Contacts of the strand formed by residues 46 - 51 (chain A) in PDB entry 1VH7
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 GLU 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ARG* 2.9 38.0 + - - -
6A ILE 3.6 2.8 + - - -
7A ILE* 3.4 23.9 - - + +
8A ALA 3.2 12.0 + - - -
44A ILE* 2.9 18.0 - - - +
45A ASP* 1.3 88.3 - - + +
47A LEU* 1.3 67.2 + - - +
48A VAL* 6.1 0.5 - - - +
75A ILE* 4.0 2.0 - - - -
76A PRO* 3.3 31.8 - - + +
78A THR* 4.7 3.1 + - - -
99A LYS* 2.8 31.7 + - - -
199A ILE* 5.7 0.5 - - - +
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Residues in contact with LEU 47 (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 ALA* 3.4 18.4 - - + +
10A LEU* 4.1 11.4 - - + -
36A GLY* 3.7 28.3 - - - +
39A TYR* 4.2 13.9 - - + -
44A ILE* 3.9 13.9 - - + -
46A GLU* 1.3 84.6 - - - +
48A VAL* 1.3 68.7 + - - +
49A PHE* 3.8 23.3 - - + -
73A ILE* 3.5 28.7 - - + -
75A ILE* 4.0 8.5 - - + -
76A PRO 3.1 5.1 + - - -
77A PHE* 3.2 6.8 - - + -
78A THR* 2.9 24.2 + - - -
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Residues in contact with VAL 48 (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 ILE* 3.7 21.3 - - + -
8A ALA 2.9 9.9 + - - +
9A CYS* 3.3 12.9 - - - -
10A LEU* 2.7 35.0 + - - +
46A GLU* 6.1 0.9 - - - +
47A LEU* 1.3 79.7 - - - +
49A PHE* 1.3 59.9 + - - +
50A LEU* 3.9 30.7 - - + -
78A THR* 3.4 27.1 - - + +
101A SER* 5.7 0.7 - - - -
169A LEU* 4.8 12.1 - - + -
199A ILE* 5.8 3.4 - - + -
222A LEU* 4.0 13.9 - - + -
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Residues in contact with PHE 49 (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 LEU* 3.4 38.4 - - + +
12A VAL* 4.3 7.0 - - + -
32A PRO* 3.8 17.9 - - + -
33A VAL* 5.6 0.2 - - - -
36A GLY* 4.9 0.9 - - - -
47A LEU* 3.8 34.5 - - + -
48A VAL* 1.3 75.1 - - - +
50A LEU* 1.3 63.0 + - - +
51A ASP 4.0 0.7 - - - -
65A LEU* 4.1 28.7 - - + -
69A VAL* 3.7 38.4 - - + -
73A ILE* 6.0 0.2 - - + -
77A PHE* 3.9 20.4 - + + -
78A THR 2.9 11.2 + - - +
79A VAL* 3.4 10.1 - - + +
80A GLY 2.9 25.5 + - - +
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Residues in contact with LEU 50 (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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9A CYS* 3.8 20.2 - - - -
10A LEU 3.0 8.9 + - - +
11A ASP* 3.5 19.1 - - - +
12A VAL* 2.9 26.1 + - - +
48A VAL* 3.9 20.2 - - + -
49A PHE* 1.3 80.8 - - - +
51A ASP* 1.3 61.1 + - - +
52A ILE* 4.1 5.1 + - + +
80A GLY* 3.3 23.8 - - - +
81A GLY* 4.2 4.5 - - - +
101A SER* 4.9 9.9 - - - +
169A LEU* 5.9 5.2 - - + -
222A LEU* 6.3 0.2 - - + -
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Residues in contact with ASP 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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12A VAL* 3.4 23.0 - - + +
13A LYS* 4.3 0.7 - - - -
14A ASP 4.4 0.2 + - - -
15A GLY 5.2 0.3 + - - -
49A PHE 4.0 1.2 - - - +
50A LEU* 1.3 73.4 - - - +
52A ILE* 1.4 67.9 + - - +
53A THR* 2.6 45.1 + - - -
58A LYS* 3.0 29.5 + - - +
61A THR* 4.2 7.3 - - - +
62A MET* 3.5 36.8 - - + +
65A LEU* 5.5 3.1 - - + +
79A VAL* 5.7 0.9 - - + -
80A GLY 2.9 8.7 + - - +
81A GLY* 3.6 12.5 - - - -
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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