Contacts of the helix formed by residues 35 - 51 (chain B) in PDB entry 1NVP
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 ASP 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B PHE* 4.7 0.7 - - - -
33B GLY 3.8 3.4 + - - -
34B VAL* 1.3 77.6 - - - +
36B GLU* 1.3 67.4 + - - +
37B GLN* 2.6 48.4 + - + +
38B VAL* 2.9 30.6 + - + +
39B LEU 3.7 1.6 + - - -
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Residues in contact with GLU 36 (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 ARG* 2.5 45.9 + - - +
29B PHE* 5.9 2.0 - - - -
30B LEU* 4.7 21.2 - - + +
34B VAL 3.4 3.7 + - - -
35B ASP* 1.3 76.0 + - - +
37B GLN* 1.3 62.2 + - - +
38B VAL 3.2 0.2 - - - -
39B LEU* 3.2 20.3 + - + +
40B MET* 3.2 21.4 + - + +
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Residues in contact with GLN 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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35B ASP* 2.6 34.0 + - + +
36B GLU* 1.3 73.5 - - - +
38B VAL* 1.3 64.9 + - + +
40B MET* 3.1 10.9 + - - +
41B GLU* 2.9 21.3 + - - +
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Residues in contact with VAL 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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29B PHE* 4.2 2.7 - - + -
34B VAL* 3.5 16.6 - - + -
35B ASP* 2.9 23.5 + - + +
37B GLN* 1.3 79.4 - - + +
39B LEU* 1.3 62.1 + - - +
41B GLU* 3.0 10.9 + - - +
42B LEU* 2.9 21.5 + - - +
22D LEU* 4.4 11.6 - - + +
27D GLN* 4.0 31.6 - - + +
28D ILE* 3.7 30.5 - - + -
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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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22B ILE* 4.0 21.7 - - + +
25B VAL* 3.5 29.8 - - + -
26B ARG* 3.5 58.6 - - + +
29B PHE* 3.7 31.2 - - + -
35B ASP 3.7 1.0 + - - -
36B GLU* 3.2 19.3 + - + +
38B VAL* 1.3 79.3 - - - +
40B MET* 1.3 63.1 + - - +
42B LEU* 3.1 15.9 + - + +
43B LYS* 3.1 12.8 + - - +
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Residues in contact with MET 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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22B ILE* 5.2 4.0 - - - -
26B ARG* 3.9 25.6 - - - +
36B GLU* 3.2 21.1 + - + +
37B GLN* 3.1 10.2 + - - +
39B LEU* 1.3 77.9 - - - +
41B GLU* 1.3 65.7 + - - +
43B LYS* 3.4 22.3 + - + +
44B THR* 3.0 27.6 + - - +
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Residues in contact with GLU 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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37B GLN 2.9 12.1 + - - +
38B VAL* 3.0 11.5 + - - +
40B MET* 1.3 72.9 - - - +
42B LEU* 1.3 56.1 + - - +
44B THR* 3.1 7.7 + - - -
45B LEU* 2.7 55.1 + - + +
22D LEU* 3.7 12.7 - - + +
27D GLN* 2.9 39.9 + - - +
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Residues in contact with LEU 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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22B ILE* 4.4 17.3 - - + -
25B VAL* 5.1 1.1 - - + -
29B PHE* 3.9 24.5 - - + -
38B VAL 2.9 10.5 + - - +
39B LEU* 3.1 13.9 - - + +
41B GLU* 1.3 78.0 - - - +
43B LYS* 1.3 58.3 + - - +
45B LEU* 3.1 3.5 + - - +
46B TRP* 2.8 33.4 + - + +
15D LEU* 4.5 10.8 - - + -
18D SER* 4.0 17.7 - - - -
19D LEU* 3.6 31.6 - - + -
22D LEU* 3.7 21.5 - - + +
36D VAL* 4.3 14.8 - - + -
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Residues in contact with LYS 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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18B ILE* 4.0 14.6 - - + -
