Contacts of the helix formed by residues 82 - 102 (chain B) in PDB entry 3V9M
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 PRO 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LYS* 1.3 105.0 - - + +
83B GLY* 1.3 70.1 + - - +
85B LYS* 3.8 1.9 + - - +
86B SER* 3.5 12.6 + - - +
201B SO4 3.5 9.6 + - - -
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO* 1.3 77.7 - - - +
84B CYS* 1.3 68.7 + - - -
85B LYS 3.0 0.9 + - - -
86B SER* 3.1 3.2 + - - -
87B PHE* 2.9 23.8 + - - +
201B SO4 3.8 9.9 - - - -
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Residues in contact with CYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LYS 4.4 4.9 - - - -
59B GLY 4.1 4.3 - - - -
60B CYS* 2.0 63.2 - - + -
65B THR* 3.8 12.1 - - + +
83B GLY* 1.3 70.7 - - - -
85B LYS* 1.3 55.9 + - - +
87B PHE* 4.3 2.5 - - - -
88B VAL* 2.8 34.7 + - - +
201B SO4 2.8 27.8 + - - +
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Residues in contact with LYS 85 (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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65B THR* 3.6 16.2 - - + -
66B LEU* 3.4 29.0 + - - +
67B TYR* 3.5 6.4 - - + +
80B SER* 3.7 22.2 - - - +
81B LYS* 3.4 35.8 - - + +
82B PRO 4.0 4.0 - - - +
84B CYS* 1.3 75.2 - - - +
86B SER* 1.3 57.1 + - - +
89B CYS* 3.0 32.4 + - - +
201B SO4 2.9 28.4 + - - +
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B CYS* 5.0 3.8 - - - +
80B SER* 2.5 28.1 + - - -
81B LYS 2.5 19.8 + - - -
82B PRO* 3.6 9.5 - - - +
83B GLY 3.1 7.7 + - - -
85B LYS* 1.3 74.1 - - - +
87B PHE* 1.3 63.2 + - - +
89B CYS* 3.9 3.0 - - - +
90B ALA* 3.0 24.1 + - - +
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Residues in contact with PHE 87 (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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51B CYS* 3.4 19.5 - - - -
54B GLN* 3.8 21.3 - - + -
55B ALA* 3.4 39.7 - - + -
58B LYS* 3.5 29.8 - - + -
60B CYS* 5.1 2.5 - - - -
83B GLY 2.9 17.1 + - - +
84B CYS* 3.8 7.2 - - - +
86B SER* 1.3 76.1 - - - +
88B VAL* 1.3 63.2 + - - +
90B ALA* 3.2 9.5 + - + +
91B CYS* 3.1 26.2 + - - -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B TYR* 4.2 9.2 - - + -
55B ALA* 4.0 16.6 - - + -
60B CYS* 4.2 6.3 - - + -
62B PRO* 3.5 43.5 - - + +
65B THR* 3.6 23.6 - - + +
67B TYR* 4.1 13.0 - - + -
84B CYS 2.8 23.6 + - - +
87B PHE* 1.3 70.0 - - + +
89B CYS* 1.3 65.5 + - - +
91B CYS* 3.1 7.6 + - - +
92B ASP* 3.1 24.1 + - - +
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Residues in contact with CYS 89 (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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8B MET* 3.6 18.1 - - - +
67B TYR* 3.5 32.2 - - + -
68B SER 4.1 2.9 - - - -
69B TRP* 4.0 3.1 - - - -
78B CYS* 2.0 60.2 - - + -
80B SER* 4.9 1.1 - - - -
85B LYS 3.0 20.9 + - - +
86B SER* 3.9 2.7 - - - +
88B VAL* 1.3 76.2 - - - +
90B ALA* 1.3 56.0 + - - +
92B ASP* 3.3 1.2 + - - -
93B ALA 2.9 26.5 + - - -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B CYS* 5.1 0.4 - - - -
78B CYS* 3.7 7.5 - - - -
86B SER 3.0 14.3 + - - +
87B PHE* 3.4 12.1 - - + +
89B CYS* 1.3 75.3 - - - +
91B CYS* 1.3 65.7 + - - +
93B ALA* 4.1 2.1 - - - +
94B ALA* 3.0 26.7 + - - +
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Residues in contact with CYS 91 (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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48B HIS* 3.5 10.9 - - + -
51B CYS* 2.0 67.8 - - + +
52B TYR* 4.0 18.8 - - + -
55B ALA* 4.9 0.7 - - - -
87B PHE* 3.1 28.1 + - - -
88B VAL* 3.1 10.3 + - - +
90B ALA* 1.3 75.8 - - - +
92B ASP* 1.3 59.1 + - - +
94B ALA* 3.5 5.0 + - - +
95B ALA* 3.1 22.2 + - - +
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Residues in contact with ASP 92 (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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1B ASN 4.0 3.3 - - - +
5B PHE* 3.3 34.9 - - + +
8B MET* 3.6 6.5 - - - -
48B HIS* 2.9 13.7 + - - -
52B TYR* 2.7 31.2 + - - -
67B TYR* 2.7 36.1 + - - +
88B VAL* 3.1 13.4 + - - +
89B CYS 3.8 1.6 - - - +
91B CYS* 1.3 78.5 - - - +
93B ALA* 1.3 60.6 + - - +
95B ALA 3.3 0.3 + - - -
96B ALA* 2.8 28.8 + - - +
