Contacts of the helix formed by residues 123 - 131 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A VAL 2.9 10.7 + - - +
119A ASN* 3.7 15.5 - - - +
122A LEU* 1.3 75.5 - - - +
124A LEU* 1.3 79.7 + - + +
126A PRO* 3.3 15.1 - - - +
127A ILE* 3.4 30.0 - - + +
139A TRP* 3.2 42.9 + + - +
143A PHE* 3.6 19.3 - + - -
150A GLY* 3.5 29.6 - - - -
151A CYS 3.6 16.2 - - - +
152A PHE* 4.9 0.2 - - - +
194A ALA* 3.3 38.1 - - + +
195A ALA 4.1 2.7 - - - -
196A VAL* 3.7 13.6 - - + +
214A LEU* 5.1 0.4 - - + -
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Residues in contact with LEU 124 (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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80A LEU 3.6 23.8 - - - +
81A ALA* 3.8 21.3 - - + -
84A VAL* 3.8 18.8 - - + -
119A ASN* 2.9 28.9 + - - +
120A ASN* 3.6 6.7 - - - +
123A TYR* 1.3 94.6 - - + +
125A GLY* 1.3 66.7 + - - +
127A ILE* 3.2 5.1 + - - +
128A LEU* 2.9 26.5 + - - +
140A VAL* 3.9 36.5 - - + +
143A PHE* 3.9 8.7 - - + +
144A THR* 4.5 2.0 - - + -
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Residues in contact with GLY 125 (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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95A TYR* 5.5 0.9 - - - -
120A ASN 3.0 15.1 + - - -
121A SER* 3.3 12.5 + - - -
123A TYR 3.4 0.2 - - - -
124A LEU* 1.3 76.0 - - - +
126A PRO* 1.3 62.1 - - - +
128A LEU* 3.2 6.2 + - - +
129A LYS* 2.9 28.8 + - - +
270A MET* 3.9 18.5 - - - +
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Residues in contact with PRO 126 (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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121A SER 3.4 7.6 - - - +
122A LEU 3.1 28.7 - - - +
123A TYR 3.3 9.6 - - - +
125A GLY* 1.3 90.8 - - - +
127A ILE* 1.3 52.0 + - - +
129A LYS* 4.5 0.4 - - + -
130A PHE* 2.7 47.3 + - + +
152A PHE* 5.2 0.9 - - + -
196A VAL* 4.2 14.6 - - + -
254A LEU* 3.9 15.8 - - + +
263A ILE* 4.1 9.4 - - + -
267A THR* 3.4 24.9 - - + +
270A MET* 4.3 0.6 - - + -
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Residues in contact with ILE 127 (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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123A TYR* 3.4 56.8 - - + +
124A LEU* 3.2 6.6 + - - +
126A PRO* 1.3 75.2 - - - +
128A LEU* 1.3 59.4 + - - +
131A GLY* 2.8 30.2 + - - -
135A GLN* 3.9 29.6 - - + +
136A LYS* 3.9 5.3 - - - +
139A TRP* 3.8 14.4 - - + +
140A VAL* 3.4 21.5 - - + -
196A VAL* 4.4 3.4 - - + -
214A LEU* 3.9 22.7 - - + -
254A LEU* 4.3 9.0 - - + -
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Residues in contact with LEU 128 (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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83A ASP* 4.0 13.5 - - + +
84A VAL* 3.4 40.4 - - + +
85A PRO* 4.1 7.9 - - + -
88A LEU* 3.6 30.7 - - + -
124A LEU 2.9 16.4 + - - +
125A GLY* 3.7 8.5 - - - +
127A ILE* 1.3 78.8 - - - +
129A LYS* 1.3 63.5 + - - +
136A LYS* 3.5 27.6 + - + +
140A VAL* 4.1 16.8 - - + -
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Residues in contact with LYS 129 (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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125A GLY 2.9 19.9 + - - +
126A PRO* 4.5 0.9 - - + -
128A LEU* 1.3 75.3 - - - +
130A PHE* 1.3 89.8 + - + +
131A GLY 5.1 0.7 - - - +
266A GLN* 2.7 35.0 + - + +
270A MET* 4.8 18.4 - - + +
341A PHE* 5.8 7.5 - - - -
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Residues in contact with PHE 130 (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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126A PRO* 2.7 29.0 + - + +
129A LYS* 1.3 99.1 - - + +
131A GLY* 1.3 63.2 + - - +
132A SER 4.0 0.2 + - - -
135A GLN* 4.6 0.3 - - - +
254A LEU* 3.8 17.7 - - + +
255A GLY* 4.1 14.9 + - - +
259A MET* 3.8 21.8 - - + -
262A LYS* 4.7 5.8 - - - -
263A ILE* 3.7 52.0 - - + -
266A GLN* 3.4 30.5 - - + -
267A THR* 4.5 2.2 - - - -
270A MET* 5.8 0.7 - - + -
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Residues in contact with GLY 131 (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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127A ILE* 2.8 20.9 + - - -
128A LEU 4.8 0.5 - - - +
129A LYS 3.8 0.7 - - - +
130A PHE* 1.3 82.5 - - - +
132A SER* 1.3 67.3 + - - -
135A GLN* 3.4 15.5 - - - -
136A LYS* 3.4 15.0 + - - -
254A LEU* 3.5 9.5 - - - +
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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