Contacts of the helix formed by residues 25 - 37 (chain B) in PDB entry 1NVT
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 PHE 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B HIS* 3.8 27.4 - + - -
24B SER* 1.3 73.1 + - - +
26B SER* 1.3 64.2 + - - +
27B PRO* 3.3 3.4 - - - -
28B ILE* 3.1 13.8 + - + +
29B MET* 3.0 22.6 + - - +
231B TYR* 4.0 22.9 + + + +
232B ASN* 3.7 28.0 - - + -
256B LEU* 4.9 7.6 - - + -
281B ILE* 4.3 21.3 - - + +
284B LYS* 3.9 37.5 - - + -
285B ILE* 3.6 31.6 - - + -
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Residues in contact with SER 26 (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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16B LEU* 4.8 4.1 - - - +
24B SER* 3.2 13.5 + - - -
25B PHE* 1.3 79.2 - - - +
27B PRO* 1.3 66.4 - - - +
29B MET* 3.2 19.4 + - - +
30B HIS* 3.0 36.6 + - - -
43B TYR* 3.5 25.6 + - - -
69B ASN* 4.4 3.3 + - - -
256B LEU* 4.6 9.3 - - - +
259B GLN* 5.5 2.4 + - - -
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Residues in contact with PRO 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.8 0.4 - - + -
8A ASN* 4.1 19.5 - - - +
9A ALA* 3.9 20.0 - - + +
16B LEU* 5.5 0.2 - - + -
24B SER* 3.5 16.2 - - - +
25B PHE 3.4 4.7 - - - -
26B SER* 1.3 94.7 - - - +
28B ILE* 1.3 55.9 + - - +
31B ASN* 2.8 41.6 + - - +
43B TYR* 3.4 37.7 - - + +
44B VAL 4.6 1.6 - - - -
45B ALA* 4.4 11.2 - - + -
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Residues in contact with ILE 28 (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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7A ILE 3.6 20.9 - - - +
8A ASN* 4.2 11.0 - - + -
24B SER 5.0 2.5 - - - +
25B PHE* 3.1 22.9 + - + +
27B PRO* 1.3 76.5 - - + +
29B MET* 1.3 67.5 + - - +
31B ASN* 4.5 1.9 - - - +
32B ALA* 3.3 22.2 + - - +
280B ALA* 3.5 32.5 - - + +
281B ILE* 4.5 1.6 - - - +
284B LYS* 3.3 46.2 - - + +
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Residues in contact with MET 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE 3.0 6.8 + - - +
26B SER* 3.5 21.8 - - - +
28B ILE* 1.3 80.7 - - - +
30B HIS* 1.3 75.7 + - + +
32B ALA* 3.4 4.2 + - - +
33B ALA* 3.2 20.3 + - - +
256B LEU* 3.3 54.5 - - + +
257B ILE* 4.0 11.7 - - - -
259B GLN* 5.1 0.7 - - - +
260B GLY* 4.3 3.4 - - - -
277B MET* 3.7 39.1 - - + +
280B ALA* 4.7 1.1 - - - -
281B ILE* 3.5 23.5 - - + +
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Residues in contact with HIS 30 (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 SER* 3.0 28.3 + - - +
29B MET* 1.3 96.2 - - + +
31B ASN* 1.3 60.7 + - - +
33B ALA* 3.3 4.5 + - - +
34B PHE* 2.8 41.9 + - + -
43B TYR* 3.4 33.2 - + + -
69B ASN* 3.6 24.2 - - - -
259B GLN* 5.7 0.7 - - - -
260B GLY* 3.7 27.8 + - - -
264B PHE* 3.7 24.9 - + + -
267B TRP* 3.7 15.2 - + - -
277B MET* 5.2 2.2 - - - -
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Residues in contact with ASN 31 (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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7A ILE* 3.8 22.0 + - - +
