Contacts of the strand formed by residues 16 - 23 (chain P) in PDB entry 1JVP
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 16 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12P GLU* 3.9 0.2 - - - -
13P GLY* 2.8 29.4 + - - -
14P THR 3.2 5.5 + - - -
15P TYR* 1.3 82.1 - - - +
17P VAL* 1.3 66.5 + - - -
18P VAL* 4.1 1.4 + - - +
33P LYS* 4.2 11.8 - - - -
34P LYS 3.4 13.9 - - - -
36P ARG* 3.8 12.7 - - - +
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Residues in contact with VAL 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P LYS* 3.5 22.4 - - + +
11P GLY 3.4 14.8 - - - +
12P GLU* 3.5 27.1 - - + +
13P GLY 5.4 0.2 - - - +
16P GLY* 1.3 74.8 - - - -
18P VAL* 1.3 64.4 + - - +
19P TYR* 3.5 30.7 + - + +
32P LEU 3.6 1.6 - - - +
33P LYS* 3.4 2.6 - - - -
34P LYS* 3.2 33.2 + - + +
36P ARG* 6.1 4.0 - - + +
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Residues in contact with VAL 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P LYS* 3.6 4.2 - - - +
10P ILE* 2.9 46.8 + - + +
11P GLY* 3.1 24.1 + - - +
12P GLU* 5.3 1.6 - - - +
13P GLY 5.7 0.4 - - - +
16P GLY 4.6 2.5 - - - +
17P VAL* 1.3 76.6 - - - +
19P TYR* 1.3 65.4 + - - +
31P ALA* 4.2 15.3 - - + -
32P LEU 3.4 8.1 - - - +
33P LYS* 3.7 30.5 - - + -
80P PHE* 6.4 0.9 - - + -
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Residues in contact with TYR 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P LYS* 3.7 51.4 + - + -
8P GLU* 3.3 7.4 - - - +
9P LYS* 3.6 38.3 + - + -
10P ILE* 3.8 5.2 - - - -
17P VAL* 3.5 32.5 - - + +
18P VAL* 1.3 76.9 - - - +
20P LYS* 1.3 67.1 + - - +
21P ALA 3.5 0.2 + - - -
31P ALA* 3.3 4.0 - - - -
32P LEU* 2.6 53.7 + - + +
34P LYS* 5.6 9.2 - - + -
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Residues in contact with LYS 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6P LYS* 3.7 1.6 - - - -
7P VAL* 2.7 54.3 + - + +
8P GLU* 2.6 33.0 + - + +
10P ILE* 3.6 23.5 - - + +
19P TYR* 1.3 71.9 - - - +
21P ALA* 1.3 55.1 + - - +
29P VAL* 3.8 31.2 - - + -
30P VAL 3.5 5.8 - - - +
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Residues in contact with ALA 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P PHE* 4.3 12.6 - - + -
5P GLN 3.2 17.0 - - - +
6P LYS* 4.2 4.9 - - + -
7P VAL* 4.1 5.6 - - - -
19P TYR 3.5 0.4 + - - -
20P LYS* 1.3 76.8 - - - +
22P ARG* 1.3 59.5 + - - +
29P VAL* 3.4 6.1 - - - +
30P VAL* 2.8 43.6 + - + +
32P LEU* 3.9 27.4 - - + -
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Residues in contact with ARG 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4P PHE* 3.5 3.4 - - - -
5P GLN* 2.9 42.2 + - - +
7P VAL* 4.3 5.3 - - - +
21P ALA* 1.3 74.1 - - - +
23P ASN* 1.3 61.6 + - - +
24P LYS* 2.9 5.9 + - - -
27P GLY* 4.8 4.5 - - - -
28P GLU 3.2 8.5 - - - -
29P VAL* 4.4 4.9 - - - +
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Residues in contact with ASN 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P ASN* 3.7 9.4 - - - +
4P PHE* 3.7 32.7 - - + -
22P ARG* 1.3 68.3 - - - +
24P LYS* 1.3 52.5 + - - +
25P LEU* 2.8 26.3 + - - +
26P THR* 2.9 39.2 + - - +
27P GLY* 2.6 31.9 + - - -
28P GLU* 2.7 26.1 + - + +
30P VAL* 5.7 0.4 - - + -
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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