Contacts of the helix formed by residues 1151 - 1161 (chain D) in PDB entry 6VVT
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 HIS1151 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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569D ALA 3.3 20.3 + - - +
570D SER* 4.9 5.2 - - - +
916D GLU 3.8 13.0 - - - -
917D THR* 3.1 26.1 + - - +
920D PHE* 2.3 34.4 + + - -
921D ALA* 4.2 0.4 - - + -
922D ARG* 3.9 22.2 - - + -
982D MET* 3.2 26.5 - - + +
1149D SER 4.3 0.4 - - - -
1150D ILE* 1.3 76.6 - - - +
1152D ASP* 1.3 70.2 + - - +
1153D LYS* 3.0 37.6 + - + +
1154D HIS* 3.0 24.7 + - + +
1155D ILE* 3.9 0.9 + - - +
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Residues in contact with ASP1152 (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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917D THR* 2.9 27.2 + - - +
918D SER* 3.2 25.4 - - - -
922D ARG* 3.3 20.1 + - - +
1136D VAL* 4.0 21.4 - - + +
1140D GLN* 4.2 12.3 - - - +
1150D ILE 3.9 2.4 - - - +
1151D HIS* 1.3 72.0 - - - +
1153D LYS* 1.3 57.2 + - - +
1155D ILE* 3.0 10.8 + - - +
1156D GLU* 2.8 35.8 + - - +
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Residues in contact with LYS1153 (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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921D ALA 3.2 14.7 + - - -
922D ARG* 4.4 7.1 - - - +
964D VAL* 5.2 2.5 - - + -
978D TYR* 2.7 62.1 + - + +
979D GLY 3.6 1.0 - - - -
980D ARG 3.0 27.7 + - - +
982D MET* 3.3 23.3 - - + +
1151D HIS* 3.0 29.2 + - + +
1152D ASP* 1.3 79.2 - - - +
1154D HIS* 1.3 63.0 + - + +
1156D GLU* 3.3 17.5 + - - +
1157D VAL* 2.8 36.0 + - - +
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Residues in contact with HIS1154 (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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568D PRO 3.1 27.3 + - - -
569D ALA* 3.4 24.3 + - - -
978D TYR* 3.9 21.0 + - - -
982D MET* 4.0 9.4 - - + +
994D VAL* 5.1 1.4 - - - +
997D VAL* 4.0 10.3 - - + -
998D ALA* 3.4 42.3 - - + +
1001D SER* 3.5 17.5 - - - -
1002D ILE* 4.1 3.4 - - + -
1150D ILE* 4.1 11.4 - - + -
1151D HIS* 3.0 23.9 + - + +
1153D LYS* 1.3 80.3 - - + +
1155D ILE* 1.3 63.2 + - - +
1157D VAL* 3.2 9.5 + - - -
1158D ILE* 3.3 11.1 + - - +
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Residues in contact with ILE1155 (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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1002D ILE* 3.9 18.8 - - + -
1036D PHE* 4.2 7.6 - - + -
1136D VAL* 3.7 29.2 - - + +
1139D VAL* 3.6 34.8 - - + -
1140D GLN* 3.0 42.8 - - + +
1143D TYR* 5.3 2.9 - - + -
1150D ILE* 4.5 10.8 - - + -
1151D HIS 4.6 0.7 - - - +
1152D ASP* 3.0 7.5 + - - +
1154D HIS* 1.3 74.8 - - - +
1156D GLU* 1.3 58.7 + - - +
1158D ILE* 3.0 5.1 + - - +
1159D VAL* 2.8 37.4 + - + +
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Residues in contact with GLU1156 (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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896D ILE* 3.8 8.0 - - - +
922D ARG* 2.5 41.8 + - - -
963D SER* 2.7 25.9 + - - -
964D VAL* 3.6 14.9 + - + +
965D LEU* 3.6 21.2 - - + +
1136D VAL* 4.0 19.2 - - + +
1152D ASP* 2.8 30.7 + - + +