5B SER* 4.1 17.7 + - - +
27B PRO 2.8 27.7 + - - +
28B ILE* 4.5 1.8 - - - +
30B HIS* 1.3 76.2 - - - +
32B ALA* 1.3 62.6 + - - +
34B PHE* 3.3 7.2 + - - +
35B LYS* 3.0 32.7 + - + +
41B TYR 4.4 0.7 - - - +
42B VAL* 3.5 12.7 - - - +
43B TYR* 2.8 44.3 + - - -
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Residues in contact with ALA 32 (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 3.3 18.3 + - - +
29B MET 3.4 5.2 - - - +
30B HIS 3.2 0.4 - - - -
31B ASN* 1.3 79.4 - - - +
33B ALA* 1.3 57.0 + - - +
35B LYS* 3.6 7.8 + - - +
36B ASP* 3.1 27.7 + - - +
276B VAL* 3.6 15.7 - - + +
280B ALA* 3.6 22.0 - - + -
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Residues in contact with ALA 33 (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 MET 3.2 12.4 + - - +
30B HIS* 3.3 2.0 + - - +
32B ALA* 1.3 78.4 - - - +
34B PHE* 1.3 64.9 + - - +
36B ASP* 3.5 5.4 + - - +
37B LYS* 3.3 23.2 + - - +
264B PHE* 3.4 27.8 - - + -
272B PRO* 4.0 9.8 - - + +
273B ASN 5.0 1.8 - - - +
276B VAL* 4.0 8.9 - - + +
277B MET* 4.0 22.0 - - + -
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Residues in contact with PHE 34 (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 ILE* 3.6 27.1 - - + -
30B HIS* 2.8 30.2 + - + +
31B ASN* 3.5 12.8 - - - +
33B ALA* 1.3 76.9 - - - +
35B LYS* 1.3 62.7 + - + +
37B LYS* 3.2 3.5 + - - -
38B GLY 3.1 3.5 + - - -
39B LEU* 3.0 40.3 + - + +
41B TYR* 3.5 53.6 - + + +
42B VAL 4.1 0.9 - - - -
43B TYR* 3.8 27.1 - + + -
264B PHE* 3.4 33.2 - + - -
267B TRP* 4.7 5.4 - + + -
268B THR* 5.3 4.3 - - - -
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Residues in contact with LYS 35 (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 GLY* 4.5 2.7 - - - -
2B PRO* 2.9 39.8 + - - +
3B LEU 3.5 9.9 - - - +
4B GLY 2.6 32.7 + - - +
5B SER* 4.1 16.8 - - - +
6B MET* 4.7 2.4 - - - +
31B ASN* 3.0 18.7 + - + +
32B ALA* 3.8 6.5 - - - +
34B PHE* 1.3 79.6 - - + +
36B ASP* 1.3 65.7 + - - +
38B GLY* 3.0 15.0 + - - +
39B LEU 5.1 1.6 - - - +
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Residues in contact with ASP 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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32B ALA 3.1 18.4 + - - +
33B ALA* 3.8 4.6 - - - +
34B PHE 3.4 0.2 - - - -
35B LYS* 1.3 75.9 - - - +
37B LYS* 1.3 77.6 + - - +
38B GLY 3.8 0.3 + - - -
273B ASN* 3.4 26.1 + - - +
276B VAL* 3.9 25.5 - - + +
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Residues in contact with LYS 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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33B ALA 3.3 13.1 + - - +
34B PHE 3.2 1.6 + - - +
35B LYS 3.1 0.4 - - - -
36B ASP* 1.3 102.4 + - - +
38B GLY* 1.3 62.3 + - - +
39B LEU* 3.4 24.0 + - + +
264B PHE* 5.1 2.2 - - + -
270B VAL* 3.7 24.7 - - + -
271B GLU 3.5 22.2 + - - +
272B PRO* 5.0 4.0 - - + -
273B ASN* 4.3 13.1 - - - +
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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