Contacts of the helix formed by residues 123 - 131 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D VAL 2.9 11.3 + - - +
119D ASN* 3.7 17.9 - - - +
122D LEU* 1.3 75.6 - - - +
124D LEU* 1.3 79.1 + - + +
125D GLY 3.3 0.9 - - - -
126D PRO* 3.2 14.6 - - - +
127D ILE* 3.4 31.1 - - + +
139D TRP* 2.7 43.8 + + - +
143D PHE* 3.7 21.7 - + + -
150D GLY* 3.7 22.4 - - - -
151D CYS 3.8 19.1 - - - +
194D ALA* 3.4 36.8 - - + +
195D ALA 4.4 2.5 - - - -
196D VAL* 3.9 13.4 - - + +
214D LEU* 5.4 0.4 - - + -
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Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D LEU 3.3 26.2 - - - +
81D ALA* 3.6 20.9 - - + -
84D VAL* 3.9 14.6 - - + -
119D ASN* 2.9 31.0 + - - +
120D ASN* 3.6 6.7 - - - +
123D TYR* 1.3 90.7 - - + +
125D GLY* 1.3 63.9 + - - +
127D ILE* 3.2 6.0 + - - +
128D LEU* 3.0 28.1 + - + +
140D VAL* 3.6 47.5 - - + +
143D PHE 3.8 6.3 - - - +
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Residues in contact with GLY 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D TYR* 5.7 0.7 - - - -
120D ASN 3.1 14.1 + - - -
121D SER* 3.5 11.1 + - - -
124D LEU* 1.3 76.6 - - - +
126D PRO* 1.3 68.2 - - - +
128D LEU* 3.5 10.2 + - - +
129D LYS* 3.1 24.8 + - - +
270D MET* 3.8 17.9 - - - +
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Residues in contact with PRO 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D SER 3.4 8.5 - - - +
122D LEU 3.0 29.4 - - - +
123D TYR 3.2 10.3 - - - +
125D GLY* 1.3 90.5 - - - +
127D ILE* 1.3 54.9 + - - +
129D LYS* 4.5 0.4 - - + -
130D PHE* 2.8 42.3 + - + +
152D PHE* 5.0 0.9 - - + -
196D VAL* 4.3 13.5 - - + -
254D LEU* 3.8 17.9 - - + +
263D ILE* 4.2 9.0 - - + -
267D THR* 3.6 24.7 - - + +
270D MET* 4.2 1.3 - - + -
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Residues in contact with ILE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D TYR* 3.4 57.2 - - + +
124D LEU 3.2 3.0 + - - +
126D PRO* 1.3 73.7 - - - +
128D LEU* 1.3 63.0 + - - +
131D GLY* 2.9 30.6 + - - +
135D GLN* 4.0 29.8 - - + +
136D LYS* 3.6 7.1 - - - +
139D TRP* 3.9 14.6 - - + +
140D VAL* 3.6 21.5 - - + -
196D VAL* 4.5 3.4 - - + -
214D LEU* 4.0 22.2 - - + -
254D LEU* 4.3 5.2 - - + -
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D ASP* 3.8 20.0 - - + +
84D VAL* 3.6 31.9 - - + -
85D PRO* 4.0 13.2 - - + -
88D LEU* 3.8 27.8 - - + -
120D ASN 5.8 0.7 - - - +
124D LEU* 3.0 23.8 + - + +
125D GLY* 3.8 7.6 - - - +
127D ILE* 1.3 77.7 - - - +
129D LYS* 1.3 61.0 + - - +
136D LYS* 3.2 30.1 + - + +
140D VAL* 4.4 10.1 - - + -
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Residues in contact with LYS 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D GLY 3.1 18.4 + - - +
126D PRO* 4.5 0.2 - - + -
128D LEU* 1.3 80.3 - - - +
130D PHE* 1.3 90.4 + - + +
131D GLY 3.7 0.6 - - - +
266D GLN* 2.9 36.0 + - + +
270D MET* 4.8 17.8 - - + -
341D PHE* 6.2 1.6 - - - -
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Residues in contact with PHE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PRO* 2.8 31.1 + - + +
129D LYS* 1.3 111.1 - - + +
131D GLY* 1.3 64.0 + - - +
132D SER 4.1 0.2 + - - -
135D GLN* 4.7 0.2 - - - +
254D LEU* 3.6 18.2 - - + +
255D GLY* 3.8 15.1 + - - +
259D MET* 3.9 17.3 - - + -
262D LYS* 4.0 22.4 - - - -
263D ILE* 3.7 47.6 - - + -
266D GLN* 3.8 21.1 - - + -
267D THR* 4.7 1.6 - - - -
270D MET* 6.0 0.4 - - + -
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Residues in contact with GLY 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ILE* 2.9 20.3 + - - -
129D LYS 3.7 1.1 - - - +
130D PHE* 1.3 81.0 - - - +
132D SER* 1.3 66.7 + - - -
135D GLN* 3.5 15.3 - - - -
136D LYS* 3.4 15.0 + - - -
254D LEU* 3.6 8.4 - - - +
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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