Contacts of the strand formed by residues 99 - 102 (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 LYS 99 (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* 4.0 0.6 - - - +
46A GLU* 2.8 34.8 + - - -
76A PRO* 5.0 9.8 - - - +
77A PHE 3.2 4.4 + - - -
78A THR* 3.2 26.7 - - - +
79A VAL 3.1 20.4 + - - -
93A ILE* 4.8 1.6 - - - -
97A ALA* 3.5 7.3 - - - +
98A ASP* 1.3 87.9 - - + +
100A VAL* 1.3 68.2 + - - +
123A GLN 3.3 24.7 - - - +
124A ALA* 3.3 9.9 - - - +
126A VAL* 3.8 11.4 - - + -
167A GLU* 2.6 32.4 + - - +
199A ILE* 5.6 1.4 - - - +
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Residues in contact with VAL 100 (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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78A THR* 3.8 4.0 - - - -
79A VAL* 3.3 15.7 - - + +
83A ILE* 3.9 21.8 - - + -
89A ALA* 3.9 28.0 - - + +
92A LEU* 4.4 2.7 - - + -
93A ILE* 3.7 27.4 - - + -
99A LYS* 1.3 79.1 - - - +
101A SER* 1.3 59.5 + - - +
102A ILE* 4.1 5.3 + - + -
116A ILE* 4.3 16.2 - - + -
124A ALA 2.9 15.7 + - - +
125A VAL* 4.9 3.4 - - + +
126A VAL* 2.9 25.3 + - - +
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Residues in contact with SER 101 (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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48A VAL* 5.7 0.7 - - - -
50A LEU* 4.9 9.6 - - - +
78A THR* 3.7 16.1 - - - +
79A VAL 3.0 10.7 + - - -
80A GLY* 3.8 20.5 - - - -
81A GLY 4.5 2.1 + - - -
83A ILE* 3.8 7.8 - - - +
100A VAL* 1.3 74.9 - - - +
102A ILE* 1.3 66.6 + - - +
103A ASN* 5.6 0.2 - - - +
126A VAL* 3.2 14.8 + - - +
128A ALA* 3.5 24.8 - - - +
169A LEU* 4.5 6.6 - - - +
264A PO4 5.0 2.6 + - - -
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Residues in contact with ILE 102 (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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83A ILE* 3.9 35.7 - - + +
100A VAL* 4.9 5.2 - - + +
101A SER* 1.3 80.2 - - - +
103A ASN* 1.3 63.1 + - - +
106A ALA* 3.8 25.4 - - + +
112A LEU* 4.2 15.7 - - + -
113A ILE* 3.9 20.6 - - + -
116A ILE* 4.1 28.5 - - + -
125A VAL* 4.2 7.9 - - + -
126A VAL 3.0 10.1 + - - +
127A VAL* 3.5 8.8 - - + +
128A ALA 2.9 22.7 + - - +
264A PO4 5.0 2.0 - - - -
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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