Contacts of the helix formed by residues 123 - 131 (chain F) in PDB entry 2VIG
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 TYR 123 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118F VAL 2.9 11.6 + - - +
119F ASN* 3.6 12.8 - - - +
122F LEU* 1.3 76.4 - - - +
124F LEU* 1.3 85.2 + - + +
126F PRO* 3.3 14.7 - - - +
127F ILE* 3.4 32.0 - - + +
139F TRP* 2.9 40.1 + + - -
143F PHE* 3.7 16.5 - + - -
150F GLY* 3.5 20.9 - - - -
151F CYS* 3.8 26.0 - - - +
194F ALA* 3.2 38.7 - - + +
195F ALA 4.3 3.1 - - - -
196F VAL* 3.8 11.6 - - + +
214F LEU* 5.2 0.4 - - + -
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Residues in contact with LEU 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F LEU 3.5 25.1 - - - +
81F ALA* 3.8 5.6 - - + -
84F VAL* 3.8 28.3 - - + -
119F ASN* 2.9 27.2 + - - +
120F ASN* 3.7 6.1 - - - +
123F TYR* 1.3 97.1 - - + +
125F GLY* 1.3 63.4 + - - +
127F ILE* 3.2 6.6 + - + +
128F LEU* 3.0 28.2 + - + +
139F TRP 3.9 0.2 - - - +
140F VAL* 3.7 41.3 - - + +
143F PHE* 3.8 9.4 - - + +
144F THR* 4.5 2.0 - - + -
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Residues in contact with GLY 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95F TYR* 5.6 0.2 - - - -
120F ASN 3.1 15.3 + - - -
121F SER* 3.3 12.5 + - - -
124F LEU* 1.3 77.9 - - - +
126F PRO* 1.3 67.2 - - - +
128F LEU* 3.3 7.0 + - - +
129F LYS* 3.1 21.1 + - - +
270F MET* 3.7 19.0 - - - +
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Residues in contact with PRO 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F SER 3.5 7.0 - - - +
122F LEU 3.3 22.9 - - - +
123F TYR 3.3 10.1 - - - +
125F GLY* 1.3 87.2 - - - +
127F ILE* 1.3 60.9 + - - +
129F LYS* 4.4 1.8 - - + -
130F PHE* 2.7 42.6 + - + +
152F PHE* 5.2 0.4 - - + -
196F VAL* 4.2 14.6 - - + -
254F LEU* 4.1 14.8 - - + +
263F ILE* 4.2 10.8 - - + -
267F THR* 3.4 27.1 - - + +
270F MET* 4.0 1.1 - - + -
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Residues in contact with ILE 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F TYR* 3.4 58.8 - - + +
124F LEU* 3.2 7.6 + - - +
126F PRO* 1.3 76.7 - - - +
128F LEU* 1.3 58.4 + - - +
131F GLY* 2.8 28.2 + - - -
135F GLN* 4.2 30.1 - - + +
136F LYS* 3.7 5.7 - - - +
139F TRP* 3.8 11.2 - - + +
140F VAL* 3.8 17.5 - - + -
196F VAL* 4.3 4.5 - - + -
214F LEU* 3.7 24.7 - - + -
254F LEU* 4.1 10.5 - - + -
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Residues in contact with LEU 128 (chain F).
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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83F ASP 4.0 7.6 - - - +
84F VAL* 3.4 42.0 - - + -
85F PRO* 4.0 10.3 - - + -
88F LEU* 3.3 34.3 - - + -
124F LEU 3.0 16.9 + - - +
125F GLY* 3.8 8.5 - - - +
127F ILE* 1.3 77.9 - - - +
129F LYS* 1.3 59.1 + - - +
136F LYS* 3.4 32.5 + - + +
140F VAL* 4.2 11.7 - - + -
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Residues in contact with LYS 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F GLY 3.1 15.8 + - - +
126F PRO* 4.4 0.2 - - + -
127F ILE 3.3 0.2 - - - -
128F LEU* 1.3 79.4 - - - +
130F PHE* 1.3 92.6 + - + +
131F GLY 3.7 0.6 - - - +
266F GLN* 2.6 32.9 + - + +
270F MET* 4.5 19.1 - - + -
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Residues in contact with PHE 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F PRO* 2.7 28.6 + - + +
129F LYS* 1.3 103.4 - - + +
131F GLY* 1.3 62.6 + - - +
132F SER 4.0 0.2 + - - -
135F GLN* 4.6 0.5 - - - +
254F LEU* 3.9 14.1 - - + -
255F GLY* 3.9 18.7 + - - +
259F MET* 3.8 23.8 - - + -
262F LYS* 5.7 0.4 - - + -
263F ILE* 3.8 47.1 - - + -
266F GLN* 3.6 35.9 - - + -
267F THR* 4.7 1.6 - - - -
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Residues in contact with GLY 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F ILE* 2.8 20.7 + - - -
129F LYS 3.7 0.7 - - - -
130F PHE* 1.3 80.8 - - - +
132F SER* 1.3 68.1 + - - -
135F GLN* 3.5 15.3 - - - -
136F LYS* 3.4 15.5 + - - -
254F LEU* 3.6 9.2 - - - +
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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