Contacts of the strand formed by residues 10 - 17 (chain W) in PDB entry 4JPB
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 GLU 10 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8W LEU* 3.9 9.9 - - + +
9W LYS* 1.3 107.6 + - + +
11W PHE* 1.3 62.9 + - - +
12W GLU 4.3 0.5 + - - -
103W ARG* 3.1 50.0 + - - +
104W ILE 3.8 7.9 + - - +
105W THR* 3.9 13.2 - - - +
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Residues in contact with PHE 11 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9W LYS* 3.6 11.4 + - + +
10W GLU* 1.3 77.8 - - - +
12W GLU* 1.3 71.0 + - - +
13W VAL* 5.0 2.0 - - + -
26W ASP* 3.7 17.0 - - + -
28W ASP* 4.9 9.2 - - - -
102W LEU 3.6 0.3 - - - +
103W ARG* 3.2 8.0 - - - -
104W ILE* 2.5 64.0 + - + +
105W THR* 5.1 0.2 - - - -
106W GLU* 4.0 34.1 - - + -
109W LEU* 6.3 0.4 - - + -
123W LYS* 5.8 2.5 - - + -
135W TYR* 3.3 34.8 - + - -
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Residues in contact with GLU 12 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W GLU 4.3 0.8 + - - -
11W PHE* 1.3 78.4 - - - +
13W VAL* 1.3 63.2 + - - +
26W ASP* 3.9 2.8 - - - +
27W VAL* 3.0 45.0 + - + +
28W ASP* 5.0 1.9 - - - +
101W VAL* 3.7 25.6 - - + +
102W LEU 3.4 4.5 - - - +
103W ARG* 3.2 39.6 + - + +
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Residues in contact with VAL 13 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W PHE* 5.0 2.7 - - + -
12W GLU* 1.3 80.2 - - - +
14W LEU* 1.3 61.4 + - - +
15W SER 5.0 0.2 - - - +
24W ALA* 3.9 19.1 - - + -
25W PHE 3.5 10.3 - - - +
26W ASP* 4.2 5.8 - - - -
27W VAL* 4.0 4.3 - - - +
101W VAL* 3.3 9.4 - - - +
102W LEU* 2.9 57.2 + - + +
104W ILE* 4.1 25.8 - - + -
126W VAL* 6.1 3.4 - - + -
133W ILE* 6.2 0.2 - - + -
135W TYR* 3.9 30.5 - - + +
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Residues in contact with LEU 14 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13W VAL* 1.3 72.7 - - - +
15W SER* 1.3 59.6 + - - +
16W PHE* 3.5 10.6 - - + -
24W ALA* 3.0 22.6 - - - -
25W PHE* 3.0 18.4 + - + +
27W VAL* 4.7 6.9 - - + +
30W ILE* 4.2 29.6 - - + -
33W VAL* 3.7 29.6 - - + -
82W ILE* 4.5 9.9 - - + -
98W VAL* 3.6 24.9 - - + -
100W GLY* 3.5 22.0 - - - +
101W VAL* 4.1 12.1 - - + -
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Residues in contact with SER 15 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13W VAL 4.0 1.0 + - - -
14W LEU* 1.3 73.6 - - - +
16W PHE* 1.3 55.4 + - - +
22W ALA* 6.0 0.2 - - - -
23W LEU 3.2 10.5 - - - -
24W ALA* 3.7 7.4 - - - -
98W VAL* 3.7 4.6 - - - +
99W LEU* 2.7 50.2 + - - +
100W GLY 2.9 19.1 + - - -
102W LEU* 3.7 23.0 - - - +
133W ILE* 4.2 16.5 - - - +
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Residues in contact with PHE 16 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14W LEU* 3.5 21.1 - - + -
15W SER* 1.3 75.0 - - - +
17W GLU* 1.3 63.9 + - - +
18W ILE* 4.4 2.5 - - + -
22W ALA* 3.4 6.1 - - - +
23W LEU* 2.9 58.8 + - + +
24W ALA* 3.7 10.3 - - - -
25W PHE* 3.5 40.8 - + - -
65W LEU* 3.7 13.7 - - + -
82W ILE* 3.5 16.8 - - + -
95W VAL* 3.6 33.2 - - + -
97W ARG 3.3 16.8 - - - +
98W VAL* 4.0 7.0 - - + -
99W LEU* 3.9 6.5 - - - +
136W LEU* 4.3 1.6 - - + -
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Residues in contact with GLU 17 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16W PHE* 1.3 76.6 - - - +
18W ILE* 1.3 64.7 + - - +
19W ASP* 3.5 10.5 - - - +
20W GLU* 4.1 16.5 + - - +
21W GLN 3.4 13.7 - - - +
22W ALA* 4.5 2.2 - - + +
95W VAL* 4.2 1.0 - - - +
96W ASP* 3.0 30.9 + - + +
97W ARG* 2.9 41.8 + - + +
99W LEU* 3.8 20.2 - - + +
131W ARG* 5.7 4.4 + - - +
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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