Contacts of the helix formed by residues 1140 - 1156 (chain B) in PDB entry 3CQG
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 PHE1140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1083B TRP* 4.4 24.3 - - + +
1141B GLU* 1.3 53.9 + - - +
1142B PHE* 2.8 27.0 + - + +
1143B VAL* 3.6 11.2 + - + +
1144B LEU* 4.2 4.4 + - - +
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Residues in contact with GLU1141 (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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1128B ALA* 5.6 9.9 - - + -
1140B PHE* 1.3 68.0 - - - +
1142B PHE* 1.3 65.8 + - - +
1143B VAL 3.4 0.9 - - - -
1144B LEU* 3.8 14.2 - - + +
1145B LYS* 3.5 19.8 + - - +
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Residues in contact with PHE1142 (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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1140B PHE* 2.8 19.1 + - + +
1141B GLU* 1.3 76.6 - - - +
1143B VAL* 1.3 65.0 + - + +
1145B LYS* 3.8 3.6 + - - +
1146B ALA* 3.5 14.7 + - - +
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Residues in contact with VAL1143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083B TRP* 3.2 37.2 - - + +
1140B PHE* 3.6 7.9 + - + +
1142B PHE* 1.3 80.5 - - + +
1144B LEU* 1.3 65.8 + - - +
1145B LYS 3.2 2.0 - - - -
1146B ALA* 2.9 11.0 + - + +
1147B ASN* 2.8 45.5 + - - +
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Residues in contact with LEU1144 (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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1083B TRP* 5.0 5.6 - - + -
1124B ASP* 5.8 3.4 - - - +
1127B GLN* 6.1 3.6 - - - +
1128B ALA* 6.0 5.8 - - + -
1140B PHE 4.2 3.7 + - - +
1141B GLU* 3.6 20.1 + - + +
1142B PHE 3.4 0.6 - - - -
1143B VAL* 1.3 78.6 - - - +
1145B LYS* 1.3 51.4 + - - +
1147B ASN* 3.4 8.4 + - - +
1148B TYR* 2.8 35.0 + - - +
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Residues in contact with LYS1145 (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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1124B ASP* 5.6 1.6 - - - -
1141B GLU 3.5 12.0 + - - +
1142B PHE 4.1 3.6 - - - +
1143B VAL 3.2 0.4 - - - -
1144B LEU* 1.3 76.6 - - - +
1146B ALA* 1.3 56.4 + - - +
1148B TYR* 3.1 10.5 - - - -
1149B GLU* 2.7 36.6 + - - +
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Residues in contact with ALA1146 (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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1142B PHE 3.5 5.6 + - - +
1143B VAL* 2.9 28.2 + - + +
1145B LYS* 1.3 78.0 - - - +
1147B ASN* 1.3 62.7 + - - +
1149B GLU* 3.2 8.4 + - - +
1150B TYR* 3.0 24.8 + - - +
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Residues in contact with ASN1147 (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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1078B LEU* 6.0 0.2 - - - +
1083B TRP* 3.2 20.5 - - - +
1097B LYS* 6.0 1.0 - - - +
1098B ASP* 3.9 19.4 + - - +
1101B PHE* 6.6 0.4 - - + -
1143B VAL* 2.8 41.1 + - - +
1144B LEU* 3.8 6.1 - - - +
1146B ALA* 1.3 72.9 - - - +
1148B TYR* 1.3 54.3 + - - +
1149B GLU 2.8 5.2 - - - -
1150B TYR* 3.1 8.4 + - - +
1151B TYR* 2.6 37.7 + - - +
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Residues in contact with TYR1148 (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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1124B ASP* 3.1 33.3 - - + +
1144B LEU 2.8 19.9 + - - +
1145B LYS* 3.0 13.4 + - - +
1147B ASN* 1.3 74.7 - - - +
1149B GLU* 1.3 55.5 + - - +
1151B TYR* 4.1 10.3 - - - +
1152B VAL* 3.2 19.2 + - - +
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Residues in contact with GLU1149 (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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1145B LYS 2.7 14.6 + - - +
1146B ALA* 3.2 9.4 - - - +
1148B TYR* 1.3 78.8 - - - +
1150B TYR* 1.3 61.7 + - - +
1151B TYR 3.0 4.0 - - - -
1152B VAL* 3.1 24.4 + - - +
1153B GLN* 3.3 6.8 + - - +
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Residues in contact with TYR1150 (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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1146B ALA 3.0 15.5 + - - +
1147B ASN* 3.8 9.4 - - - +
1149B GLU* 1.3 75.2 - - - +
1151B TYR* 1.3 56.2 + - - +
1153B GLN* 3.8 8.0 + - - +
1154B GLY* 3.2 20.8 + - - -
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Residues in contact with TYR1151 (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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1101B PHE* 6.0 7.9 - - + -
1147B ASN 2.6 22.0 + - - +
1148B TYR* 4.1 9.6 - - - -
1150B TYR* 1.3 71.8 - - - +
1152B VAL* 1.3 58.2 + - + +
1154B GLY* 2.9 2.4 + - - +
1155B GLN* 2.7 57.3 + - - +
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Residues in contact with VAL1152 (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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1148B TYR 3.2 22.7 - - - +
1149B GLU* 3.2 11.9 - - - +
1151B TYR* 1.3 76.1 - - - +
1153B GLN* 1.3 61.0 + - - +
1155B GLN* 4.0 2.6 - - - -
1156B ILE* 2.8 53.6 + - + +
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Residues in contact with GLN1153 (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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1149B GLU 3.3 7.1 + - - +
1150B TYR* 4.1 9.2 - - - +
1151B TYR 3.3 0.2 - - - -
1152B VAL* 1.3 80.2 - - - +
1154B GLY* 1.3 61.7 + - - +
1156B ILE* 3.6 24.4 - - + +
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Residues in contact with GLY1154 (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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1105B LEU* 6.2 4.3 - - - -
1119B LEU* 5.0 4.4 - - - +
1150B TYR 3.2 13.2 + - - -
1151B TYR* 2.9 8.3 + - - -
1153B GLN* 1.3 78.5 - - - +
1155B GLN* 1.3 62.6 + - - +
1156B ILE 3.3 4.3 + - - -
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Residues in contact with GLN1155 (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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1101B PHE* 5.5 3.0 - - - -
1119B LEU* 3.2 69.7 + - + +
1120B PRO* 3.8 9.7 - - + +
1122B VAL* 5.2 4.6 - - - +
1151B TYR* 2.7 41.1 + - - +
1152B VAL* 4.3 2.2 - - - +
1154B GLY* 1.3 72.2 - - - +
1156B ILE* 1.3 62.0 + - + +
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Residues in contact with ILE1156 (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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1152B VAL* 2.8 44.4 + - + +
1153B GLN* 3.6 24.0 - - + +
1154B GLY 4.0 7.4 - - - -
1155B GLN* 1.3 84.9 - - + +
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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