Contacts of the strand formed by residues 112 - 118 (chain B) in PDB entry 2VGB
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 MET 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B ILE* 4.1 7.6 - - - +
92B ALA* 3.9 26.9 - - + -
94B ILE* 4.6 5.6 - - - -
104B LEU* 4.4 17.5 - - + +
107B MET* 2.9 34.6 + - + +
108B ILE* 3.7 38.6 + - + +
111B GLY* 1.3 78.6 - - - +
113B ASN* 1.3 65.6 + - - +
114B ILE 3.5 21.1 - - - +
115B ALA* 4.4 13.7 - - + -
134B VAL* 5.3 3.1 - - + -
149B ARG* 6.0 2.3 - - - +
150B PRO 5.4 0.2 - - - +
151B VAL* 4.1 28.5 - - + +
418B VAL* 3.7 9.6 - - + +
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Residues in contact with ASN 113 (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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86B ARG* 2.4 34.1 + - - +
89B SER* 3.2 15.5 + - - -
90B ILE 2.9 17.2 + - - +
111B GLY* 3.3 12.7 + - - -
112B MET* 1.3 77.8 + - - +
114B ILE* 1.3 64.5 + - + +
149B ARG* 6.1 4.8 - - - +
150B PRO 4.9 1.2 + - - -
151B VAL* 3.6 11.3 - - - -
152B ALA 3.0 22.5 + - - -
507B HIS* 3.8 33.9 - - + +
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Residues in contact with ILE 114 (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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89B SER* 4.9 1.6 - - - -
90B ILE 3.1 2.6 + - - +
91B ILE* 3.8 36.3 - - + -
92B ALA 2.9 26.5 + - - -
112B MET* 3.5 8.7 - - - +
113B ASN* 1.3 92.2 - - + +
115B ALA* 1.3 70.7 + - - +
151B VAL* 4.6 0.2 - - - -
152B ALA* 3.7 19.7 - - + +
154B ALA* 4.0 18.4 - - + -
282B ILE* 4.4 6.1 - - + -
284B PHE* 4.6 1.8 - - + -
401B CYS* 4.5 3.4 - - - -
507B HIS* 4.2 20.4 - - + +
508B LEU* 4.0 25.8 - - + -
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Residues in contact with ALA 115 (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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92B ALA 3.5 4.0 - - - -
94B ILE* 4.0 24.7 - - + -
112B MET* 4.4 8.7 - - - -
114B ILE* 1.3 73.0 - - - +
116B ARG* 1.3 57.5 + - - +
117B LEU* 3.9 3.9 + - + -
134B VAL* 4.1 22.2 - - + -
151B VAL* 4.1 1.9 - - + +
152B ALA 3.0 14.8 + - - +
153B ILE* 3.5 5.7 - - + +
154B ALA* 2.7 33.6 + - - +
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Residues in contact with ARG 116 (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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91B ILE* 3.8 13.9 - - + -
92B ALA 2.7 17.9 + - - +
93B THR* 3.0 40.5 + - + +
94B ILE* 3.0 25.3 + - - +
114B ILE 3.9 0.2 + - - -
115B ALA* 1.3 74.4 - - - +
117B LEU* 1.3 62.1 + - - +
118B ASN* 4.0 17.2 - - - +
154B ALA* 3.5 4.5 - - - +
156B ASP* 2.5 40.8 + - + +
284B PHE* 4.0 15.8 - - + -
313B LYS* 4.0 0.4 - - - +
403B MET* 3.5 37.9 - - - +
405B SER* 3.9 8.7 + - - -
581B PGA 2.7 29.5 + - - -
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Residues in contact with LEU 117 (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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94B ILE* 4.3 17.0 - - + -
115B ALA* 4.8 3.8 - - + +
116B ARG* 1.3 77.4 - - - +
118B ASN* 1.3 59.1 + - - +
119B PHE* 3.4 23.1 + - + -
127B HIS* 3.9 21.3 - - + +
130B SER* 4.1 22.9 - - - -
131B ILE* 3.8 34.8 - - + +
134B VAL* 5.4 1.6 - - + -
153B ILE* 4.2 19.5 - - + -
154B ALA 2.8 18.0 + - - +
155B LEU* 4.6 1.3 - - - -
156B ASP* 2.6 35.0 + - - +
280B VAL* 4.9 5.4 - - + -
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Residues in contact with ASN 118 (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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93B THR* 4.1 19.1 - - + +
94B ILE 5.3 3.7 + - - +
116B ARG* 3.8 25.1 + - - +
117B LEU* 1.3 69.8 - - - +
119B PHE* 1.3 57.0 + - - +
120B SER* 2.9 29.5 + - - -
121B HIS* 3.1 40.6 + - + +
127B HIS* 3.6 6.5 - - - -
156B ASP* 3.9 5.8 - - - -
163B ARG* 6.0 0.2 - - - +
581B PGA 4.4 5.3 + - - -
586B K 3.2 9.5 - - - -
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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