Contacts of the strand formed by residues 30 - 36 (chain W) in PDB entry 2JA7
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 ALA 30 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23W PRO* 4.2 2.1 - - - +
24W ASP* 3.4 22.9 + - + +
27W ALA 3.9 14.1 + - - +
28W PRO 3.7 0.4 - - - +
29W ASN* 1.3 77.7 + - - +
31W VAL* 1.3 71.7 + - - +
74W ARG* 3.9 25.6 - - - +
75W ILE 3.0 14.4 - - - +
76W GLN* 4.0 13.7 - - + +
83W PRO* 5.3 1.5 - - - +
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Residues in contact with VAL 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21W ILE* 3.3 34.5 - - + -
22W ASP 3.5 9.9 - - - +
23W PRO* 4.9 4.3 - - + -
24W ASP* 4.1 1.6 - - - +
30W ALA* 1.3 81.8 - - - +
32W VAL* 1.3 81.6 + - - +
33W ILE* 4.0 11.9 - - + -
73W LEU 4.2 0.4 - - - -
74W ARG* 3.0 11.0 - - - +
75W ILE* 2.7 37.7 + - + +
83W PRO* 3.5 28.9 - - + -
84W LYS* 5.4 4.9 - - + -
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Residues in contact with VAL 32 (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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551M TYR* 3.2 28.5 - - + +
20W LYS 3.5 2.4 - - - +
21W ILE* 3.7 0.3 - - - -
22W ASP* 3.0 41.7 + - + +
24W ASP* 3.8 28.3 - - + +
31W VAL* 1.3 84.3 - - - +
33W ILE* 1.3 63.1 + - - +
34W THR* 3.9 1.8 + - - +
72W LYS* 4.0 24.9 - - + +
73W LEU 3.3 3.6 - - - +
74W ARG* 4.5 5.2 - - + -
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Residues in contact with ILE 33 (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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19W LEU* 3.3 34.8 - - + -
20W LYS 3.4 7.6 - - - +
21W ILE* 3.4 32.8 - - + -
31W VAL* 4.0 9.9 - - + -
32W VAL* 1.3 75.8 - - - +
34W THR* 1.3 60.0 + - - +
35W PHE* 3.3 21.2 - - + -
72W LYS* 3.4 1.0 - - - -
73W LEU* 2.7 40.6 + - + +
75W ILE* 4.0 17.7 - - + -
84W LYS* 5.8 3.6 - - + -
87W LEU* 3.4 30.5 - - + -
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Residues in contact with THR 34 (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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18W LYS 3.1 13.0 - - - +
19W LEU* 3.6 0.9 - - - -
20W LYS* 2.9 52.6 + - - +
22W ASP* 5.1 4.9 + - - -
32W VAL* 3.9 3.2 + - - +
33W ILE* 1.3 70.2 - - - +
35W PHE* 1.3 63.3 + - - +
36W GLU* 3.5 26.6 + - + +
70W ARG* 4.8 9.9 - - - +
71W PHE 3.3 6.5 - - - +
72W LYS* 3.3 30.8 - - + +
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Residues in contact with PHE 35 (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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258O ILE* 4.1 14.8 - - + -
18W LYS* 3.3 6.7 - - + -
19W LEU* 3.5 22.0 - - + -
33W ILE* 3.3 28.9 - - + -
34W THR* 1.3 70.3 - - - +
36W GLU* 1.3 59.4 + - - +
38W GLU* 4.0 10.7 - - + +
42W LEU* 4.0 9.2 - - + -
46W ILE* 3.8 25.8 - - + -
70W ARG* 2.9 28.7 - - - +
71W PHE* 2.6 60.0 + + + +
73W LEU* 3.6 27.6 - - + -
87W LEU* 4.5 11.4 - - + -
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Residues in contact with GLU 36 (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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12W LEU* 5.1 3.4 - - + -
16W GLU* 3.5 26.6 - - + +
17W SER 3.5 23.8 - - - +
18W LYS* 3.0 22.0 + - - +
20W LYS* 3.9 15.2 + - - +
34W THR* 3.5 17.3 + - + +
35W PHE* 1.3 70.1 - - - +
37W LYS* 1.3 91.6 + - + +
38W GLU* 3.0 14.1 + - - +
69W ALA 4.1 2.1 - - - +
70W ARG* 3.0 43.9 + - - -
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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