Contacts of the helix formed by residues 70 - 83 (chain B) in PDB entry 1PVS
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 VAL 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B VAL* 3.9 31.4 - - + -
44B TYR* 3.7 46.7 - - + -
67B LEU* 3.2 14.1 - - + +
69B PRO* 1.3 80.7 - - - +
71B ALA* 1.3 65.9 + - - +
72B ALA* 3.3 2.9 - - - -
73B GLU* 3.1 10.1 + - + +
74B CYS* 3.1 20.0 + - - -
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Residues in contact with ALA 71 (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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2B TYR* 3.4 33.2 - - + +
63B LEU* 3.5 26.5 - - + -
67B LEU 3.0 1.2 + - - -
68B GLU* 3.0 17.1 + - - +
69B PRO 3.6 0.6 + - - -
70B VAL* 1.3 76.0 - - - +
72B ALA* 1.3 51.7 + - - +
74B CYS* 2.9 6.8 + - - +
75B LEU* 2.7 38.6 + - - +
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Residues in contact with ALA 72 (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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70B VAL* 3.2 1.2 + - - -
71B ALA* 1.3 78.1 - - - +
73B GLU* 1.3 57.8 + - - +
75B LEU* 3.2 15.8 + - + +
76B ALA* 2.9 26.5 + - - +
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Residues in contact with GLU 73 (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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41B VAL* 4.2 18.4 - - + -
70B VAL* 3.1 13.4 + - + +
72B ALA* 1.3 74.7 - - - +
74B CYS* 1.3 61.8 + - - +
76B ALA* 3.2 9.1 + - - +
77B LYS* 2.9 57.4 + - - +
80B ARG* 3.3 25.7 + - - -
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Residues in contact with CYS 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.1 23.3 - - + -
41B VAL* 4.3 12.3 - - - -
48B VAL* 4.7 0.7 - - + -
63B LEU* 3.9 21.1 - - + -
67B LEU* 4.0 31.9 - - - -
70B VAL* 3.1 19.0 + - - -
71B ALA 2.9 11.6 + - - +
73B GLU* 1.3 77.5 - - - +
75B LEU* 1.3 60.2 + - - +
77B LYS* 3.3 8.7 + - - +
78B MET* 3.1 29.5 + - - +
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Residues in contact with LEU 75 (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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2B TYR* 3.7 51.4 - - + -
4B LEU* 3.8 25.9 - - + +
61B ILE* 3.8 29.4 - - + -
63B LEU* 5.0 2.2 - - + -
71B ALA 2.7 20.7 + - - +
72B ALA* 3.5 14.8 - - + +
73B GLU 3.2 0.2 - - - -
74B CYS* 1.3 76.5 - - - +
76B ALA* 1.3 61.8 + - - +
78B MET* 3.2 9.1 + - - +
79B SER* 3.0 21.5 + - - -
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Residues in contact with ALA 76 (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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72B ALA 2.9 14.2 + - - +
73B GLU* 3.5 20.9 - - - +
75B LEU* 1.3 77.2 - - - +
77B LYS* 1.3 61.8 + - - +
79B SER* 2.5 26.6 + - - +
80B ARG* 3.1 30.2 + - - +
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.3 23.6 - - + -
40B ALA 5.6 1.3 - - - -
41B VAL* 4.1 17.5 - - + +
73B GLU* 2.9 46.0 + - - +
74B CYS* 3.3 5.3 + - - +
76B ALA* 1.3 76.0 - - - +
78B MET* 1.3 62.1 + - + +
80B ARG* 3.3 21.8 + - - +
81B LEU* 3.0 27.0 + - - +
110B CYS 3.5 7.4 - - - +
111B VAL* 2.9 41.8 + - + +
112B ASP* 4.3 14.3 + - - +
