Contacts of the strand formed by residues 50 - 56 (chain A) in PDB entry 1V1A
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 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.9 6.4 - - - +
4A VAL* 3.2 15.0 - - + +
6A THR* 4.0 11.2 - - + -
40A ALA* 3.2 46.4 - - + +
43A LEU* 3.7 11.0 - - + -
44A ALA* 3.5 23.3 - - + +
48A VAL 3.2 6.2 + - - +
49A LYS* 1.3 75.4 - - - +
51A GLY* 1.3 73.0 + - - +
73A GLY 4.4 3.0 + - - +
74A VAL* 3.7 7.2 - - + -
75A ASP* 3.1 22.3 + - - +
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Residues in contact with GLY 51 (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 LEU* 4.0 5.9 - - - +
4A VAL 2.9 10.5 + - - -
5A VAL* 3.2 5.6 - - - +
6A THR* 2.5 35.7 + - - +
50A VAL* 1.3 80.7 - - - +
52A PHE* 1.3 56.9 + - - -
75A ASP* 3.6 5.8 - - - -
122A TYR* 3.5 21.5 - - - -
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Residues in contact with PHE 52 (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* 3.2 23.6 - - - +
7A ALA* 3.9 0.7 - - - -
8A GLY 3.6 29.8 - - - -
10A PRO* 3.4 23.6 - - + -
36A GLU* 3.7 30.7 - - + -
37A VAL* 3.6 25.1 - - + -
40A ALA* 4.4 1.8 - - + -
51A GLY* 1.3 75.6 - - - -
53A VAL* 1.3 74.1 + - - +
54A GLY* 3.8 6.1 - - - -
69A LEU* 4.5 11.0 - - + -
74A VAL* 3.4 22.7 - - + +
75A ASP 3.1 15.9 + - - +
76A LEU* 4.2 3.0 - - + -
78A HIS 4.4 1.2 + - - -
79A PHE* 3.7 30.3 + + - +
122A TYR* 4.7 0.7 + - - -
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Residues in contact with VAL 53 (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 VAL* 4.0 10.3 - - + -
6A THR 2.9 8.3 + - - -
7A ALA* 3.4 31.8 - - + +
8A GLY 3.5 6.9 + - - +
52A PHE* 1.3 80.0 - - - +
54A GLY* 1.3 59.7 + - - +
55A ARG* 5.1 2.2 - - - +
78A HIS* 3.7 22.4 - - + +
113A LEU* 4.5 9.7 - - + +
117A ALA* 5.0 2.5 - - + -
118A PHE* 3.8 33.7 - - + -
122A TYR* 3.6 34.5 - - + -
145A PHE* 4.9 4.9 - - + -
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Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLY 4.1 7.6 - - - -
52A PHE* 3.8 14.9 - - - -
53A VAL* 1.3 79.5 - - - +
55A ARG* 1.3 70.6 + - - -
78A HIS 3.6 3.8 + - - -
79A PHE* 3.1 23.1 - - - +
80A ARG 3.2 13.2 + - - -
113A LEU* 4.6 8.1 - - - -
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Residues in contact with ARG 55 (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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8A GLY 4.9 0.2 + - - -
10A PRO* 3.9 12.7 - - - +
53A VAL* 5.1 2.2 - - - +
54A GLY* 1.3 83.0 + - - -
56A VAL* 1.3 65.9 + - - +
78A HIS* 3.5 21.6 + - - +
79A PHE* 4.1 0.8 - - - -
80A ARG* 3.0 34.0 + - - +
82A ALA* 4.4 17.5 - - + +
86A THR* 5.6 0.3 - - - +
109A ALA 3.6 19.3 - - - +
110A GLY* 3.1 28.5 + - - -
112A ALA* 6.0 2.0 - - + -
113A LEU* 5.0 18.6 - - + +
117A ALA* 3.1 31.9 + - - +
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Residues in contact with VAL 56 (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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10A PRO* 4.1 7.2 - - + -
55A ARG* 1.3 76.7 - - - +
57A GLY* 1.3 68.2 + - - +
62A GLY* 3.5 18.2 - - - +
65A VAL* 3.6 28.3 - - + -
79A PHE* 3.3 37.5 - - + -
80A ARG 3.6 1.2 + - - -
81A ARG* 3.2 31.2 - - + -
82A ALA 2.9 20.3 + - - +
86A THR* 3.9 8.5 - - + +
109A ALA* 3.9 3.1 - - - -
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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