Contacts of the helix formed by residues 123 - 131 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B VAL 3.0 10.1 + - - +
119B ASN* 3.7 12.3 - - - +
122B LEU* 1.3 77.1 - - - +
124B LEU* 1.3 83.0 + - + +
126B PRO* 3.4 10.0 - - - +
127B ILE* 3.3 36.5 - - + +
139B TRP* 2.8 42.6 + + - +
143B PHE* 3.6 20.1 - + - -
150B GLY* 3.7 11.7 - - - -
151B CYS* 3.7 33.7 - - - +
194B ALA* 3.2 38.4 - - + +
195B ALA 4.3 2.2 - - - -
196B VAL* 3.7 12.4 - - + +
214B LEU* 5.3 0.4 - - + -
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU 3.4 26.0 - - - +
81B ALA* 3.9 18.2 - - + -
84B VAL* 4.1 14.8 - - + -
119B ASN* 3.1 22.3 + - - +
120B ASN* 3.8 6.5 - - - +
123B TYR* 1.3 98.8 - - + +
125B GLY* 1.3 60.2 + - - +
127B ILE* 3.3 4.9 + - - +
128B LEU* 2.9 34.4 + - - +
140B VAL* 3.7 42.2 - - + +
143B PHE* 3.9 10.1 - - + +
144B THR* 4.5 1.3 - - + -
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B TYR* 5.8 0.4 - - - -
120B ASN 3.2 11.9 + - - -
121B SER* 3.6 10.5 + - - -
124B LEU* 1.3 78.0 - - - +
126B PRO* 1.3 63.0 - - - +
128B LEU* 3.3 10.1 + - - +
129B LYS* 3.0 28.9 + - - +
270B MET* 4.0 16.9 - - - +
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Residues in contact with PRO 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B SER 3.5 8.3 - - - +
122B LEU 3.2 27.4 - - - +
123B TYR 3.4 9.6 - - - +
125B GLY* 1.3 87.1 - - - +
127B ILE* 1.3 54.7 + - - +
129B LYS* 4.4 0.2 - - + -
130B PHE* 2.7 48.4 + - + +
152B PHE* 5.1 0.9 - - + -
196B VAL* 4.4 13.5 - - + -
198B PHE* 5.9 0.4 - - + -
254B LEU* 4.0 14.3 - - + +
263B ILE* 4.1 12.3 - - + -
267B THR* 3.4 25.6 - - + +
270B MET* 4.4 1.3 - - + -
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TYR* 3.3 57.9 - - + +
124B LEU* 3.3 7.1 + - - +
125B GLY 3.2 1.0 - - - -
126B PRO* 1.3 75.4 - - - +
128B LEU* 1.3 59.0 + - - +
131B GLY* 2.8 32.8 + - - -
135B GLN 4.1 18.6 - - - +
136B LYS* 3.9 9.4 - - + -
139B TRP* 4.0 13.2 - - + +
140B VAL* 3.5 20.2 - - + -
196B VAL* 4.5 1.6 - - + -
214B LEU* 3.9 26.9 - - + -
254B LEU* 4.3 9.9 - - + -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASP* 3.8 21.8 - - + +
84B VAL* 3.7 31.4 - - + -
85B PRO* 3.9 11.7 - - + -
88B LEU* 3.7 30.1 - - + -
124B LEU 2.9 19.9 + - - +
125B GLY* 3.5 7.4 - - - +
127B ILE* 1.3 77.4 - - - +
129B LYS* 1.3 61.2 + - - +
136B LYS* 3.4 30.8 + - + +
140B VAL* 4.7 6.7 - - + -
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLY 3.0 18.1 + - - +
126B PRO* 4.4 0.2 - - + -
128B LEU* 1.3 77.2 - - - +
130B PHE* 1.3 86.5 + - + +
131B GLY 5.3 0.2 - - - -
266B GLN* 2.7 43.3 + - + +
270B MET* 4.4 17.7 - - + +
335B LYS* 6.2 1.1 - - - +
341B PHE* 5.9 6.1 - - - -
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Residues in contact with PHE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PRO* 2.7 34.1 + - + +
129B LYS* 1.3 103.6 - - + +
131B GLY* 1.3 61.1 + - - +
254B LEU* 3.7 17.7 - - + +
255B GLY* 3.9 14.7 + - - +
259B MET* 5.5 8.1 - - + -
262B LYS* 5.5 7.0 - - + -
263B ILE* 3.7 55.6 - - + -
266B GLN* 3.3 33.7 - - + -
267B THR* 4.8 1.3 - - - -
270B MET* 5.6 0.2 - - + -
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Residues in contact with GLY 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ILE* 2.8 20.9 + - - -
128B LEU 4.8 0.2 - - - +
129B LYS 3.8 0.2 - - - -
130B PHE* 1.3 81.3 - - - +
132B SER* 1.3 65.4 + - - -
135B GLN* 3.3 16.4 - - - -
136B LYS* 3.4 17.0 + - - -
254B LEU* 3.4 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