Contacts of the strand formed by residues 106 - 112 (chain B) in PDB entry 2VGO
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 ASN 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B PRO* 6.1 2.7 - - + -
100B GLY 3.9 4.9 - - - +
101B LYS* 3.5 26.9 - - - +
105B GLY* 1.3 73.5 - - - -
107B VAL* 1.3 62.0 + - - +
108B TYR* 3.6 32.7 + - + +
121B LEU 3.7 1.6 - - - +
122B LYS* 3.5 1.0 - - - -
123B VAL* 2.9 32.6 + - + +
125B PHE* 5.5 7.1 - - - -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PRO* 3.7 2.8 - - - +
99B LEU* 2.7 36.1 + - + +
100B GLY 3.0 13.1 + - - +
102B GLY* 4.1 7.2 - - - +
106B ASN* 1.3 75.6 - - - +
108B TYR* 1.3 56.6 + - - +
120B ALA* 3.8 19.1 - - + -
121B LEU 3.5 9.0 - - - +
122B LYS* 3.8 29.6 - - + +
1359B AD5 3.5 54.5 - - + +
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 4.1 27.1 - - + -
97B ARG 3.5 2.0 - - - +
98B PRO* 3.9 34.3 - - + -
99B LEU* 4.1 3.4 - - - -
106B ASN* 3.6 34.7 + - + -
107B VAL* 1.3 76.5 - - - +
109B LEU* 1.3 70.7 + - - +
120B ALA* 3.3 4.2 - - - -
121B LEU* 2.8 51.4 + - + +
123B VAL* 3.7 26.5 - - + -
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Residues in contact with LEU 109 (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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95B ILE* 3.8 0.7 - - - -
96B GLY* 2.8 24.5 + - - -
97B ARG* 2.7 54.8 + - + +
99B LEU* 3.7 12.1 - - + +
108B TYR* 1.3 74.9 - - - +
110B ALA* 1.3 59.6 + - - +
118B ILE* 3.6 23.8 - - + -
119B MET 3.7 5.2 - - - +
172B PHE* 3.8 36.3 - - + -
801C TRP* 4.1 16.4 - - + -
802C ALA* 4.2 3.1 - - + -
807C LEU* 3.8 24.9 - - + -
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Residues in contact with ALA 110 (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 PHE* 4.4 13.5 - - + -
94B ASP 3.2 12.3 - - - +
95B ILE* 4.1 16.4 - - + -
108B TYR 4.9 0.2 - - - -
109B LEU* 1.3 75.0 - - - +
111B ARG* 1.3 61.0 + - - +
112B GLU 4.2 0.2 - - - -
118B ILE* 3.3 7.1 - - - +
119B MET* 2.8 39.3 + - + +
121B LEU* 4.1 19.7 - - + +
801C TRP* 3.6 5.8 - - - -
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Residues in contact with ARG 111 (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 PHE* 3.3 4.6 - - - -
94B ASP* 2.8 67.3 + - + +
110B ALA* 1.3 73.4 - - - +
112B GLU* 1.3 64.8 + - - +
113B LYS* 3.4 2.0 + - - -
116B LYS* 3.5 67.8 - - - +
117B PHE 3.4 6.3 - - - +
118B ILE* 4.3 7.0 - - + -
801C TRP* 3.7 48.5 - - + +
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Residues in contact with GLU 112 (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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88B PHE* 4.2 16.1 - - + -
92B ASP* 3.6 13.2 - - - +
93B PHE* 3.8 25.8 - - + -
110B ALA 4.2 0.4 - - - -
111B ARG* 1.3 69.6 - - - +
113B LYS* 1.3 60.9 + - - +
114B GLN* 3.3 24.2 + - - +
115B ASN* 3.0 25.6 + - - +
116B LYS* 2.9 27.9 + - - -
117B PHE 2.8 15.8 + - - +
119B MET* 4.1 6.2 - - + +
825C TYR* 2.7 46.2 + - + +
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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