Contacts of the helix formed by residues 100 - 111 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C PRO 5.2 1.0 + - - -
99C ARG* 1.3 80.1 - - - +
101C VAL* 1.3 64.0 + - - +
102C GLU* 3.5 5.9 + - - +
103C ARG* 3.1 27.4 + - - +
104C LEU* 2.9 21.3 + - - +
133C ASN* 4.5 1.8 - - - -
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Residues in contact with VAL 101 (chain C).
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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99C ARG 3.4 3.0 + - - -
100C SER* 1.3 69.9 - - - +
102C GLU* 1.3 61.9 + - + +
104C LEU* 3.2 10.4 + - - +
105C LYS* 2.9 52.4 + - - +
133C ASN* 3.8 33.3 + - + +
136C GLU* 3.8 35.9 - - + +
137C ALA* 3.9 7.6 - - - +
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Residues in contact with GLU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C SER* 3.2 5.5 + - - +
101C VAL* 1.3 79.6 - - + +
103C ARG* 1.3 69.5 + - - +
105C LYS* 2.9 46.3 + - - +
106C GLU* 3.3 23.7 + - - +
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Residues in contact with ARG 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ALA 3.0 27.6 - - - +
98C SER* 4.0 11.4 - - - -
100C SER* 3.1 25.6 + - - +
102C GLU* 1.3 75.5 - - - +
104C LEU* 1.3 66.5 + - - +
106C GLU* 2.7 50.4 + - - +
107C MET* 3.0 19.4 + - - +
414C PRO* 4.3 14.8 - - + +
415C VAL* 4.5 9.1 - - + +
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ILE* 3.7 20.6 - - + -
98C SER 3.1 20.9 - - - +
99C ARG* 3.3 24.0 - - - +
100C SER 2.9 27.3 + - - +
101C VAL* 3.5 4.3 - - - +
103C ARG* 1.3 74.3 - - - +
105C LYS* 1.3 64.0 + - - +
107C MET* 2.9 13.3 + - - +
108C ILE* 2.8 29.4 + - + +
112C MET* 4.5 15.2 - - + +
133C ASN* 4.1 16.2 - - + -
134C VAL* 4.3 14.4 - - + +
137C ALA* 3.4 20.9 - - + -
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Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 2.9 31.1 + - - +
102C GLU* 2.9 43.2 + - - +
103C ARG 3.1 0.2 - - - -
104C LEU* 1.3 75.2 - - - +
106C GLU* 1.3 62.7 + - + +
108C ILE* 3.3 3.3 + - - +
109C LYS* 3.0 30.2 + - + +
136C GLU* 5.1 0.9 - - - -
137C ALA* 3.9 13.2 - - + +
140C SER* 3.4 36.2 - - - +
141C PHE* 4.1 16.1 - - + -
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLU 3.3 12.2 + - - +
103C ARG* 2.7 49.4 + - - +
105C LYS* 1.3 75.2 - - + +
107C MET* 1.3 57.3 + - - +
109C LYS* 3.2 15.6 + - + +
110C ALA* 2.8 29.3 + - - +
415C VAL* 3.8 24.2 - - + +
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Residues in contact with MET 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA* 3.6 31.0 - - + -
94C ILE* 5.1 2.5 - - + -
98C SER* 3.7 29.4 - - - -
103C ARG* 3.0 11.7 + - - +
104C LEU* 2.9 17.8 + - + +
106C GLU* 1.3 73.4 - - - +
108C ILE* 1.3 66.2 + - - +
110C ALA* 3.3 7.2 + - - +
111C GLY 3.1 6.1 + - - -
112C MET* 2.9 39.6 + - + +
408C THR* 4.1 15.9 - - + -
414C PRO* 4.5 9.4 - - - -
415C VAL* 3.6 25.8 - - + -
418C VAL* 4.0 9.4 - - + +
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Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C LEU* 2.8 18.3 + - + +
105C LYS 3.6 6.1 - - - +
107C MET* 1.3 75.7 - - - +
109C LYS* 1.3 64.9 + - - +
111C GLY* 2.8 17.5 + - - -
112C MET* 3.7 29.6 + - + +
134C VAL* 6.1 0.4 - - + -
137C ALA* 4.0 12.3 - - + +
138C VAL* 3.7 43.7 - - + +
141C PHE* 4.2 16.2 - - + -
149C ARG* 4.1 35.5 - - + +
151C VAL* 4.0 15.9 - - + -
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Residues in contact with LYS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LYS* 3.0 22.3 + - + +
106C GLU* 3.4 17.0 - - + +
108C ILE* 1.3 76.6 - - - +
110C ALA* 1.3 60.4 + - - +
111C GLY* 3.5 0.7 + - - -
141C PHE* 4.1 24.3 - - + -
149C ARG* 4.2 23.7 + - - +
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Residues in contact with ALA 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C GLU 2.8 16.2 + - - +
107C MET* 3.7 7.0 - - - +
108C ILE 3.0 0.4 - - - -
109C LYS* 1.3 78.5 - - - +
111C GLY* 1.3 56.4 + - - +
415C VAL* 4.2 11.9 - - + -
418C VAL* 3.7 16.2 - - + +
419C LYS* 3.7 32.5 - - + +
422C HIS* 3.8 21.7 + - - +
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Residues in contact with GLY 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ARG* 3.2 25.4 + - - -
90C ILE* 4.0 3.4 - - - +
107C MET 3.1 0.4 + - - -
108C ILE 2.8 16.4 + - - -
109C LYS 3.3 0.6 - - - -
110C ALA* 1.3 74.0 - - - +
112C MET* 1.3 69.2 + - - +
113C ASN* 3.2 18.8 + - - +
149C ARG* 6.5 0.2 - - - -
418C VAL* 4.0 6.7 - - - -
422C HIS* 5.1 0.9 - - - -
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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