Contacts of the helix formed by residues 36 - 46 (chain B) in PDB entry 1PVI
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 GLY 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B ILE* 4.1 16.6 - - - +
30B ASP 3.8 15.9 - - - -
31B ILE* 3.9 7.3 + - - -
33B GLN 2.9 14.1 + - - -
34B ASP 3.4 1.0 - - - -
35B ASN* 1.3 75.4 - - - +
37B GLY* 1.3 64.8 + - - +
39B LEU* 2.9 6.5 + - - +
40B LEU* 2.8 22.6 + - - +
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Residues in contact with GLY 37 (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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13A TRP* 5.5 0.2 - - - -
32A PHE* 3.8 15.2 - - - -
19B TYR* 2.6 44.6 + - - -
31B ILE* 3.0 19.4 + - - +
35B ASN 3.4 0.6 - - - -
36B GLY* 1.3 71.3 - - - +
38B LYS* 1.3 62.6 + - - +
40B LEU* 3.0 11.3 + - - +
41B GLN* 3.5 4.4 + - - +
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Residues in contact with LYS 38 (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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13A TRP* 6.3 0.2 - - + -
30A ASP* 3.2 35.6 + - - -
32A PHE* 3.6 16.2 - - + -
35B ASN* 3.0 32.3 + - + +
37B GLY* 1.3 72.3 - - - +
39B LEU* 1.3 61.9 + - - +
41B GLN* 3.3 17.2 - - - +
42B VAL* 3.5 4.4 + - - +
71B SER* 3.9 15.3 - - - +
72B ILE 5.2 2.9 + - - +
73B ASN* 4.8 7.9 - - - +
104B TYR* 2.6 51.0 + - + +
106B GLY 2.9 28.5 + - - -
107B ILE* 3.9 9.0 - - + +
11C G 5.9 0.9 - - - -
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Residues in contact with LEU 39 (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 ILE* 3.8 24.0 - - + -
35B ASN* 2.6 26.3 + - + +
36B GLY* 3.5 5.2 - - - +
38B LYS* 1.3 72.0 - - - +
40B LEU* 1.3 69.3 + - - +
42B VAL* 3.5 8.0 + - + +
43B LEU* 3.3 21.8 + - + +
50B VAL* 4.3 16.8 - - + -
54B ARG* 4.8 4.5 - - - +
57B ASN* 4.5 30.1 - - + +
69B LEU* 3.5 39.3 - - + +
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Residues in contact with LEU 40 (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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9A LEU* 4.6 5.2 - - + -
19B TYR* 3.4 39.0 - - + +
22B LEU* 4.1 14.4 - - + +
23B ALA* 3.4 38.8 - - + +
26B HIS* 4.1 19.3 - - + +
28B ILE* 4.1 13.4 - - + +
36B GLY 2.8 10.8 + - - +
37B GLY 3.0 9.6 + - - +
39B LEU* 1.3 75.9 - - - +
41B GLN* 1.3 64.6 + - - +
43B LEU* 2.9 19.6 + - + +
44B LEU* 3.1 25.5 + - + +
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Residues in contact with GLN 41 (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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6A LEU* 6.1 0.7 - - + -
9A LEU* 3.7 26.3 - - + +
10A LEU* 6.1 3.0 - - - +
13A TRP* 3.2 44.6 - - + -
37B GLY 3.5 2.4 + - - +
38B LYS* 3.3 10.9 + - - +
40B LEU* 1.3 79.9 - - - +
42B VAL* 1.3 63.5 + - + +
43B LEU 3.2 0.2 + - - -
44B LEU* 3.4 1.6 + - - +
45B ILE* 3.1 36.1 + - + +
104B TYR* 2.8 36.5 + - - +
108B ALA* 5.2 0.4 - - - +
109B ILE* 4.1 22.3 - - + +
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Residues in contact with VAL 42 (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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38B LYS 3.5 4.4 + - - +
39B LEU* 4.0 13.5 - - + +
40B LEU 3.3 0.8 - - - -
41B GLN* 1.3 78.3 - - - +
43B LEU* 1.3 54.3 + - - +
45B ILE* 4.5 5.2 - - - -
46B THR* 2.6 56.9 + - + +
48B LEU* 5.4 0.7 - - + -
69B LEU* 4.1 21.8 - - + -
71B SER* 5.7 0.7 - - - +
100B ILE* 4.6 13.2 - - + -
102B ALA* 3.7 29.4 - - + -
104B TYR* 3.7 12.8 - - - +
109B ILE* 4.1 7.9 - - + -
112B ILE* 4.6 6.3 - - + -
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Residues in contact with LEU 43 (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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26B HIS* 4.3 23.1 - - + +
28B ILE* 4.7 5.2 - - + -
39B LEU* 3.3 21.3 + - + +
40B LEU* 2.9 12.9 + - + +
42B VAL* 1.3 76.8 - - - +
44B LEU* 1.3 60.9 + - + +
45B ILE 3.0 0.2 + - - -
46B THR* 4.0 0.9 - - - -
47B GLY* 2.6 37.9 + - - -
48B LEU* 3.2 46.2 + - + +
49B THR* 4.0 0.9 - - - +
50B VAL* 3.5 27.6 - - + +
59B ALA* 4.1 11.9 - - + -
69B LEU* 4.5 8.7 - - + -
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Residues in contact with LEU 44 (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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2A SER* 3.6 0.9 - - - -
3A HIS* 2.9 49.2 + - + +
5A ASP* 3.9 11.2 - - + +
6A LEU* 3.9 37.1 - - + +
9A LEU* 3.9 26.5 - - + -
22B LEU* 5.1 4.5 - - + -
26B HIS* 3.4 41.5 - - + +
40B LEU* 3.1 21.2 + - + +
41B GLN 4.2 4.3 - - - +
43B LEU* 1.3 77.3 - - + +
45B ILE* 1.3 61.1 + - - +
47B GLY 3.9 0.5 + - - -
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Residues in contact with ILE 45 (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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2A SER* 3.4 19.9 + - - +
6A LEU* 4.4 24.2 - - + -
41B GLN* 3.1 24.3 + - + +
42B VAL* 3.8 3.8 - - - +
43B LEU 3.1 0.6 - - - -
44B LEU* 1.3 79.5 - - - +
46B THR* 1.3 63.2 + - + +
47B GLY 3.1 4.7 + - - -
109B ILE* 4.6 15.7 - - + -
112B ILE* 4.5 17.9 - - + -
156B ILE* 6.2 0.4 - - + -
157B TYR* 4.1 41.1 - - + -
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Residues in contact with THR 46 (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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2A SER 5.1 1.8 - - - -
42B VAL* 2.6 40.2 + - + +
45B ILE* 1.3 78.6 - - + +
47B GLY* 1.3 62.9 + - - +
48B LEU* 3.3 31.6 + - + +
100B ILE* 5.2 4.0 - - + -
112B ILE* 4.2 15.0 - - + -
156B ILE* 4.1 27.8 - - + -
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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
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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