Contacts of the strand formed by residues 2 - 9 (chain A) in PDB entry 3JVX
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 ARG 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A HIS 3.9 1.0 + - - -
1A MET* 1.3 71.6 - - - +
3A VAL* 1.3 62.9 + - - +
4A SER* 3.4 23.6 - - - +
91A GLU 2.8 18.0 + - - +
92A GLU* 3.3 20.3 + - + -
93A ILE* 2.9 29.8 + - - +
110A ASP* 3.9 18.3 + - + +
111A LYS* 3.7 32.8 - - - +
159A GLU* 5.0 8.9 + - - -
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Residues in contact with VAL 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1A HIS* 3.8 31.2 - - + +
1A MET* 4.0 8.3 - - + +
2A ARG* 1.3 73.8 - - - +
4A SER* 1.3 60.7 + - - +
5A PHE* 4.6 4.0 - - + -
84A PHE* 4.1 17.7 - - + -
93A ILE* 4.0 5.8 - - + -
95A ILE* 3.8 30.3 - - + -
105A PHE* 4.8 5.4 - - + -
108A TYR* 3.5 24.7 - - + +
109A VAL* 3.6 9.2 - - - +
110A ASP* 2.8 35.3 + - - -
111A LYS 3.3 4.0 + - - -
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Residues in contact with SER 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 3.4 13.4 + - - +
3A VAL* 1.3 73.7 - - - +
5A PHE* 1.3 56.6 + - - +
92A GLU* 2.6 28.1 + - - -
93A ILE 2.9 15.8 + - - +
94A PHE* 3.3 10.9 - - - -
95A ILE* 2.7 34.8 + - - +
111A LYS* 3.2 13.9 - - - +
113A TYR* 3.6 16.5 - - - -
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Residues in contact with PHE 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A VAL* 4.6 0.7 - - + -
4A SER* 1.3 73.7 - - - +
6A MET* 1.3 61.0 + - - +
7A VAL* 4.1 0.4 - - + -
95A ILE* 3.6 31.9 - - + +
102A TYR* 3.3 47.3 - + + -
105A PHE* 3.7 12.3 - - + -
106A LEU* 3.7 31.6 - - + -
109A VAL* 3.5 27.8 - - + -
111A LYS 2.8 7.3 + - - -
112A LEU* 3.6 17.9 - - + -
113A TYR* 2.9 33.7 + - - +
127A PHE* 3.6 25.8 - + + -
130A MET* 5.1 0.9 - - - -
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Residues in contact with MET 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A SER 4.0 0.4 + - - -
5A PHE* 1.3 72.1 - - - +
7A VAL* 1.3 55.5 + - - +
31A TYR* 4.3 10.5 - - + -
32A VAL* 4.0 13.2 - - + -
35A THR* 3.9 32.8 - - + -
36A THR* 4.2 10.5 - - + -
94A PHE* 4.0 14.6 - - + -
95A ILE 2.8 16.1 + - - +
96A PHE* 3.9 22.9 - - + -
102A TYR* 2.5 23.6 + - - -
113A TYR* 3.6 28.7 - - + +
115A THR* 5.6 0.2 - - - -
208A EKB 2.9 44.0 + - - +
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 5.1 0.4 - - + -
6A MET* 1.3 70.9 - - - +
8A ALA* 1.3 64.3 + - - +
9A MET* 4.9 0.4 - - + -
15A ILE* 3.8 16.2 - - + -
102A TYR* 3.2 35.4 - - + +
112A LEU* 4.2 5.4 - - + -
113A TYR 3.1 6.1 + - - +
114A ILE* 3.4 30.4 - - + -
115A THR 2.9 23.4 + - - -
127A PHE* 3.7 29.8 - - + -
207A NDP 3.4 6.7 - - - +
208A EKB 3.3 14.7 + - - -
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Residues in contact with ALA 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 1.3 73.5 - - - +
9A MET* 1.3 60.5 + - - +
15A ILE* 3.4 7.3 - - - +
23A TRP* 3.3 20.5 - - + -
28A GLU* 4.0 7.0 - - - +
115A THR* 3.4 16.4 - - - +
117A ILE* 4.4 6.1 - - + -
207A NDP 2.8 35.9 + - - +
208A EKB 3.5 27.3 - - + +
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Residues in contact with MET 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A VAL* 4.3 2.2 - - + -
8A ALA* 1.3 75.1 - - - +
10A ASP* 1.3 69.8 + - - +
11A GLU 5.7 1.1 - - - +
13A ARG* 3.6 46.4 - - + +
14A VAL 3.3 12.1 - - - +
15A ILE* 3.7 12.6 - - + -
23A TRP* 4.0 4.5 - - - -
114A ILE* 3.5 31.4 - - + -
115A THR 3.0 9.9 + - - +
116A LYS* 3.5 19.7 - - + -
117A ILE* 2.8 27.4 + - - +
127A PHE* 3.9 17.7 - - + -
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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