Contacts of the helix formed by residues 1167 - 1180 (chain J) in PDB entry 4XLQ
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 SER1167 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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916J TYR* 3.4 13.5 + - - -
920J LEU* 3.8 16.6 - - - +
1145J TYR* 3.8 7.6 - - - -
1165J TYR 4.2 1.6 - - - -
1166J LEU* 1.3 73.8 - - - +
1168J LEU* 1.3 64.5 + - - +
1169J GLU* 3.0 5.2 + - - +
1170J ASP* 2.9 19.2 + - - -
1171J VAL* 2.6 40.6 + - - +
1207J TYR* 3.2 24.4 + - - -
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Residues in contact with LEU1168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776J GLU* 5.6 4.5 - - - +
913J ASP* 5.0 10.8 - - - +
916J TYR* 3.6 43.0 + - + +
917J GLN* 4.6 12.6 - - - +
920J LEU* 5.6 0.7 - - + -
1141J GLU* 3.8 27.1 - - + +
1145J TYR* 3.7 14.2 - - + -
1167J SER* 1.3 78.5 + - - +
1169J GLU* 1.3 56.5 + - - +
1171J VAL* 4.2 6.1 - - + -
1172J HIS* 2.9 67.6 + - + +
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Residues in contact with GLU1169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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920J LEU* 6.1 3.1 - - + -
1158J ARG* 4.8 11.6 + - - -
1164J ARG* 4.9 6.2 + - - -
1167J SER* 3.0 4.6 + - - +
1168J LEU* 1.3 77.3 - - - +
1170J ASP* 1.3 74.5 + - - +
1172J HIS* 3.3 5.5 + - - +
1173J PHE* 2.9 34.1 + - + +
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Residues in contact with ASP1170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1160J LEU* 5.4 3.1 - - + -
1164J ARG* 3.0 40.0 + - + +
1165J TYR 3.1 16.4 - - - +
1166J LEU* 3.6 11.8 - - + -
1167J SER* 3.2 32.2 + - - +
1169J GLU* 1.3 84.8 - - - +
1171J VAL* 1.3 62.4 + - - +
1173J PHE* 3.0 11.5 - - - +
1174J LEU* 2.9 29.7 + - + +
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Residues in contact with VAL1171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140J ILE* 3.6 31.0 - - + +
1141J GLU* 4.7 10.1 - - + -
1144J LEU* 4.0 10.5 - - + +
1145J TYR* 3.6 35.9 - - + +
1166J LEU* 4.4 6.7 - - + -
1167J SER 2.6 24.3 + - - +
1168J LEU* 3.8 6.7 - - - +
1170J ASP* 1.3 72.5 - - - +
1172J HIS* 1.3 63.2 + - + +
1174J LEU* 3.0 14.8 + - + +
1175J ILE* 2.9 35.8 + - + +
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Residues in contact with HIS1172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1137J ARG* 6.0 1.2 - - - +
1141J GLU* 4.3 11.8 + - + -
1168J LEU* 2.9 53.9 + - + +
1169J GLU* 3.8 4.7 - - - +
1171J VAL* 1.3 78.8 - - + +
1173J PHE* 1.3 66.3 + - - +
1175J ILE* 3.1 26.3 + - + +
1176J LYS* 2.9 33.6 + - + +
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Residues in contact with PHE1173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155J ALA* 5.2 0.9 - - + -
1156J LEU* 4.0 24.7 - - + +
1158J ARG* 3.7 57.7 - - + -
1160J LEU* 6.1 4.9 - - + -
1164J ARG* 4.8 9.9 - - - +
1169J GLU* 2.9 25.7 + - + +
1170J ASP* 3.0 16.4 + - - +
1172J HIS* 1.3 75.5 - - - +
1174J LEU* 1.3 64.0 + - + +
1176J LYS* 3.5 7.1 + - - +
1177J ALA* 3.0 25.3 + - + +