1153D LYS* 3.5 8.5 - - - +
1155D ILE* 1.3 72.6 - - - +
1157D VAL* 1.3 53.8 + - - +
1159D VAL 3.1 0.4 + - - +
1160D ARG* 2.7 36.7 + - - +
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Residues in contact with VAL1157 (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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880D SER* 4.6 2.9 - - - -
883D VAL* 4.0 21.3 - - + -
964D VAL* 4.1 20.0 - - + -
973D VAL* 6.3 0.7 - - + -
978D TYR* 4.4 5.2 - - + -
994D VAL* 3.9 22.4 - - + -
995D GLY* 3.7 30.5 - - - +
998D ALA* 4.0 5.8 - - + -
1153D LYS 2.8 28.1 + - - +
1154D HIS* 3.5 8.5 - - - +
1155D ILE 3.2 0.2 - - - -
1156D GLU* 1.3 76.4 - - - +
1158D ILE* 1.3 63.1 + - - +
1160D ARG* 3.6 10.3 + - - +
1161D GLN* 3.6 17.3 - - - +
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Residues in contact with ILE1158 (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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876D LEU* 4.1 19.3 - - + +
879D VAL* 4.7 3.1 - - + -
880D SER* 3.2 33.4 - - - +
995D GLY 4.5 1.1 - - - +
998D ALA* 4.5 2.0 - - + -
999D ALA 4.4 11.9 - - - +
1002D ILE* 3.7 17.9 - - + -
1036D PHE* 3.3 33.9 - - + -
1154D HIS 3.3 12.8 + - - +
1155D ILE 3.0 7.0 + - - +
1157D VAL* 1.3 74.8 - - - +
1159D VAL* 1.3 64.9 - - - +
1161D GLN* 3.2 18.7 + - - +
1162D MET* 3.9 7.8 - - + +
1211D ILE* 4.2 17.7 - - + +
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Residues in contact with VAL1159 (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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965D LEU* 4.4 0.9 - - + -
1036D PHE* 4.9 3.6 - - + -
1132D GLN* 3.5 44.3 + - + +
1135D LEU* 4.1 26.2 - - + -
1136D VAL* 3.7 21.8 - - + -
1139D VAL* 5.8 0.7 - - + -
1155D ILE* 2.8 31.5 + - + +
1156D GLU* 3.8 3.8 - - - +
1158D ILE* 1.3 70.5 - - - +
1160D ARG* 1.3 66.4 + - - +
1162D MET* 2.9 33.7 + - + +
1163D LEU* 3.8 2.8 + - + -
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Residues in contact with ARG1160 (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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883D VAL* 4.7 4.9 - - - +
964D VAL* 3.2 28.0 - - - +
965D LEU* 4.1 8.2 - - + +
967D CYS* 4.4 14.6 + - - +
969D SER 4.6 6.1 + - - -
972D GLY 3.3 19.0 + - - -
973D VAL* 3.9 15.6 - - - +
1132D GLN* 4.2 14.2 + - - +
1156D GLU 2.7 20.7 + - - +
1157D VAL* 3.7 8.5 - - - +
1159D VAL* 1.3 73.6 - - - +
1161D GLN* 1.3 75.5 + - - +
1162D MET 3.2 1.4 + - - -
1163D LEU 3.6 9.4 + - - -
1164D ARG* 3.7 25.5 + - + +
2003D SO4 1.3 45.3 + - - -
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Residues in contact with GLN1161 (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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879D VAL* 3.7 37.0 + - + +
880D SER* 4.5 4.3 - - - -
882D ASP* 6.3 0.6 - - - +
883D VAL* 3.5 25.1 - - + +
1157D VAL 3.6 14.3 - - - +
1158D ILE 3.2 8.5 + - - +
1159D VAL 3.0 1.2 + - - -
1160D ARG* 1.3 106.7 + - - +
1162D MET* 1.3 61.4 + - - +
1163D LEU 3.6 0.2 - - - -
1164D ARG* 3.4 40.4 + - - +
1209D MET* 4.7 2.1 - - - +
1214D ALA* 3.9 16.8 - - - +
2003D SO4 4.6 3.6 + - - -
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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