Contacts of the strand formed by residues 112 - 118 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ILE* 4.1 7.2 - - - +
92A ALA* 3.8 27.6 - - + +
94A ILE* 4.8 4.5 - - - -
104A LEU* 4.4 16.2 - - + -
107A MET* 3.0 31.1 + - + +
108A ILE* 3.7 37.5 - - + +
111A GLY* 1.3 79.4 - - - +
113A ASN* 1.3 67.1 + - - +
114A ILE 3.7 21.5 - - - +
115A ALA* 4.5 10.3 - - + -
134A VAL* 5.3 3.6 - - + -
149A ARG* 5.9 2.1 - - - +
151A VAL* 4.1 30.2 - - + +
418A VAL* 3.7 10.5 - - + +
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Residues in contact with ASN 113 (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 ARG* 2.5 33.6 + - - +
89A SER* 3.1 13.3 + - - -
90A ILE 3.0 16.5 + - - +
111A GLY 3.2 13.1 + - - -
112A MET* 1.3 76.1 + - - +
114A ILE* 1.3 65.7 + - + +
149A ARG* 6.2 3.6 - - - +
150A PRO 4.9 1.4 + - - -
151A VAL* 3.5 11.9 - - - -
152A ALA 3.0 22.4 + - - -
507A HIS* 3.6 40.3 - - + +
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Residues in contact with ILE 114 (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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89A SER* 4.9 1.6 - - - -
90A ILE 3.1 3.5 + - - +
91A ILE* 3.5 34.8 - - + -
92A ALA 2.9 27.0 + - - -
112A MET* 3.7 7.1 - - - +
113A ASN* 1.3 89.1 - - + +
115A ALA* 1.3 73.5 + - - +
151A VAL* 4.6 0.2 - - - -
152A ALA* 3.6 19.1 - - + -
154A ALA* 4.0 18.2 - - + -
282A ILE* 4.4 6.3 - - + -
284A PHE* 4.7 2.0 - - + -
401A CYS* 4.5 7.2 - - - -
507A HIS* 4.1 20.2 - - + +
508A LEU* 3.9 27.6 - - + -
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Residues in contact with ALA 115 (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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92A ALA 3.5 3.8 - - - -
94A ILE* 4.0 23.3 - - + -
112A MET* 4.5 8.1 - - - -
114A ILE* 1.3 75.6 - - - +
116A ARG* 1.3 55.8 + - - +
117A LEU* 4.0 4.4 + - + -
134A VAL* 4.1 24.2 - - + -
151A VAL* 4.2 1.9 - - + +
152A ALA 2.9 14.6 + - - +
153A ILE* 3.4 6.1 - - + +
154A ALA* 2.7 34.1 + - - +
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Residues in contact with ARG 116 (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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91A ILE* 3.7 13.7 - - + -
92A ALA 2.8 16.7 + - - +
93A THR* 3.0 40.7 + - - +
94A ILE* 3.0 26.0 + - - +
115A ALA* 1.3 72.8 - - - +
117A LEU* 1.3 62.0 + - - +
118A ASN* 4.1 15.6 - - - +
154A ALA* 3.4 4.5 - - - +
156A ASP* 2.5 42.0 + - + -
284A PHE* 3.9 16.4 - - + -
313A LYS* 4.0 0.8 - - - +
403A MET* 3.5 33.4 - - - +
405A SER* 3.8 13.3 + - - -
581A PGA 3.1 30.1 + - - -
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ILE* 4.2 17.5 - - + -
115A ALA* 5.0 3.6 - - + -
116A ARG* 1.3 74.8 - - - +
118A ASN* 1.3 59.7 + - - +
119A PHE* 3.3 24.3 + - + -
127A HIS* 3.9 20.6 - - + +
130A SER* 4.1 23.3 - - - -
131A ILE* 3.7 35.2 - - + +
134A VAL* 5.4 2.0 - - + -
153A ILE* 4.2 17.9 - - + -
154A ALA 2.8 17.1 + - - +
155A LEU* 4.6 1.6 - - - -
156A ASP* 2.6 33.0 + - - -
280A VAL* 4.9 6.1 - - + -
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Residues in contact with ASN 118 (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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93A THR* 4.2 11.3 - - + +
94A ILE 5.3 3.7 + - - +
116A ARG* 3.9 30.1 + - - +
117A LEU* 1.3 70.0 - - - +
119A PHE* 1.3 57.1 + - - +
120A SER* 3.0 29.2 + - - -
121A HIS* 3.1 38.9 + - + +
127A HIS* 3.6 7.7 - - - -
156A ASP* 4.0 5.8 - - - -
581A PGA 4.5 4.9 + - - -
582A K 3.1 12.9 - - - -
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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