Contacts of the strand formed by residues 1 - 9 (chain A) in PDB entry 3VF1
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 MET 1 (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* 1.3 79.8 + - - +
2A LYS* 1.3 87.6 - - + +
3A TYR* 3.3 31.3 + - + +
57A SER* 3.1 6.7 - - - -
58A GLY 3.0 40.6 + - - +
60A ASP* 3.1 41.9 - - + +
89A LYS* 4.0 6.5 - - + -
90A ILE* 3.3 50.5 - - + +
92A GLU* 5.5 2.0 - - - -
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Residues in contact with LYS 2 (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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0A HIS 3.9 3.8 + - - +
1A MET* 1.3 94.0 - - + +
3A TYR* 1.3 66.0 + - - +
4A LYS* 5.1 6.3 - - + +
56A GLN 3.3 9.4 - - - +
57A SER* 4.5 2.2 - - - +
88A GLU* 4.3 15.5 + - - +
89A LYS* 3.8 16.7 + - - +
90A ILE* 3.7 45.1 - - + +
97A SER* 5.5 1.6 - - - -
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Residues in contact with TYR 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 MET* 3.3 32.5 - - + +
2A LYS* 1.3 81.8 - - - +
4A LYS* 1.3 59.5 + - - +
5A ILE* 3.6 13.3 + - + -
25A LEU* 3.5 31.6 - - + -
33A THR* 3.8 14.8 - - + -
36A PHE* 3.8 20.2 - + - -
54A TYR 3.5 3.3 - - - +
55A ASP* 3.6 0.7 - - - -
56A GLN* 2.7 48.1 + - + +
58A GLY 4.7 2.5 - - - -
59A VAL 3.1 19.8 + - - -
61A VAL* 3.3 25.6 + - + +
64A ILE* 4.9 0.4 - - + -
87A ILE* 4.5 4.3 - - + -
88A GLU 3.8 1.6 - - - -
89A LYS* 3.6 30.5 - - + -
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Residues in contact with LYS 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 LYS* 4.3 7.3 - - + +
3A TYR* 1.3 70.2 - - - +
5A ILE* 1.3 59.6 + - - +
6A THR* 3.7 8.1 + - - +
53A THR* 3.6 28.3 - - + -
54A TYR 3.4 2.9 - - - -
55A ASP* 3.8 18.8 - - - +
86A ILE 3.3 5.7 - - - +
87A ILE* 4.4 0.2 - - - -
88A GLU* 2.9 62.5 + - + +
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Residues in contact with ILE 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 TYR* 4.3 12.1 - - + +
4A LYS* 1.3 73.0 - - - +
6A THR* 1.3 59.4 + - - +
7A VAL* 4.3 11.4 - - + -
23A ILE* 3.8 37.2 - - + -
25A LEU* 4.6 6.3 - - + -
36A PHE* 4.3 10.5 - - + -
38A LEU* 4.7 8.5 - - + -
54A TYR* 2.7 51.9 + - + +
56A GLN* 4.2 19.5 - - + -
85A VAL* 3.8 24.7 - - + -
86A ILE 3.6 2.9 - - - -
87A ILE* 4.1 17.7 - - + +
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Residues in contact with THR 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 LYS* 4.2 9.7 + - - +
5A ILE* 1.3 73.7 - - - +
7A VAL* 1.3 61.7 + - - +
8A GLU* 4.0 8.0 + - + +
51A THR* 3.3 33.4 - - + -
52A ASP 3.5 2.7 - - - -
53A THR* 3.5 20.8 + - - +
85A VAL* 3.4 4.0 - - - +
86A ILE* 2.7 59.2 + - + +
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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 ILE* 4.3 9.6 - - + -
6A THR* 1.3 76.5 - - - +
8A GLU* 1.3 65.7 + - - +
9A THR* 3.8 1.0 + - - -
38A LEU* 4.0 26.9 - - + -
51A THR* 3.5 3.5 - - - -
52A ASP* 2.9 37.8 + - + +
54A TYR* 4.2 11.7 - - + -
80A TRP* 3.5 34.3 - - + -
82A ILE* 3.9 28.5 - - + -
84A LYS 4.0 2.5 - - - -
85A VAL* 4.5 10.5 - - + +
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Residues in contact with GLU 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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6A THR* 4.9 4.9 - - + +
7A VAL* 1.3 75.4 - - - +
9A THR* 1.3 62.4 + - - +
50A GLY 3.7 6.5 - - - +
51A THR* 4.0 19.0 + - + +
82A ILE* 3.6 3.6 - - - +
83A ALA* 2.8 34.5 + - + +
84A LYS* 3.0 45.8 + - + +
86A ILE* 3.8 21.2 - - + +
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Residues in contact with THR 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 3.8 1.0 + - - -
8A GLU* 1.3 74.4 - - - +
10A GLY* 1.3 74.4 + - - +
12A LEU 4.6 6.3 - - - +
13A ARG* 6.4 0.2 - - - -
40A LYS* 4.1 8.8 + - - -
42A PHE* 4.5 13.5 - - + -
48A SER* 5.5 0.4 - - - -
49A GLY* 3.4 36.4 + - - +
50A GLY 3.1 10.0 + - - +
52A ASP* 4.3 2.8 + - - -
80A TRP* 3.0 36.3 + - + +
81A TYR 3.4 14.6 - - - +
82A ILE* 4.5 0.2 - - - +
83A ALA* 4.0 3.4 - - - +
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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