Contacts of the strand formed by residues 96 - 101 (chain A) in PDB entry 1VD6
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 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A LEU* 4.6 17.0 - - + -
11A LEU* 4.0 15.0 - - + -
37A ASP* 3.1 14.3 + - + +
38A GLY* 3.0 22.7 - - - -
39A VAL* 3.2 5.0 + - - +
94A GLN 4.1 7.9 - - - +
95A ALA* 1.3 76.7 - - - +
97A PHE* 1.3 69.2 + - - +
124A GLY* 3.3 19.5 - - - +
126A TRP* 3.8 24.2 - - + -
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Residues in contact with PHE 97 (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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32A LEU* 4.4 6.1 - - + -
39A VAL* 3.6 27.6 - - + -
41A LEU* 4.3 5.6 - - + -
85A VAL* 3.4 28.9 - - + -
86A LEU* 3.7 31.6 - - + -
88A LEU* 4.2 9.0 - - + -
89A LYS* 3.8 42.6 - - + -
95A ALA* 3.6 29.8 - - + -
96A VAL* 1.3 75.3 - - - +
98A ASN* 1.3 59.7 + - - +
99A VAL* 3.8 0.4 - - + -
124A GLY 2.8 18.6 + - - +
125A VAL* 3.2 8.7 - - + +
126A TRP* 3.0 28.8 + - - -
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Residues in contact with ASN 98 (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 LEU* 5.2 2.2 - - + -
39A VAL 2.9 14.5 + - - +
40A GLU* 3.2 23.1 - - + +
41A LEU* 2.9 27.3 + - - +
97A PHE* 1.3 71.8 - - - +
99A VAL* 1.3 63.8 + - - +
100A GLU 3.7 0.5 + - - -
126A TRP* 3.3 47.1 + - + +
128A SER* 3.0 29.4 + - - +
168A HIS* 3.5 15.0 + - - -
212A ILE* 3.7 9.0 - - - +
300A GOL 4.6 0.7 + - - -
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Residues in contact with VAL 99 (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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41A LEU* 3.6 14.1 - - + +
43A VAL* 3.7 35.0 - - + -
82A LEU* 3.8 28.5 - - + -
86A LEU* 4.4 4.7 - - + -
97A PHE 4.6 0.4 - - - +
98A ASN* 1.3 73.9 - - - +
100A GLU* 1.3 62.1 + - - +
115A LEU* 4.4 15.3 - - + -
119A LEU* 5.0 2.2 - - + -
125A VAL* 3.9 21.8 - - + -
126A TRP 2.9 10.1 + - - +
127A VAL* 3.2 12.7 - - + +
128A SER 2.9 22.0 + - - -
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Residues in contact with GLU 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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40A GLU* 3.3 14.8 - - - +
41A LEU 2.8 10.8 + - - +
42A ASP* 3.4 7.3 - - - +
43A VAL* 3.0 28.0 + - - +
98A ASN 3.7 1.6 + - - -
99A VAL* 1.3 71.9 - - - +
101A LEU* 1.3 66.8 + - - +
102A LYS* 2.7 37.1 + - + +
128A SER* 3.3 12.5 + - - +
129A SER* 4.6 0.4 - - - -
130A PHE* 3.3 17.8 + - - -
150A LEU* 3.4 23.3 - - + -
300A GOL 2.6 38.4 + - - +
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Residues in contact with LEU 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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43A VAL* 4.0 9.4 - - + +
45A PRO* 4.7 0.7 - - + -
51A PHE* 3.8 28.5 - - + -
99A VAL 3.6 2.8 + - - -
100A GLU* 1.3 71.6 - - - +
102A LYS* 1.3 71.5 + - - +
103A SER* 4.1 13.3 + - - +
108A GLY 4.5 1.8 - - - +
111A ALA* 4.4 2.0 - - + -
112A ALA* 3.7 37.0 - - + +
115A LEU* 4.0 23.8 - - + -
127A VAL* 4.0 8.1 - - + -
128A SER 3.0 8.2 + - - +
129A SER* 3.4 24.9 + - - -
130A PHE 4.9 0.5 + - - -
134A ALA* 4.4 11.4 - - + -
138A LEU* 4.3 9.9 - - + -
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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