Contacts of the strand formed by residues 18 - 25 (chain J) in PDB entry 3IT8
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 18 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8J THR 4.3 0.4 - - - -
9J VAL* 2.9 7.3 - - - +
10J THR* 2.8 37.0 + - - +
12J LYS* 2.9 40.9 - - + +
16J LEU* 4.0 2.7 + - - -
17J TYR* 1.3 75.7 - - - +
19J GLY* 1.3 59.9 + - - +
20J VAL* 6.0 2.0 - - + -
35J TYR 4.7 3.5 - - - +
37J HIS* 3.0 26.0 + - - -
70J TYR* 4.0 1.1 - - - -
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Residues in contact with GLY 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8J THR 3.2 6.5 - - - -
9J VAL* 4.2 0.7 - - - -
18J ASP* 1.3 79.5 + - - +
20J VAL* 1.3 65.6 + - - +
34J SER* 3.1 4.9 - - - -
35J TYR* 2.9 29.7 + - - +
66J PHE* 3.9 7.2 - - - -
70J TYR* 3.8 24.6 - - - -
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Residues in contact with VAL 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J ASN 3.7 1.0 - - - +
7J TYR* 3.5 2.4 - - - -
8J THR* 2.8 47.6 + - + +
10J THR* 5.7 1.6 - - - +
18J ASP* 6.0 1.6 - - + -
19J GLY* 1.3 79.3 - - - +
21J PHE* 1.3 61.0 + - - +
22J TYR* 4.3 14.4 - - + +
32J LYS* 4.5 15.0 - - - +
33J ILE 3.1 10.5 - - - +
34J SER* 4.0 11.9 - - - -
66J PHE* 3.9 5.6 - - - -
325J NAG 3.9 23.3 - - - +
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Residues in contact with PHE 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J TYR* 3.9 16.2 - + + -
6J ASN 3.1 12.6 - - - -
7J TYR* 3.4 46.2 - + + -
20J VAL* 1.3 77.2 - - - +
22J TYR* 1.3 82.1 + - - +
23J ASP* 3.9 13.9 - - + -
31J THR* 4.4 3.8 - - + -
32J LYS* 3.3 7.1 - - - +
33J ILE* 2.8 50.7 + - + +
64J TYR* 3.2 46.2 - + + -
66J PHE* 3.7 21.3 - + + -
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Residues in contact with TYR 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J LYS 3.5 1.2 - - - +
5J TYR* 3.5 5.4 - - - -
6J ASN* 2.9 44.0 + - + +
20J VAL* 4.3 18.4 - - + +
21J PHE* 1.3 85.0 - - - +
23J ASP* 1.3 59.8 + - - +
24J HIS* 3.9 23.1 - - + -
29J LEU* 3.9 22.2 - - + -
31J THR 3.5 1.3 - - - -
32J LYS* 3.6 42.3 + - + -
325J NAG 3.3 35.8 + - - -
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Residues in contact with ASP 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3J LEU* 3.6 4.3 - - - +
4J LYS 3.6 3.1 - - - -
5J TYR* 3.1 16.8 - - - -
21J PHE* 3.9 9.2 - - + -
22J TYR* 1.3 72.3 - - - +
24J HIS* 1.3 59.6 + - - +
29J LEU* 3.7 4.0 - - - +
30J VAL* 2.7 41.7 + - - +
31J THR* 3.0 28.4 + - - +
64J TYR* 2.8 23.0 + - - -
170J TYR* 2.6 36.6 + - - -
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Residues in contact with HIS 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2J THR* 3.7 0.9 - - - +
3J LEU* 3.4 4.5 - - - +
4J LYS* 2.8 69.3 + - + +
6J ASN* 5.9 0.7 - - + -
22J TYR* 3.9 31.9 - + + +
23J ASP* 1.3 76.1 + - - +
25J TYR* 1.3 58.9 + - - +
26J ASN 3.8 11.5 + - - +
27J ASP* 4.4 8.5 + - - -
28J GLN 3.4 3.3 + - - -
29J LEU* 3.5 40.1 + - + +
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Residues in contact with TYR 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1J ILE* 3.2 30.0 - - + +
2J THR 3.3 15.5 - - - -
3J LEU* 4.4 2.9 - - + -
24J HIS* 1.3 70.0 - - - +
26J ASN* 1.3 87.4 + - - +
28J GLN* 2.7 27.6 + - + +
30J VAL* 3.8 19.4 - - + +
50J TRP* 4.1 7.6 - + + -
167J ILE* 4.1 17.9 - - + -
170J TYR* 3.5 32.5 - + + -
171J GLN* 3.3 27.6 - - - +
174J ALA* 3.7 29.4 - - + -
178J ILE* 3.9 9.2 - - + -
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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