Contacts of the strand formed by residues 25 - 31 (chain A) in PDB entry 1QGV
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A ARG* 1.3 72.6 - - - +
26A VAL* 1.3 60.1 + - - +
27A VAL* 3.9 12.3 - - + -
55A PHE 2.9 11.2 + - - +
56A ALA* 3.2 24.9 - - + -
57A VAL* 2.9 23.6 + - - +
83A PHE* 5.2 3.1 - - + -
84A PHE 3.3 9.9 - - - +
85A PHE* 3.8 18.8 - - + -
116A ILE* 4.0 11.0 - - + +
119A VAL* 4.3 14.1 - - + +
120A TYR* 3.3 38.8 - - + +
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Residues in contact with VAL 26 (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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17A ALA 3.7 14.1 - - - +
18A ILE* 4.3 15.0 - - + +
21A GLU* 3.5 39.3 - - + +
24A ARG 4.0 1.3 - - - +
25A VAL* 1.3 72.0 - - - +
27A VAL* 1.3 60.7 + - - +
28A ILE* 3.9 24.9 - - + -
57A VAL* 3.5 4.3 - - + -
59A TYR* 3.9 22.4 - - + -
82A MET 3.7 1.2 - - - +
83A PHE* 3.6 4.7 - - - -
84A PHE* 2.8 48.0 + - + +
86A ARG 6.4 0.2 - - - +
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Residues in contact with VAL 27 (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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25A VAL* 3.9 22.2 - - + -
26A VAL* 1.3 73.8 - - - +
28A ILE* 1.3 61.6 + - - +
45A LEU* 4.4 10.1 - - + -
56A ALA* 4.2 9.6 - - + -
57A VAL 2.8 16.2 + - - +
58A ILE* 3.3 21.1 - - + +
59A TYR* 2.9 26.5 + - - +
81A VAL* 3.4 29.2 - - + -
82A MET 3.6 3.1 - - - -
83A PHE* 4.0 19.3 - - + -
116A ILE* 4.2 12.8 - - + -
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Residues in contact with ILE 28 (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 LEU* 4.7 7.6 - - + -
14A VAL* 3.9 24.5 - - + -
17A ALA* 5.3 0.2 - - + -
18A ILE* 4.1 10.5 - - + -
26A VAL* 3.9 15.3 - - + -
27A VAL* 1.3 79.2 - - - +
29A ARG* 1.3 63.4 + - - +
30A PHE* 3.2 32.5 + - + -
59A TYR* 3.4 13.2 - - + +
61A VAL* 3.6 21.1 - - + -
81A VAL* 3.4 3.5 - - - -
82A MET 2.8 39.4 + - - +
84A PHE* 3.8 25.8 - - + -
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Residues in contact with ARG 29 (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 HIS* 4.1 2.0 + - - -
27A VAL* 5.3 1.0 - - - +
28A ILE* 1.3 71.6 - - - +
30A PHE* 1.3 61.1 + - - +
31A GLY 3.7 9.7 + - - +
33A ASP* 2.8 37.2 + - - +
38A CYS* 4.3 6.9 - - - +
41A MET* 4.1 10.5 - - + -
42A ASP* 2.6 41.3 + - - +
45A LEU* 4.1 12.1 - - + +
59A TYR 2.9 7.9 + - - +
60A LEU* 3.7 33.8 - - + +
61A VAL* 2.8 56.6 + - - +
79A CYS* 3.4 31.1 - - - -
80A THR 3.4 7.0 - - - +
81A VAL* 4.3 4.2 - - + +
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Residues in contact with PHE 30 (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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14A VAL* 4.4 5.8 - - + -
28A ILE* 3.2 45.3 - - + -
29A ARG* 1.3 75.4 - - - +
31A GLY* 1.3 57.0 + - - +
61A VAL* 3.6 33.0 - - + -
63A ILE* 3.9 4.2 - - + +
69A PHE* 3.9 29.6 - + + -
72A MET* 4.6 0.9 - - + -
73A TYR* 3.4 35.8 - + + -
78A PRO 4.1 2.1 - - - +
79A CYS* 3.9 1.2 - - - -
80A THR* 2.7 40.4 + - - +
82A MET* 3.0 39.9 - - + -
84A PHE* 5.1 0.9 - + - -
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Residues in contact with GLY 31 (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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29A ARG* 3.7 3.5 + - - +
30A PHE* 1.3 75.9 - - - +
32A HIS* 1.3 61.5 + - - -
38A CYS* 3.6 13.9 - - - -
61A VAL 3.2 6.2 + - - +
62A ASP* 3.2 9.2 - - - -
63A ILE* 2.9 42.4 + - - +
77A ASP 4.9 4.0 - - - -
79A CYS* 4.2 2.9 - - - -
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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