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Residues in contact with ALA 93 (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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8B MET* 3.3 15.9 - - - -
76B PRO* 3.7 27.5 - - + +
78B CYS* 4.1 11.9 - - - -
89B CYS 2.9 20.5 + - - +
90B ALA* 4.1 3.1 - - - +
92B ASP* 1.3 73.6 - - - +
94B ALA* 1.3 63.7 + - - +
96B ALA* 3.3 2.4 + - - +
97B LYS* 3.0 34.5 + - - +
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Residues in contact with ALA 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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47B VAL* 6.2 3.8 - - + -
90B ALA 3.0 19.3 + - - +
91B CYS* 3.7 4.9 - - - +
93B ALA* 1.3 76.9 - - - +
95B ALA* 1.3 61.8 + - - +
97B LYS* 3.3 13.1 + - - +
98B CYS* 3.0 23.8 + - - +
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.6 16.8 - - + -
44B CYS 5.0 2.7 - - - +
48B HIS* 3.3 42.6 - - + -
91B CYS 3.1 7.5 + - - +
94B ALA* 1.3 76.3 - - - +
96B ALA* 1.3 57.6 + - - +
98B CYS* 3.1 6.5 + - - +
99B PHE* 2.8 45.1 + - + -
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Residues in contact with ALA 96 (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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5B PHE* 4.0 4.2 - - + -
8B MET* 3.7 39.5 - - + +
9B ILE* 3.9 14.1 - - + +
12B ALA* 3.4 11.9 - - + +
76B PRO* 3.9 6.5 - - + -
92B ASP 2.8 17.9 + - - +
93B ALA 3.5 4.7 - - - +
95B ALA* 1.3 76.9 - - - +
97B LYS* 1.3 61.7 + - - +
99B PHE* 3.4 3.3 + - - +
100B ALA* 3.1 18.4 + - - +
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Residues in contact with LYS 97 (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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12B ALA* 4.2 7.4 - - + -
75B VAL* 3.5 30.0 - - + +
76B PRO* 4.0 20.5 + - + -
93B ALA* 3.0 22.0 + - - +
94B ALA* 3.5 11.2 - - - +
96B ALA* 1.3 76.3 - - - +
98B CYS* 1.3 61.9 + - - +
100B ALA* 3.4 4.8 + - - +
101B LYS* 3.3 41.8 + - - +
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Residues in contact with CYS 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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40B GLU* 5.2 2.1 - - - +
43B ARG 5.2 0.2 - - - -
44B CYS* 2.0 59.9 - - + +
47B VAL* 6.1 2.5 - - - -
94B ALA 3.0 17.3 + - - +
95B ALA* 3.5 7.2 - - - +
97B LYS* 1.3 74.9 - - - +
99B PHE* 1.3 65.2 + - - +
101B LYS* 3.3 14.9 + - - +
102B ALA* 3.4 9.2 + - - +
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Residues in contact with PHE 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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5B PHE* 3.9 18.6 - + - -
9B ILE* 3.8 38.1 - - + -
13B ASN* 6.5 0.2 - - + -
22B TYR* 3.7 46.9 + + + -
41B LEU* 3.4 20.2 - - + +
44B CYS* 3.5 23.1 - - + -
45B CYS* 3.5 31.9 - - - -
48B HIS* 5.5 2.2 - + + -
95B ALA* 2.8 29.9 + - + +
96B ALA* 3.7 5.4 - - - +
98B CYS* 1.3 71.0 - - - +
100B ALA* 1.3 62.8 - - - +
102B ALA* 3.2 21.7 + - - +
203B PEG 4.2 7.4 - - - -
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Residues in contact with ALA 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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12B ALA* 3.5 33.4 - - + +
13B ASN* 3.8 18.0 - - + +
22B TYR* 5.4 1.3 - - - -
96B ALA 3.1 14.1 + - - +
97B LYS* 3.6 6.3 - - - +
98B CYS 3.2 0.2 - - - -
99B PHE* 1.3 80.7 - - - +
101B LYS* 1.3 62.1 + - + +
102B ALA 3.7 2.6 + - - +
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Residues in contact with LYS 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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40B GLU* 4.1 8.6 - - - +
97B LYS* 3.3 31.7 + - - +
98B CYS* 3.3 6.8 + - - +
99B PHE 3.2 0.6 - - - -
100B ALA* 1.3 78.7 - - + +
102B ALA* 1.3 63.0 + - - +
103B PRO* 4.0 4.2 - - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 5.5 1.2 + - - -
40B GLU* 3.6 26.7 - - + +
41B LEU* 3.9 24.6 - - + +
44B CYS* 4.5 1.8 - - - -
98B CYS 3.4 13.4 + - - +
99B PHE 3.2 14.9 + - - +
100B ALA 4.3 2.8 - - - +
101B LYS* 1.3 81.0 - - - +
103B PRO* 1.3 70.6 - - + +
104B TYR* 3.6 2.8 + - - +
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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