Contacts of the helix formed by residues 87 - 91 (chain A) in PDB entry 1VDV
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 THR 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A VAL* 4.6 1.8 - - + -
11A ASN* 2.9 20.3 + - - +
30A LEU* 3.9 39.7 - - + -
36A LEU* 4.6 2.2 - - + +
39A THR* 3.9 9.6 - - - +
53A VAL* 4.2 9.4 - - + -
85A VAL* 4.2 7.2 - - + -
86A THR* 1.3 82.7 - - - +
88A VAL* 1.3 60.0 + - - +
89A GLU* 2.6 37.2 + - - +
90A GLY* 2.8 18.9 + - - -
91A ILE 3.7 3.5 + - - -
122A MET* 3.7 8.0 - - - +
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Residues in contact with VAL 88 (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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38A GLY* 3.8 22.2 - - - -
39A THR* 4.6 2.3 + - - +
87A THR* 1.3 76.8 - - - +
89A GLU* 1.3 81.6 + - - +
90A GLY 3.1 0.7 + - - -
91A ILE* 3.3 17.2 + - - +
92A GLY 3.6 1.2 - - - +
102A GLN* 3.4 13.0 + - - +
118A PRO* 4.0 22.2 - - + -
121A VAL* 4.2 8.7 - - + -
122A MET* 3.6 18.5 - - + +
586A ALA 3.2 27.1 - - - +
587A SER 3.7 16.4 - - - +
588A GLY* 3.9 3.1 - - - -
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Residues in contact with GLU 89 (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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11A ASN* 3.8 4.5 - - - +
36A LEU* 3.3 41.3 - - + +
37A ARG 3.8 0.7 + - - -
38A GLY* 3.2 27.0 + - - -
39A THR* 4.2 2.6 + - - -
87A THR* 2.6 33.0 + - - +
88A VAL* 1.3 92.7 - - + +
90A GLY* 1.3 59.5 + - - +
91A ILE 3.4 0.7 + - - -
92A GLY* 4.0 15.3 + - - +
93A SER* 5.5 2.1 - - - -
587A SER 4.4 5.8 - - - +
588A GLY 4.8 2.6 - - - +
589A GLU* 6.6 0.2 - - + -
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Residues in contact with GLY 90 (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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11A ASN* 3.2 34.0 + - - +
86A THR* 4.5 5.4 - - - +
87A THR 2.8 8.9 + - - -
89A GLU* 1.3 80.8 - - - +
91A ILE* 1.3 63.7 + - - +
210A PRO* 4.1 17.8 - - - +
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Residues in contact with ILE 91 (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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86A THR* 3.8 12.8 - - + -
87A THR 4.1 3.8 - - - +
88A VAL 3.3 11.9 + - - +
90A GLY* 1.3 80.8 - - - +
92A GLY* 1.3 59.6 + - - +
97A ARG 4.6 0.7 - - - +
99A HIS* 3.3 30.3 - - + +
101A VAL* 4.9 0.7 - - + -
102A GLN* 3.6 15.7 - - + +
121A VAL* 3.5 31.9 - - + -
122A MET* 4.2 7.2 - - + -
125A TYR* 3.5 57.9 - - + +
210A PRO* 5.4 4.3 - - + -
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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