Contacts of the strand formed by residues 95 - 100 (chain B) in PDB entry 3VF0
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 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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956A PRO* 5.4 5.2 - - + -
959A GLN* 5.6 3.4 - - - +
62B LEU* 4.4 6.5 - - + -
63B ILE 3.1 12.1 - - - +
64B ARG* 4.1 24.7 - - + +
65B GLY 5.3 0.2 - - - +
66B LEU* 4.0 2.9 - - - -
89B VAL* 3.6 3.6 - - - +
90B ASP* 2.7 52.2 + - - +
93B LYS* 3.8 19.9 - - + +
94B GLY* 1.3 83.4 - - - +
96B ALA* 1.3 57.8 + - - +
97B PHE* 3.5 16.8 - - - -
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B ILE 3.9 0.2 - - - +
62B LEU* 3.5 8.5 - - - +
63B ILE* 2.9 40.3 + - + +
66B LEU* 3.9 17.7 - - + -
75B VAL* 4.3 14.1 - - + -
88B PHE 3.2 10.1 - - - +
89B VAL* 4.1 13.5 - - + -
95B THR* 1.3 73.8 - - - +
97B PHE* 1.3 63.2 + - - +
98B VAL* 3.9 7.8 + - + -
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Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956A PRO* 3.9 28.9 - - + -
61B ILE 3.9 4.7 - - - -
62B LEU* 3.6 20.4 - - + -
86B TYR* 3.6 20.1 - - + -
87B CYS* 3.4 3.1 - - - -
88B PHE* 2.9 60.4 + + + +
90B ASP* 4.5 7.0 - - + -
95B THR* 3.5 23.8 - - - -
96B ALA* 1.3 70.1 - - - +
98B VAL* 1.3 59.6 + - - +
128B GLN* 3.8 26.2 - - + +
3003B GOL 5.1 1.8 - - - +
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ARG 3.9 0.3 - - - +
60B LYS* 3.4 2.4 - - - -
61B ILE* 2.7 51.8 + - + +
63B ILE* 4.4 5.4 - - + -
75B VAL* 4.4 0.7 - - + -
79B LEU* 3.9 18.2 - - + -
84B LEU* 3.9 14.6 - - + -
86B TYR 3.4 9.6 - - - +
87B CYS* 3.7 23.1 - - - -
96B ALA* 4.3 15.3 - - + -
97B PHE* 1.3 76.7 - - - +
99B THR* 1.3 64.8 + - - +
100B LEU* 3.8 28.0 - - + -
128B GLN* 4.0 2.0 + - - +
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Residues in contact with THR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ARG* 3.7 39.3 - - + +
60B LYS* 3.4 25.4 - - + +
84B LEU* 3.7 2.4 - - - -
85B LYS* 2.8 39.4 + - + -
86B TYR* 3.0 25.7 + - + +
98B VAL* 1.3 70.8 - - - +
100B LEU* 1.3 58.0 + - - +
128B GLN* 5.0 0.5 + - - -
181B MET* 5.5 1.1 - - + -
3003B GOL 3.2 25.5 + - - +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ARG* 2.8 40.7 + - - +
61B ILE* 4.4 12.6 - - + -
79B LEU* 5.2 4.0 - - + -
82B TYR* 3.8 25.4 - - + -
83B GLU 3.5 10.1 - - - +
84B LEU* 4.3 8.1 - - + -
85B LYS* 4.2 2.9 - - - -
98B VAL* 3.8 23.3 - - + -
99B THR* 1.3 74.5 - - - +
101B LEU* 1.3 64.8 + - - +
102B ASN 3.4 4.0 - - - +
105B GLN* 3.7 20.9 - - + +
106B ALA* 3.7 29.4 - - + +
109B ALA* 3.9 16.2 - - + -
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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