Contacts of the strand formed by residues 19 - 25 (chain J) in PDB entry 3Q3G
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 VAL 19 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11J LEU* 3.7 22.7 - - + -
13J VAL* 4.0 13.9 - - + -
17J GLU* 5.4 0.4 - - + -
18J LYS* 1.3 74.5 - - - +
20J THR* 1.3 65.0 + - - +
21J MET* 3.7 26.2 - - + -
80J THR* 3.4 4.3 - - - +
81J ILE* 2.7 42.9 + - + +
84J VAL* 3.4 44.0 - - + -
110J LEU* 4.1 6.7 - - + -
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Residues in contact with THR 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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8J PRO* 4.4 11.3 - - - +
11J LEU* 4.4 8.1 - - - +
18J LYS* 4.3 13.0 + - + +
19J VAL* 1.3 81.4 - - - +
21J MET* 1.4 66.5 + - - +
78J THR* 4.6 5.4 - - - +
79J LEU 3.4 4.5 - - - -
80J THR* 3.7 25.1 - - + +
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Residues in contact with MET 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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6J GLN* 5.6 0.2 - - - +
7J SER 3.9 2.9 - - - -
11J LEU* 5.4 0.4 - - + -
19J VAL* 3.7 15.9 - - + -
20J THR* 1.4 77.6 - - - +
22J SER* 1.3 60.0 + - - +
41J TRP* 4.0 15.3 - - + -
78J THR* 3.2 8.7 - - - -
79J LEU* 2.8 61.0 + - + +
81J ILE* 3.7 29.8 - - + -
92J TYR* 3.7 34.1 - - + -
108J THR* 3.5 36.8 - - + +
110J LEU* 4.6 3.1 - - + -
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Residues in contact with SER 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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5J THR 4.3 1.7 + - - -
6J GLN* 3.2 9.0 + - - +
7J SER* 2.8 51.9 + - - +
20J THR 4.6 0.2 + - - -
21J MET* 1.3 74.5 - - - +
23J CYS* 1.3 62.4 + - - +
24J LYS* 3.8 28.6 - - - +
41J TRP* 4.3 2.4 - - - -
77J PHE 3.6 5.8 + - - -
78J THR* 4.7 3.1 - - - +
108J THR* 5.0 0.2 + - - -
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Residues in contact with CYS 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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4J MET* 3.6 21.5 - - - -
5J THR 3.4 4.7 - - - -
6J GLN* 4.2 0.7 - - + -
22J SER* 1.3 73.8 + - - +
24J LYS* 1.3 60.9 + - - +
39J LEU* 3.7 9.2 - - - -
41J TRP* 3.5 22.4 - - + -
75J THR 3.8 1.0 - - - +
77J PHE* 2.7 44.3 + - + +
94J CYS* 2.1 47.1 - - - -
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Residues in contact with LYS 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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3J GLU 3.5 1.7 - - - +
4J MET* 3.6 2.1 - - - -
5J THR* 2.8 55.9 + - - +
22J SER* 3.8 18.8 - - - +
23J CYS* 1.3 79.7 - - - +
25J SER* 1.3 61.0 + - - +
75J THR* 3.4 3.4 - - + -
76J ASP* 3.3 36.3 - - + +
77J PHE 5.0 0.2 - - - +
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Residues in contact with SER 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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2J ILE* 3.3 12.1 - - - +
3J GLU 3.6 4.0 - - - -
4J MET* 4.1 9.0 - - - -
5J THR* 5.5 0.4 - - - -
23J CYS 4.3 0.4 - - - -
24J LYS* 1.3 73.3 - - - +
26J SER* 1.3 61.7 + - - +
27J GLN 2.4 31.1 + - - -
29J LEU* 3.4 25.6 - - - +
75J THR* 2.8 40.4 + - - +
77J PHE* 4.7 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