Contacts of the helix formed by residues 36 - 46 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ALA* 5.7 0.2 - - - +
28A ILE* 4.2 17.4 - - - +
30A ASP 3.8 10.1 - - - -
31A ILE* 3.8 9.5 - - - +
33A GLN 2.6 24.5 + - - -
34A ASP 3.0 2.6 - - - -
35A ASN* 1.3 71.3 - - - +
37A GLY* 1.3 61.4 + - - +
38A LYS 3.4 0.2 + - - -
39A LEU* 3.5 18.8 + - - +
40A LEU* 3.7 6.4 + - - +
32B PHE 3.8 1.6 + - - -
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Residues in contact with GLY 37 (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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19A TYR* 2.9 26.6 + - - -
31A ILE* 3.0 23.0 + - - -
35A ASN 3.1 1.2 + - - -
36A GLY* 1.3 75.5 - - - +
38A LYS* 1.3 59.2 + - - +
40A LEU* 4.0 6.4 + - - +
41A GLN* 4.2 3.3 + - - +
13B TRP* 5.1 0.5 - - - -
32B PHE* 3.7 31.3 - - - -
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Residues in contact with LYS 38 (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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35A ASN* 2.9 35.1 + - + +
37A GLY* 1.3 70.5 - - - +
39A LEU* 1.3 71.5 + - - +
41A GLN* 3.0 18.2 - - - +
42A VAL 3.2 1.0 + - - -
71A SER* 5.0 5.0 - - - +
72A ILE 5.2 1.0 - - - -
73A ASN* 4.3 15.4 - - - +
104A TYR* 2.8 58.8 + - + +
106A GLY 3.5 14.2 + - - -
107A ILE* 3.5 22.9 - - + +
13B TRP* 6.1 0.9 - - + -
30B ASP* 2.8 31.9 + - - -
32B PHE* 3.9 13.7 - - + -
33B GLN* 4.6 1.2 + - - -
11D G 5.3 1.6 + - - -
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Residues in contact with LEU 39 (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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28A ILE* 4.5 15.3 - - + -
34A ASP 5.5 1.1 - - - +
35A ASN* 3.2 9.8 + - + +
36A GLY* 3.6 13.7 - - - +
38A LYS* 1.3 76.9 - - - +
40A LEU* 1.3 54.0 + - - +
41A GLN 2.5 1.9 + - - -
42A VAL* 2.5 36.1 + - + +
43A LEU* 2.8 18.1 + - + -
50A VAL* 4.2 23.1 - - + -
54A ARG* 5.7 1.8 - - - +
57A ASN* 3.9 38.6 - - + +
69A LEU* 3.7 31.4 - - + -
71A SER* 4.7 12.3 + - - +
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Residues in contact with LEU 40 (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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19A TYR* 4.1 27.8 - - + +
22A LEU* 4.1 7.6 - - + +
23A ALA* 3.3 40.6 - - + +
26A HIS* 3.7 35.0 - - + +
28A ILE* 4.2 8.9 - - + +
36A GLY 3.7 6.3 + - - +
37A GLY* 4.2 9.6 - - - +
39A LEU* 1.3 77.4 - - - +
41A GLN* 1.3 55.9 + - - +
43A LEU* 3.8 10.4 - - + +
44A LEU* 3.0 46.8 + - + +
9B LEU* 4.3 9.6 - - + -
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Residues in contact with GLN 41 (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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19A TYR* 5.1 0.4 - - - +
37A GLY 4.2 3.3 + - - +
38A LYS* 3.0 14.3 + - - +
39A LEU 2.5 4.2 + - - -
40A LEU* 1.3 72.8 - - - +
42A VAL* 1.3 66.2 + - + +
44A LEU* 3.1 4.4 + - - +
45A ILE* 2.9 40.0 + - + +
104A TYR* 3.4 22.8 - - + +
107A ILE 4.2 1.4 - - - +
109A ILE* 3.5 33.8 - - + +
6B LEU* 5.5 1.6 - - + -
9B LEU* 4.2 27.6 - - + +
10B LEU* 6.3 0.4 - - - +
13B TRP* 4.1 34.0 - - + +
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Residues in contact with VAL 42 (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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38A LYS 3.3 4.7 - - - +
39A LEU* 2.5 19.4 + - + +
41A GLN* 1.3 73.2 - - - +
43A LEU* 1.3 59.0 + - - +
45A ILE* 4.7 1.3 - - - -
46A THR* 2.7 37.7 + - + +
48A LEU* 5.3 1.8 - - + -
69A LEU* 4.6 18.8 - - + -
71A SER* 5.5 2.5 - - - +
100A ILE* 4.7 14.6 - - + -
102A ALA* 4.0 15.5 - - + -
104A TYR* 3.0 27.6 - - + +
109A ILE* 4.6 4.3 - - + -
112A ILE* 4.2 23.6 - - + -
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Residues in contact with LEU 43 (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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26A HIS* 4.0 11.0 - - + +
28A ILE* 3.9 16.4 - - + -
39A LEU* 2.8 23.2 + - + +
40A LEU* 3.8 8.7 - - - +
42A VAL* 1.3 73.3 - - - +
44A LEU* 1.3 62.1 + - + +
46A THR* 4.1 2.5 - - - -
47A GLY* 2.7 34.3 + - - -
48A LEU* 3.4 37.4 + - + +
49A THR* 4.1 2.2 - - + +
50A VAL* 3.3 38.4 - - + +
59A ALA* 4.3 11.9 - - + -
69A LEU* 4.5 12.8 - - + -
3B HIS* 4.9 0.3 - - - +
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Residues in contact with LEU 44 (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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22A LEU* 4.3 15.0 - - + -
26A HIS* 3.7 33.9 - - + +
40A LEU* 3.0 30.4 + - + +
41A GLN* 3.8 3.1 - - - +
43A LEU* 1.3 80.8 - - + +
45A ILE* 1.3 59.8 + - - +
47A GLY 4.1 0.5 + - - -
2B SER* 3.1 2.7 - - - -
3B HIS* 2.8 46.4 + - + +
5B ASP* 3.8 14.4 - - + +
6B LEU* 3.8 39.3 - - + +
9B LEU* 4.4 9.2 - - + -
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Residues in contact with ILE 45 (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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41A GLN* 2.9 29.2 + - + +
42A VAL 4.0 2.9 - - - +
44A LEU* 1.3 77.3 - - - +
46A THR* 1.3 61.5 + - + +
109A ILE* 4.0 31.4 - - + -
112A ILE* 4.6 7.9 - - + -
157A TYR* 3.5 41.7 - - + +
2B SER* 2.9 36.1 + - - +
6B LEU* 4.0 21.8 - - + -
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Residues in contact with THR 46 (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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42A VAL* 2.7 27.1 + - + +
45A ILE* 1.3 79.1 - - + +
47A GLY* 1.3 62.4 + - - +
48A LEU* 3.3 31.8 + - + +
100A ILE* 5.6 1.3 - - + -
112A ILE* 4.0 23.8 - - + -
156A ILE* 4.3 22.0 - - + -
157A TYR* 6.1 0.4 - - + -
2B SER* 5.4 1.9 - - - -
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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