLU* 3.8 6.1 - - - +
90B ASP* 1.3 69.8 - - - +
92B VAL* 1.3 62.1 + - - +
94B ASP* 3.6 6.9 - - - +
95B LEU* 2.8 33.6 + - - +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.4 22.7 - - + -
12B VAL* 3.6 13.9 - - + -
24B LEU* 3.7 11.7 - - + -
26B LEU* 3.4 18.9 - - + +
31B ILE* 4.8 2.2 - - + -
65B LEU* 3.3 24.5 - - + -
77B PHE* 6.1 0.2 - - + -
79B PHE* 3.4 17.9 - - + -
88B GLU 2.8 29.5 + - - +
89B ARG 3.8 3.8 - - - +
91B ALA* 1.3 72.0 - - - +
93B LYS* 1.3 57.7 + - - +
95B LEU 3.8 0.2 - - - -
96B LEU* 2.8 42.4 + - + +
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASN* 5.0 9.2 - - + +
53B GLN* 3.0 17.8 - - + +
55B ILE* 3.7 30.3 - - + -
65B LEU* 3.9 9.4 - - + +
89B ARG 2.8 19.8 + - - +
90B ASP* 2.7 41.2 + - - +
92B VAL* 1.3 77.0 - - - +
94B ASP* 1.3 85.4 + - - +
96B LEU 3.1 0.7 + - - -
97B GLN* 2.6 66.6 + - - +
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP* 2.6 20.9 + - - +
91B ALA* 3.6 7.8 - - - +
93B LYS* 1.3 103.7 + - - +
95B LEU* 1.3 58.1 + - - +
97B GLN* 3.2 6.4 + - - +
98B GLN* 2.9 40.8 + - + +
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.1 23.1 - - + -
10B LEU* 3.6 32.1 - - + -
26B LEU* 3.9 15.3 - - + -
91B ALA 2.8 21.0 + - - +
92B VAL 4.0 2.5 - - - +
94B ASP* 1.3 73.7 - - - +
96B LEU* 1.3 52.3 + - - +
98B GLN* 3.1 11.8 - - + +
99B LEU* 2.6 63.8 + - + +
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.2 6.3 - - + -
31B ILE* 4.5 6.7 - - + -
47B TYR* 3.3 39.9 - - + +
53B GLN* 3.2 25.6 - - + +
65B LEU* 3.8 5.8 - - + -
67B LEU* 3.7 29.4 - - + -
92B VAL* 2.8 43.0 + - + +
95B LEU* 1.3 73.7 - - - +
97B GLN* 1.3 57.4 + - - +
98B GLN 2.9 4.5 - - - -
99B LEU* 4.2 1.8 - - - +
100B LEU* 2.5 47.0 + - + +
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASN* 2.8 47.9 + - - +
407A ASP* 4.1 8.7 - - - +
53B GLN* 3.1 19.5 - - - +
93B LYS* 2.6 55.3 + - - +
94B ASP* 3.7 7.0 + - - +
96B LEU* 1.3 72.3 - - - +
98B GLN* 1.3 60.3 + - + +
101B PRO* 3.1 22.8 - - - +
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Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ASP* 2.9 25.1 + - + +
95B LEU* 3.1 18.8 - - + +
97B GLN* 1.3 85.9 + - - +
99B LEU* 1.3 62.2 + - + +
101B PRO* 3.9 3.6 - - - +
102B LYS* 2.6 49.7 + - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 4.5 9.2 - - + -
26B LEU* 5.6 0.4 - - + -
27B MET 4.1 4.0 - - - +
28B ALA* 3.1 25.8 - - - +
47B TYR* 3.4 35.7 - - + +
95B LEU* 2.6 51.0 + - + +
96B LEU* 4.0 1.8 - - - +
98B GLN* 1.3 76.1 - - + +
100B LEU* 1.3 66.8 + - - +
102B LYS* 3.0 20.8 + - - +
103B PHE* 3.1 30.3 - - + -
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ASP* 3.7 10.5 - - - +
47B TYR* 3.3 34.4 - - + +
50B ILE* 3.3 46.2 - - + -
52B CYS* 4.5 2.5 - - - +
53B GLN* 3.6 28.9 - - + +
96B LEU* 2.5 33.1 + - + +
99B LEU* 1.3 71.0 - - - +
101B PRO* 1.4 60.5 - - + +
103B PHE* 2.9 6.8 + - - +
104B LYS* 2.8 42.7 + - - +
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Residues in contact with PRO 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ASP* 4.5 4.7 - - - +
410A ASP* 5.8 0.2 - - - +
96B LEU 3.6 0.4 - - - +
97B GLN* 3.1 28.3 - - - +
98B GLN 3.9 5.8 - - - +
99B LEU 3.7 0.9 - - - -
100B LEU* 1.4 95.9 - - + +
102B LYS* 1.3 61.6 + - + +
103B PHE 3.2 0.6 + - - -
104B LYS* 3.6 30.5 - - + +
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLN* 2.6 50.6 + - - +
99B LEU* 3.0 19.3 + - - +
100B LEU 3.0 0.4 + - - -
101B PRO* 1.3 81.1 - - + +
103B PHE* 1.3 74.8 + - + +
104B LYS 4.9 0.2 - - - -
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Residues in contact with PHE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ALA* 3.3 27.8 - - + -
29B GLU* 4.0 26.7 - - + -
46B MET* 5.7 4.9 - - + -
47B TYR* 3.7 28.7 - + + -
48B ALA* 3.6 22.0 - - + +
99B LEU* 3.1 33.6 + - + -
100B LEU 2.9 1.6 + - - -
102B LYS* 1.3 91.6 - - + +
104B LYS* 1.3 61.6 + - - +
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ASP* 2.6 32.2 + - - +
410A ASP* 2.7 34.0 + - - +
47B TYR 3.5 12.6 - - - +
48B ALA* 4.0 12.8 - - - +
50B ILE 3.1 22.4 - - - +
51B LYS 2.7 17.9 + - - +
70B HIS* 4.6 2.5 - - + -
100B LEU* 2.8 26.6 + - + +
101B PRO* 3.6 36.6 - - + +
102B LYS 4.9 0.3 - - - -
103B PHE* 1.3 79.5 - - - +
105B ARG* 1.3 64.2 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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