Contacts of the helix formed by residues 1144 - 1160 (chain A) in PDB entry 5O9Z
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 LYS1144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1124A ASN* 6.1 0.3 - - - +
1143A MET* 1.3 74.2 - - - +
1145A HIS* 1.3 58.4 + - - +
1147A VAL* 4.4 2.3 - - - +
1148A ASN* 2.9 32.1 + - - +
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Residues in contact with HIS1145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110A ILE* 5.7 0.7 - - - +
1143A MET* 3.4 3.6 - - + +
1144A LYS* 1.3 79.5 - - - +
1146A ASP* 1.3 57.4 + - - +
1148A ASN* 3.9 4.2 - - - +
1149A LEU* 2.9 30.8 + - - +
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Residues in contact with ASP1146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1141A ARG 4.4 10.3 - - - +
1143A MET* 3.4 25.4 + - + +
1144A LYS 3.3 0.6 - - - -
1145A HIS* 1.3 75.8 - - - +
1147A VAL* 1.3 60.4 + - - +
1149A LEU* 3.3 4.3 + - - +
1150A GLY* 2.9 25.8 + - - -
1177A VAL* 4.2 26.4 - - + +
1179A SER* 5.8 7.0 - - - -
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Residues in contact with VAL1147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124A ASN* 4.0 29.0 - - + +
1125A ILE* 5.7 1.3 - - - -
1128A TYR* 5.6 7.0 - - + -
1142A LEU* 5.8 3.6 - - + -
1143A MET 2.8 23.1 + - - +
1144A LYS* 4.4 2.0 - - - +
1146A ASP* 1.3 73.5 - - - +
1148A ASN* 1.3 57.3 + - - +
1150A GLY* 4.5 1.3 - - - +
1151A ARG* 2.9 31.7 + - - +
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Residues in contact with ASN1148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1110A ILE* 4.3 20.5 - - + +
1113A TYR* 5.0 1.7 - - - +
1124A ASN* 5.4 5.5 - - + +
1144A LYS 2.9 22.6 + - - +
1145A HIS* 3.9 5.2 - - - +
1146A ASP 3.2 0.2 - - - -
1147A VAL* 1.3 78.5 - - - +
1149A LEU* 1.3 57.4 + - - +
1151A ARG* 3.9 4.2 - - - +
1152A ALA* 2.9 30.0 + - - +
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Residues in contact with LEU1149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106A ALA* 5.2 17.5 - - + +
1109A LEU* 6.2 0.9 - - - -
1110A ILE* 4.9 5.3 - - + +
1145A HIS 2.9 19.6 + - - +
1146A ASP* 3.3 5.1 + - - +
1148A ASN* 1.3 75.5 - - - +
1150A GLY* 1.3 60.8 + - - +
1152A ALA* 3.3 6.4 + - - +
1153A VAL* 2.9 29.6 + - - +
1177A VAL* 5.6 4.7 - - + -
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Residues in contact with GLY1150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1146A ASP 2.9 16.0 + - - -
1147A VAL* 4.0 1.6 - - - -
1149A LEU* 1.3 77.3 - - - +
1151A ARG* 1.3 55.7 + - - +
1153A VAL* 3.3 6.3 + - - +
1154A PHE* 2.9 29.9 + - - +
1175A VAL* 4.7 19.8 - - - +
1177A VAL* 5.4 5.3 - - - +
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Residues in contact with ARG1151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113A TYR* 4.9 2.6 - - + +
1124A ASN* 5.8 5.8 - - + -
1147A VAL 2.9 20.1 + - - +
1148A ASN* 4.1 4.5 - - - +
1150A GLY* 1.3 75.7 - - - +
1152A ALA* 1.3 56.8 + - - +
1154A PHE* 3.8 6.3 - - - +
1155A TRP* 2.9 29.3 + - - +
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Residues in contact with ALA1152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109A LEU* 3.5 42.7 - - + +
1110A ILE 4.2 1.3 - - - +
1113A TYR* 3.7 16.5 - - + +
1148A ASN 2.9 18.8 + - - +
1149A LEU* 3.6 6.1 - - - +
1150A GLY 3.2 0.2 - - - -
1151A ARG* 1.3 76.1 - - - +
1153A VAL* 1.3 59.9 + - - +
1155A TRP* 3.2 2.7 + - - +
1156A ASP* 2.9 29.1 + - - +
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Residues in contact with VAL1153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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975A VAL* 5.3 12.8 - - + -
1109A LEU* 5.7 0.6 - - - +
1149A LEU 2.9 16.7 + - - +
1150A GLY* 3.8 5.8 - - - +
1152A ALA* 1.3 76.0 - - - +
1154A PHE* 1.3 58.2 + - - +
1156A ASP* 3.4 5.0 + - - +
1157A ILE* 2.9 31.9 + - - +
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Residues in contact with PHE1154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1150A GLY 2.9 17.7 + - - +
1151A ARG* 3.9 6.7 - - - +
1153A VAL* 1.3 76.3 - - - +
1155A TRP* 1.3 58.0 + - - +
1157A ILE* 4.2 4.4 - - - +
1158A LYS* 2.9 31.5 + - - +
1170A TRP* 4.9 17.1 - - + +
1175A VAL* 5.6 5.6 - - + -
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Residues in contact with TRP1155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113A TYR* 4.8 10.1 - - + -
1151A ARG 2.9 19.5 + - - +
1152A ALA* 3.2 7.1 + - - +
1154A PHE* 1.3 75.7 - - - +
1156A ASP* 1.3 59.7 + - - +
1158A LYS* 3.8 4.5 - - - +
1159A ASN* 2.9 30.8 + - - +
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Residues in contact with ASP1156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1152A ALA 2.9 16.7 + - - +
1153A VAL* 3.9 6.1 - - - +
1155A TRP* 1.3 75.2 - - - +
1157A ILE* 1.3 59.1 + - - +
1159A ASN* 3.3 4.9 + - - +
1160A ARG* 2.9 30.0 + - - +
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Residues in contact with ILE1157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052A VAL* 4.7 12.3 - - + +
1153A VAL 2.9 18.3 + - - +
1154A PHE* 4.2 4.5 - - - +
1156A ASP* 1.3 75.7 - - - +
1158A LYS* 1.3 61.8 + - - +
1160A ARG* 3.4 14.7 + - - +
1161A LEU* 3.6 13.3 + - - +
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Residues in contact with LYS1158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1154A PHE 2.9 21.2 + - - +
1155A TRP* 3.9 5.4 - - - +
1157A ILE* 1.3 78.5 - - - +
1159A ASN* 1.3 58.9 + - - +
1161A LEU* 3.5 16.8 + - - +
1167A THR* 6.0 2.1 - - - -
1168A VAL 5.1 11.4 - - - +
1170A TRP* 6.1 4.3 - - + -
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Residues in contact with ASN1159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1155A TRP 2.9 19.5 + - - +
1156A ASP* 3.7 5.4 - - - +
1158A LYS* 1.3 75.8 - - - +
1160A ARG* 1.3 62.2 + - - +
1161A LEU 3.4 5.1 - - - +
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Residues in contact with ARG1160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051A LEU* 3.9 17.7 - - - +
1052A VAL* 3.8 27.4 - - + +
1156A ASP 2.9 16.7 + - - +
1157A ILE* 3.8 7.9 - - - +
1158A LYS 3.3 0.6 - - - -
1159A ASN* 1.3 79.8 - - - +
1161A LEU* 1.3 59.3 + - - +
1162A PRO* 4.0 1.9 - - - +
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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