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Residues in contact with MET 78 (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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4B LEU* 4.8 0.4 - - + -
35B TYR* 5.0 8.7 - - + -
37B ARG* 5.0 4.3 - - + -
39B LEU* 4.8 6.5 - - + -
48B VAL* 3.6 36.3 - - + +
50B ALA* 4.3 11.2 - - - -
59B LEU* 5.2 0.2 - - + -
61B ILE* 4.0 26.0 - - + -
74B CYS 3.1 16.4 + - - +
75B LEU* 3.5 7.4 - - - +
76B ALA 3.2 0.2 - - - -
77B LYS* 1.3 76.5 - - + +
79B SER* 1.3 58.3 + - - +
81B LEU* 3.2 8.6 + - + -
82B PHE* 3.0 56.3 + - + +
84B LEU* 4.8 1.5 - - - +
111B VAL* 3.5 32.1 - - + -
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Residues in contact with SER 79 (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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4B LEU* 4.6 3.8 - - - -
75B LEU 3.0 11.2 + - - -
76B ALA* 2.5 27.9 + - - +
78B MET* 1.3 77.2 - - - +
80B ARG* 1.3 63.0 + - - +
83B ASP* 3.0 22.2 + - - -
84B LEU* 3.2 37.5 + - - +
85B GLN* 4.9 1.4 + - - +
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Residues in contact with ARG 80 (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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73B GLU* 3.3 23.4 + - - -
76B ALA* 3.1 28.0 + - - +
77B LYS* 3.7 28.3 - - - +
78B MET 3.2 0.2 - - - -
79B SER* 1.3 80.3 + - - +
81B LEU* 1.3 64.2 + - - +
82B PHE 3.6 0.2 + - - -
83B ASP* 3.8 6.7 + - - +
107B LEU 4.5 0.9 - - - +
109B GLY* 3.3 16.7 + - - -
110B CYS 4.2 8.9 + - - +
111B VAL 5.2 1.6 + - - -
196B MET 5.6 3.9 + - - -
197B THR* 5.8 10.2 + - - +
229B GLN* 3.2 38.1 - - - +
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Residues in contact with LEU 81 (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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15B MET* 4.5 1.6 - - - +
19B LEU* 4.1 22.7 - - + -
35B TYR* 3.6 33.9 - - + +
77B LYS 3.0 16.7 + - - +
78B MET* 3.2 8.0 + - + +
80B ARG* 1.3 79.5 - - - +
82B PHE* 1.3 83.1 + - + +
108B PRO* 3.6 7.8 - - - +
109B GLY 3.0 24.4 + - - +
110B CYS* 3.7 29.3 + - - +
111B VAL* 4.0 15.7 - - + -
226B ARG* 5.0 1.3 - - - +
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Residues in contact with PHE 82 (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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10B TYR* 2.6 34.6 + - - +
12B TRP* 3.6 29.6 - + + -
15B MET* 3.8 13.2 - - + -
16B LEU* 4.9 1.3 - - + -
19B LEU* 3.5 23.8 - - + -
35B TYR* 3.8 25.8 - + + -
50B ALA* 3.8 21.5 - - + -
59B LEU* 3.8 14.6 - - + -
78B MET* 3.0 30.9 + - - +
81B LEU* 1.3 101.7 - - + +
83B ASP* 1.3 73.2 + - - +
84B LEU* 3.3 11.6 + - + -
106B ARG* 4.1 1.2 - - - +
107B LEU 4.3 1.1 - - - -
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Residues in contact with ASP 83 (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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79B SER 3.0 9.0 + - - -
80B ARG* 3.8 5.3 + - - +
81B LEU 3.5 2.0 - - - -
82B PHE* 1.3 79.8 - - - +
84B LEU* 1.3 62.9 + - - +
85B GLN* 2.6 36.6 + - - +
86B CYS* 3.2 10.1 + - - +
106B ARG* 2.9 22.1 + - + -
107B LEU* 3.1 42.6 + - - +
229B GLN* 6.5 0.4 - - + -
231B LYS* 3.6 6.8 + - - -
266B TYR* 2.7 22.5 + - - -
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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