19B GLU* 2.8 41.1 + - - -
22B ILE* 3.9 32.5 - - + +
39B LEU 3.1 6.6 + - - +
40B MET* 3.7 25.8 - - + +
42B LEU* 1.3 80.3 - - - +
44B THR* 1.3 55.3 + - - +
46B TRP* 3.6 4.8 - - - +
47B GLU* 2.8 67.2 + - + +
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Residues in contact with THR 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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40B MET* 3.0 19.1 + - - +
41B GLU* 3.1 8.2 + - - -
43B LYS* 1.3 74.8 - - - +
45B LEU* 1.3 68.9 + - + +
47B GLU* 3.4 8.1 + - - +
48B ASN* 2.8 51.8 + - - +
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Residues in contact with LEU 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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41B GLU* 2.7 36.8 + - + +
42B LEU* 3.5 3.4 - - - +
44B THR* 1.3 73.3 - - + +
46B TRP* 1.3 57.5 + - - +
48B ASN* 3.5 5.3 + - - +
49B LYS* 3.0 36.3 + - + +
18D SER* 3.4 36.6 - - - +
21D GLU* 3.9 28.7 - - + +
22D LEU* 3.9 26.2 - - + -
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Residues in contact with TRP 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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17B VAL* 4.6 0.4 - - + -
18B ILE* 3.9 48.4 - - + +
21B VAL* 4.0 29.6 - - + -
22B ILE* 4.4 13.2 - - + -
42B LEU* 2.8 18.1 + - + +
43B LYS 3.6 3.4 - - - +
45B LEU* 1.3 76.1 - - - +
47B GLU* 1.3 65.5 + - + +
49B LYS* 3.3 10.9 + - - +
50B LEU* 3.3 11.6 + - + +
11D LEU* 3.1 36.8 + - + +
14D SER* 3.1 25.3 + - - -
15D LEU* 3.7 51.1 - - + +
18D SER* 3.2 12.3 + - - +
40D PHE* 4.2 4.7 - + - -
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Residues in contact with GLU 47 (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 ARG* 4.6 18.1 + - - +
18B ILE* 4.0 25.1 - - + +
19B GLU* 4.7 1.2 - - - +
43B LYS* 2.8 71.0 + - + +
44B THR* 4.0 6.2 + - - +
46B TRP* 1.3 71.8 - - - +
48B ASN* 1.3 67.4 + - - +
50B LEU* 3.2 20.4 + - - +
51B MET* 3.4 13.2 + - + +
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Residues in contact with ASN 48 (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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44B THR* 2.8 42.1 + - - +
45B LEU* 3.9 4.3 - - - +
47B GLU* 1.3 78.7 - - - +
49B LYS* 1.3 66.6 + - - +
51B MET* 3.0 44.0 + - + +
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Residues in contact with LYS 49 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B LEU* 3.0 17.9 + - - +
46B TRP 3.3 2.0 + - - +
48B ASN* 1.3 76.9 - - - +
50B LEU* 1.3 64.3 + - - +
51B MET 3.4 4.5 + - - -
10D THR* 5.7 1.4 - - - +
14D SER* 3.7 24.3 - - - +
17D GLU* 3.6 44.7 + - - +
18D SER* 3.6 18.9 - - - +
21D GLU* 2.5 34.0 + - - +
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Residues in contact with LEU 50 (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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14B TYR* 4.0 34.1 - - + -
15B ARG* 3.8 18.4 - - - +
18B ILE* 3.8 28.7 - - + -
46B TRP* 3.3 12.1 + - + +
47B GLU 3.2 10.4 + - - +
48B ASN 3.1 0.2 - - - -
49B LYS* 1.3 78.7 - - - +
51B MET* 1.3 63.2 + - + +
10D THR* 3.7 31.6 - - + +
11D LEU* 4.1 11.7 - - + -
14D SER* 4.2 13.9 - - - +
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Residues in contact with MET 51 (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 ARG* 5.2 11.2 - - - +
47B GLU* 3.4 8.7 + - + +
48B ASN* 3.0 46.2 + - + +
49B LYS 3.9 4.0 - - - -
50B LEU* 1.3 85.3 - - + +
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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