Contacts of the strand formed by residues 112 - 118 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D ILE* 4.0 7.6 - - - +
92D ALA* 3.9 16.8 - - + -
94D ILE* 4.7 1.8 - - - -
104D LEU* 4.4 20.4 - - + -
107D MET* 3.0 39.0 + - + +
108D ILE* 3.6 39.7 - - + +
111D GLY* 1.3 77.5 - - - +
113D ASN* 1.3 66.2 + - - +
114D ILE 3.8 20.2 - - - +
115D ALA* 4.4 13.7 - - + -
134D VAL* 5.3 2.9 - - + -
149D ARG* 6.0 2.1 - - - +
150D PRO 5.4 0.2 - - - +
151D VAL* 4.2 28.1 - - + +
418D VAL* 3.6 11.8 - - + +
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Residues in contact with ASN 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ARG* 2.4 31.7 + - - +
89D SER* 3.2 13.0 + - - -
90D ILE 2.9 17.3 + - - +
111D GLY* 3.1 13.2 + - - -
112D MET* 1.3 76.4 + - - +
114D ILE* 1.3 66.5 + - + +
149D ARG* 6.2 3.4 - - - +
150D PRO 5.0 1.0 + - - -
151D VAL* 3.6 9.5 - - - -
152D ALA 2.9 22.5 + - - -
507D HIS* 3.4 43.9 - - + +
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Residues in contact with ILE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D SER* 5.1 0.9 - - - -
90D ILE 3.2 3.7 + - - +
91D ILE* 3.4 32.9 - - + -
92D ALA 2.8 27.9 + - - +
112D MET* 3.8 6.8 - - - +
113D ASN* 1.3 90.1 - - + +
115D ALA* 1.3 72.2 + - - +
152D ALA* 3.7 17.5 - - + +
154D ALA* 3.9 19.5 - - + -
282D ILE* 4.2 8.7 - - + -
284D PHE* 4.7 1.1 - - + -
401D CYS* 4.7 2.2 - - - -
507D HIS* 4.0 22.7 - - + +
508D LEU* 3.8 29.4 - - + -
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Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ALA 3.5 4.3 - - - -
94D ILE* 4.0 21.5 - - + -
112D MET* 4.4 9.2 - - - -
114D ILE* 1.3 72.3 - - - +
116D ARG* 1.3 57.7 + - - +
117D LEU* 3.9 2.0 + - + -
134D VAL* 4.0 24.9 - - + -
151D VAL* 4.3 2.9 - - + +
152D ALA 3.0 14.9 + - - +
153D ILE* 3.4 7.5 - - + +
154D ALA* 2.7 33.6 + - - +
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Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ILE* 3.8 14.4 - - + -
92D ALA 2.7 16.7 + - - +
93D THR* 3.0 38.3 + - - +
94D ILE* 3.0 27.9 + - - +
114D ILE 3.7 0.4 + - - -
115D ALA* 1.3 72.8 - - - +
117D LEU* 1.3 63.1 + - - +
118D ASN* 4.0 13.7 - - - +
154D ALA* 3.5 4.5 - - - +
156D ASP* 2.6 41.2 + - + +
284D PHE* 4.0 15.6 - - + -
313D LYS* 4.0 0.8 - - - +
403D MET* 3.7 35.4 - - - +
405D SER* 3.8 8.7 + - - -
581D PGA 3.0 33.9 + - - -
594D K 4.0 1.6 - - - -
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Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ILE* 4.3 15.7 - - + -
115D ALA* 4.8 3.4 - - + +
116D ARG* 1.3 75.8 - - - +
118D ASN* 1.3 59.6 + - - +
119D PHE* 3.4 22.9 + - + -
127D HIS* 3.9 20.0 - - + +
130D SER* 4.1 23.6 - - - -
131D ILE* 3.8 32.8 - - + +
134D VAL* 5.5 1.8 - - + -
153D ILE* 4.1 18.8 - - + -
154D ALA 2.8 17.4 + - - +
155D LEU* 3.9 1.7 - - - -
156D ASP* 2.6 34.5 + - - +
274D PHE* 5.5 0.2 - - + -
280D VAL* 4.7 7.0 - - + -
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Residues in contact with ASN 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D THR* 4.2 19.0 - - + +
94D ILE 5.2 4.3 + - - +
116D ARG* 3.9 21.1 + - - +
117D LEU* 1.3 69.2 - - - +
119D PHE* 1.3 58.2 + - - +
120D SER* 2.9 23.0 + - - -
121D HIS* 2.9 42.6 + - + +
127D HIS* 3.5 7.3 - - - -
156D ASP* 4.0 4.9 - - - -
581D PGA 4.2 6.5 + - - -
594D K 3.0 18.4 - - - -
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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