Contacts of the helix formed by residues 100 - 111 (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 SER 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B PRO 5.4 0.8 + - - -
99B ARG* 1.3 78.2 - - - +
101B VAL* 1.3 64.7 + - - +
102B GLU* 3.6 6.4 + - - +
103B ARG* 3.0 28.6 + - - +
104B LEU* 2.9 20.9 + - - +
133B ASN* 4.6 1.6 - - - -
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Residues in contact with VAL 101 (chain B).
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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99B ARG 3.4 2.8 + - - -
100B SER* 1.3 70.6 - - - +
102B GLU* 1.3 61.8 + - + +
104B LEU* 3.2 10.1 + - - +
105B LYS* 2.9 53.5 + - - +
133B ASN* 3.8 34.2 + - + +
136B GLU* 3.8 32.8 - - + +
137B ALA* 3.9 10.7 - - - +
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Residues in contact with GLU 102 (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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100B SER* 3.1 6.2 + - - +
101B VAL* 1.3 78.0 - - + +
103B ARG* 1.3 69.9 + - - +
105B LYS* 2.9 45.7 + - - +
106B GLU* 3.3 23.2 + - - +
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Residues in contact with ARG 103 (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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97B ALA 3.0 29.2 - - - +
98B SER* 4.1 7.6 - - - -
100B SER* 3.0 29.0 + - - +
102B GLU* 1.3 76.6 - - - +
104B LEU* 1.3 66.0 + - - +
106B GLU* 2.7 51.9 + - - +
107B MET* 3.0 19.6 + - - +
414B PRO* 4.4 14.2 - - + +
415B VAL* 4.5 8.9 - - + +
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Residues in contact with LEU 104 (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* 3.6 20.6 - - + -
98B SER 3.1 20.9 - - - +
99B ARG* 3.2 31.6 - - - +
100B SER 2.9 20.0 + - - +
101B VAL* 3.5 4.3 - - - +
103B ARG* 1.3 74.8 - - - +
105B LYS* 1.3 61.9 + - - +
107B MET* 3.0 13.0 + - - +
108B ILE* 2.9 29.6 + - + +
112B MET* 4.4 15.9 - - + -
133B ASN* 4.1 15.3 - - + -
134B VAL* 4.4 13.7 - - + +
137B ALA* 3.5 19.5 - - + -
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Residues in contact with LYS 105 (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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101B VAL* 2.9 29.9 + - - +
102B GLU* 2.9 45.8 + - - +
103B ARG 3.1 0.2 - - - -
104B LEU* 1.3 76.7 - - - +
106B GLU* 1.3 62.9 + - + +
108B ILE* 3.3 2.8 + - - +
109B LYS* 3.0 30.6 + - + +
136B GLU* 5.2 0.7 - - - -
137B ALA* 4.0 11.4 - - + +
140B SER* 3.4 35.6 - - - +
141B PHE* 4.0 15.0 - - + -
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Residues in contact with GLU 106 (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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102B GLU 3.3 10.7 + - - +
103B ARG* 2.7 51.4 + - - +
105B LYS* 1.3 75.4 - - + +
107B MET* 1.3 56.0 + - - +
109B LYS* 3.4 16.0 + - + +
110B ALA* 2.9 28.4 + - - +
415B VAL* 3.7 24.2 - - + +
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Residues in contact with MET 107 (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 31.2 - - + -
93B THR 5.3 0.2 - - - +
94B ILE* 5.1 1.6 - - + -
98B SER* 3.8 28.3 - - - -
103B ARG* 3.0 13.6 + - - +
104B LEU* 3.6 15.0 - - + +
106B GLU* 1.3 74.2 - - - +
108B ILE* 1.3 64.6 + - - +
110B ALA* 3.4 6.6 + - - +
111B GLY 3.2 5.7 + - - -
112B MET* 2.9 40.7 + - + +
408B THR* 4.0 17.5 - - + -
414B PRO* 4.4 11.0 - - - -
415B VAL* 3.6 26.2 - - + -
418B VAL* 4.0 8.7 - - + +
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Residues in contact with ILE 108 (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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104B LEU* 2.9 19.8 + - + +
105B LYS 3.7 4.7 - - - +
107B MET* 1.3 74.6 - - - +
109B LYS* 1.3 63.8 + - - +
111B GLY* 2.8 17.5 + - - -
112B MET* 3.7 27.0 + - + +
134B VAL* 5.9 0.2 - - + -
137B ALA* 4.0 11.7 - - + +
138B VAL* 3.7 45.3 - - + +
141B PHE* 4.2 16.2 - - + -
149B ARG* 4.0 35.9 - - + +
151B VAL* 4.0 15.7 - - + -
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Residues in contact with LYS 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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105B LYS* 3.0 23.7 + - + +
106B GLU* 3.4 16.8 - - + +
108B ILE* 1.3 76.4 - - - +
110B ALA* 1.3 59.6 + - - +
111B GLY* 3.6 0.3 + - - -
141B PHE* 4.0 24.4 - - + -
149B ARG* 4.2 22.7 + - - +
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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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106B GLU 2.9 16.3 + - - +
107B MET* 3.8 6.1 - - - +
108B ILE 2.9 0.6 + - - -
109B LYS* 1.3 76.0 - - - +
111B GLY* 1.3 57.0 + - - +
415B VAL* 4.1 11.0 - - + -
418B VAL* 3.8 18.4 - - + +
419B LYS* 3.7 32.0 - - + +
422B HIS* 3.8 22.0 + - - +
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Residues in contact with GLY 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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86B ARG* 3.2 32.0 + - - -
90B ILE* 4.0 4.1 - - - +
108B ILE 2.8 10.5 + - - -
109B LYS 3.4 0.8 + - - -
110B ALA* 1.3 80.9 - - - +
112B MET* 1.3 69.6 + - - +
113B ASN* 3.3 12.4 + - - +
149B ARG* 6.4 0.2 - - - -
418B VAL* 4.0 6.1 - - - -
422B HIS* 5.1 0.7 - - - -
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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