Contacts of the helix formed by residues 100 - 111 (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 SER 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A PRO 5.3 0.8 + - - -
99A ARG* 1.3 78.3 - - - +
101A VAL* 1.3 64.5 + - - +
102A GLU* 3.5 6.9 + - - +
103A ARG* 3.0 27.7 + - - +
104A LEU* 2.9 21.5 + - - +
133A ASN* 4.7 1.3 - - - -
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Residues in contact with VAL 101 (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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99A ARG 3.5 2.6 + - - -
100A SER* 1.3 70.0 - - - +
102A GLU* 1.3 60.7 + - + +
104A LEU* 3.2 10.3 + - - +
105A LYS* 2.9 54.0 + - - +
133A ASN* 3.8 33.6 + - + +
136A GLU* 3.6 36.8 - - + +
137A ALA* 3.9 8.5 - - - +
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Residues in contact with GLU 102 (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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100A SER* 3.1 6.2 + - - +
101A VAL* 1.3 78.2 - - + +
103A ARG* 1.3 70.6 + - - +
105A LYS* 3.0 45.6 + - - +
106A GLU* 3.3 24.3 + - - +
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Residues in contact with ARG 103 (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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97A ALA 3.0 28.0 - - - +
98A SER* 4.1 8.7 - - - -
100A SER* 3.0 28.4 + - - +
102A GLU* 1.3 76.4 - - - +
104A LEU* 1.3 66.9 + - - +
106A GLU* 2.8 51.2 + - - +
107A MET* 3.0 18.7 + - - +
414A PRO* 4.3 15.0 - - + +
415A VAL* 4.5 9.2 - - + +
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Residues in contact with LEU 104 (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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94A ILE* 3.7 20.6 - - + -
98A SER 3.3 19.3 - - - +
99A ARG* 3.4 31.6 - - - +
100A SER 2.9 17.8 + - - +
101A VAL* 3.5 3.1 - - - +
103A ARG* 1.3 75.8 - - - +
105A LYS* 1.3 63.8 + - - +
107A MET* 3.0 14.8 + - - +
108A ILE* 2.9 30.4 + - + +
112A MET* 4.4 13.7 - - + -
130A SER 5.4 0.2 - - - +
133A ASN* 4.1 14.6 - - + -
134A VAL* 4.3 17.0 - - + +
137A ALA* 3.4 20.4 - - + -
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Residues in contact with LYS 105 (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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101A VAL* 2.9 34.6 + - - +
102A GLU* 3.0 41.2 + - - +
103A ARG 3.1 0.2 + - - -
104A LEU* 1.3 75.1 - - - +
106A GLU* 1.3 62.7 + - - +
108A ILE* 3.3 2.9 + - - +
109A LYS* 3.0 32.0 + - + +
136A GLU* 5.1 0.7 - - - -
137A ALA* 3.9 12.5 - - + +
140A SER* 3.5 35.9 - - - +
141A PHE* 4.0 14.3 - - + -
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Residues in contact with GLU 106 (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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102A GLU 3.3 13.2 + - - +
103A ARG* 2.8 48.7 + - - +
105A LYS* 1.3 74.2 - - - +
107A MET* 1.3 57.3 + - - +
109A LYS* 3.3 14.5 + - + +
110A ALA* 2.9 28.8 + - - +
415A VAL* 3.8 24.4 - - + +
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Residues in contact with MET 107 (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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92A ALA* 3.5 32.5 - - + -
94A ILE* 5.0 1.8 - - + -
98A SER* 3.6 29.6 - - - +
103A ARG* 3.0 13.9 + - - +
104A LEU* 3.0 19.0 + - + +
106A GLU* 1.3 72.1 - - - +
108A ILE* 1.3 64.9 + - - +
110A ALA* 3.3 6.6 + - - +
111A GLY 3.1 6.6 + - - -
112A MET* 3.0 40.0 + - + +
408A THR* 4.0 18.4 - - + -
414A PRO* 4.5 7.9 - - - -
415A VAL* 3.7 26.0 - - + +
418A VAL* 4.0 8.3 - - + +
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Residues in contact with ILE 108 (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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104A LEU* 2.9 19.7 + - + +
105A LYS 3.6 5.6 - - - +
107A MET* 1.3 73.6 - - - +
109A LYS* 1.3 67.9 + - - +
111A GLY* 2.9 17.2 + - - -
112A MET* 3.7 28.2 + - + +
134A VAL* 5.9 0.2 - - + -
137A ALA* 4.0 12.3 - - + +
138A VAL* 3.7 45.5 - - + +
141A PHE* 4.2 14.8 - - + -
149A ARG* 4.0 35.3 - - + +
151A VAL* 4.1 16.2 - - + -
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Residues in contact with LYS 109 (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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105A LYS* 3.0 23.0 + - + +
106A GLU* 3.4 16.4 - - + +
108A ILE* 1.3 76.6 - - - +
110A ALA* 1.3 61.0 + - - +
111A GLY* 3.6 0.3 + - - -
141A PHE* 4.1 23.4 - - + -
149A ARG* 4.4 23.7 + - - +
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Residues in contact with ALA 110 (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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106A GLU 2.9 16.9 + - - +
107A MET* 3.8 5.8 - - - +
108A ILE 2.9 0.8 + - - -
109A LYS* 1.3 77.0 - - + +
111A GLY* 1.3 57.4 + - - +
415A VAL* 4.2 11.4 - - + +
418A VAL* 3.9 15.0 - - + +
419A LYS* 3.7 32.3 - - + +
422A HIS* 3.8 24.1 - - - +
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Residues in contact with GLY 111 (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* 3.2 26.7 + - - -
90A ILE* 4.1 3.6 - - - +
107A MET 3.1 0.4 + - - -
108A ILE 2.9 8.5 + - - -
109A LYS 3.4 0.6 - - - -
110A ALA* 1.3 81.0 - - - +
112A MET* 1.3 71.6 + - - +
113A ASN* 3.2 17.5 + - - +
149A ARG* 6.4 0.2 - - - -
418A VAL* 4.1 6.1 - - - -
422A 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