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Residues in contact with LEU1174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122J LEU* 5.2 10.5 - - + -
1140J ILE* 5.8 1.3 - - + -
1144J LEU* 4.3 16.2 - - + -
1149J LEU* 5.6 3.4 - - + -
1153J VAL* 5.9 6.1 - - + -
1160J LEU* 4.9 20.2 - - + -
1166J LEU* 3.5 33.0 - - + -
1170J ASP* 2.9 23.2 + - + +
1171J VAL* 3.2 13.2 - - + +
1173J PHE* 1.3 78.7 - - + +
1175J ILE* 1.3 61.4 + - + +
1177J ALA* 3.6 5.5 - - - +
1178J ALA* 2.8 34.8 + - - +
1183J VAL* 4.5 4.6 - - + +
1186J VAL* 4.4 14.4 - - + -
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Residues in contact with ILE1175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122J LEU* 6.0 1.3 - - - -
1134J LEU* 5.5 11.7 - - + +
1137J ARG* 5.1 17.5 - - + +
1140J ILE* 4.2 26.0 - - + -
1141J GLU* 5.6 1.3 - - + -
1171J VAL* 2.9 24.1 + - + +
1172J HIS* 3.1 36.8 + - + +
1174J LEU* 1.3 76.1 - - - +
1176J LYS* 1.3 60.1 + - + +
1178J ALA* 3.4 4.2 + - - +
1179J GLU* 2.9 55.7 + - + +
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Residues in contact with LYS1176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130D ARG* 3.7 36.8 + - - +
1156J LEU* 4.7 9.0 - - + -
1172J HIS* 2.9 24.7 + - + +
1173J PHE* 3.9 5.6 - - - +
1175J ILE* 1.3 75.1 - - + +
1177J ALA* 1.3 63.0 + - - +
1179J GLU* 3.3 11.0 + - - +
1180J ALA* 3.0 22.9 + - - +
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Residues in contact with ALA1177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155J ALA* 3.8 19.7 - - + -
1156J LEU* 3.7 30.7 - - + +
1173J PHE* 3.0 19.5 + - + +
1174J LEU* 3.6 7.2 - - - +
1176J LYS* 1.3 76.4 - - - +
1178J ALA* 1.3 59.7 + - - +
1180J ALA* 2.8 20.3 + - - +
1182J GLU* 3.1 18.9 + - + +
1183J VAL* 4.3 4.9 - - + -
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Residues in contact with ALA1178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122J LEU* 3.4 24.9 - - + -
1123J PHE* 3.5 21.8 - - + -
1134J LEU* 5.7 2.9 - - + -
1174J LEU 2.8 20.5 + - - +
1175J ILE* 3.8 4.0 - - - +
1177J ALA* 1.3 71.9 - - - +
1179J GLU* 1.3 54.7 + - - +
1181J GLY* 2.7 24.8 + - - -
1183J VAL* 3.3 29.7 - - + +
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Residues in contact with GLU1179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1130D ARG* 4.1 9.6 + - - +
1131D THR* 3.1 44.2 - - + +
1132D LEU 4.1 1.0 + - - +
1123J PHE* 4.8 5.6 - - - -
1134J LEU* 4.6 22.2 - - + +
1175J ILE* 2.9 45.8 + - + +
1176J LYS* 3.3 13.4 + - - +
1178J ALA* 1.3 75.8 - - - +
1180J ALA* 1.3 56.9 + - - +
1181J GLY 3.0 3.5 + - - -
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Residues in contact with ALA1180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1125D MET* 3.1 28.0 - - + +
1130D ARG* 4.2 19.1 - - + +
1131D THR 3.8 10.5 - - - +
1132D LEU* 3.7 7.0 - - - +
1156J LEU* 4.2 11.4 - - + -
1176J LYS 3.0 10.4 + - - +
1177J ALA 2.8 12.3 + - - +
1179J GLU* 1.3 75.1 - - - +
1181J GLY* 1.3 62.2 + - - +
1182J GLU* 3.3 14.1 + - + +
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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