Contacts of the helix formed by residues 1150 - 1162 (chain A) in PDB entry 5IY8
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 ASP1150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1146A GLN* 3.4 14.5 + - + +
1147A SER 3.7 3.8 - - - +
1149A ARG* 1.3 83.1 - - + +
1151A ALA* 1.3 65.7 + - - +
1152A GLU* 2.9 15.4 + - - +
1153A ARG* 2.4 59.6 + - - +
1154A ALA* 3.4 12.3 + - - +
1334A TRP* 3.1 14.4 - - - -
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Residues in contact with ALA1151 (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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1149A ARG 4.3 0.4 + - - -
1150A ASP* 1.3 75.8 + - - +
1152A GLU* 1.3 65.6 + - - +
1154A ALA* 3.1 4.5 + - - +
1155A LYS* 2.7 38.5 + - - +
1334A TRP* 3.3 24.6 - - + +
246U ARG* 4.7 9.2 - - + -
249U GLN* 3.5 22.6 + - - +
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Residues in contact with GLU1152 (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 ASP* 2.9 14.1 + - - +
1151A ALA* 1.3 83.6 + - - +
1153A ARG* 1.3 63.5 + - + +
1155A LYS* 2.8 40.5 + - - +
1156A ASP* 3.1 21.8 + - - +
1225A LYS* 5.2 2.3 + - - -
242U LYS* 5.0 2.1 - - + +
246U ARG* 4.0 20.1 + - - -
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Residues in contact with ARG1153 (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 GLN* 3.1 57.3 + - - +
1147A SER* 3.7 27.4 - - - +
1150A ASP* 2.4 43.8 + - - +
1152A GLU* 1.3 67.8 - - - +
1154A ALA* 1.3 61.7 + - - +
1156A ASP* 3.2 7.1 + - - +
1157A ILE* 3.1 30.8 + - - +
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Residues in contact with ALA1154 (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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1143A LEU* 4.5 9.4 - - + -
1147A SER 3.8 12.9 + - - +
1150A ASP 3.4 16.1 + - - +
1151A ALA 3.1 11.4 + - - +
1153A ARG* 1.3 78.2 - - - +
1155A LYS* 1.3 56.1 + - - +
1157A ILE* 4.0 2.9 - - - +
1158A LEU* 3.0 30.5 + - - +
1310A HIS* 3.3 31.5 + - + -
1334A TRP* 3.9 5.4 - - + -
1336A LEU* 5.0 2.1 - - - +
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Residues in contact with LYS1155 (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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1151A ALA 2.7 20.5 + - - +
1152A GLU* 2.8 43.2 + - - +
1153A ARG 3.2 0.2 - - - -
1154A ALA* 1.3 75.6 - - - +
1156A ASP* 1.3 56.0 + - - +
1158A LEU* 3.7 8.3 - - + +
1159A CYS* 3.1 35.6 + - - -
1225A LYS* 5.3 11.7 - - + -
242U LYS* 3.9 25.9 + - - +
245U ILE* 3.5 42.1 - - + +
246U ARG* 4.9 3.6 - - + +
249U GLN* 3.7 25.6 - - + +
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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 GLU 3.1 13.2 + - - +
1153A ARG* 3.2 10.3 + - - +
1155A LYS* 1.3 75.4 - - - +
1157A ILE* 1.3 65.6 + - + +
1159A CYS* 3.6 5.4 + - - +
1160A ARG* 3.2 47.9 + - - +
1225A LYS* 2.4 40.7 + - - +
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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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1143A LEU* 4.0 27.6 - - + -
1147A SER* 3.5 26.7 - - - +
1153A ARG* 3.1 12.9 + - + +
1154A ALA* 4.2 4.3 - - - +
1156A ASP* 1.3 73.9 - - + +
1158A LEU* 1.3 62.8 + - - +
1160A ARG* 3.0 14.9 + - + +
1161A LEU* 2.8 30.3 + - + +
1336A LEU* 4.4 6.3 - - + -
1349A GLU* 5.6 4.0 - - + +
1350A LYS 4.4 11.9 - - - +
1351A ASP* 3.5 34.1 - - + +
1352A VAL* 4.6 9.2 - - + -
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Residues in contact with LEU1158 (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 ALA 3.0 19.8 + - - +
1155A LYS* 3.7 9.9 - - + +
1157A ILE* 1.3 73.5 - - - +
1159A CYS* 1.3 60.8 + - - +
1161A LEU* 3.2 4.7 + - + -
1162A GLU* 2.9 36.9 + - + +
1308A TYR* 2.4 66.0 - - + +
1310A HIS* 4.1 22.0 - - + +
1336A LEU* 3.5 31.4 - - + +
245U ILE* 4.8 9.9 - - + -
249U GLN* 5.6 3.4 - - + +
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Residues in contact with CYS1159 (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 LYS* 3.1 23.8 + - - +
1156A ASP* 4.0 6.7 - - - +
1158A LEU* 1.3 77.5 - - - +
1160A ARG* 1.3 61.4 + - - +
1161A LEU 3.3 0.3 + - - -
1162A GLU* 3.5 26.7 + - - +
1223A ASP* 3.2 30.3 - - - -
1224A ARG* 4.0 22.2 - - - +
1225A LYS* 4.8 9.0 - - + -
1299A GLN* 3.5 22.0 + - - +
245U ILE* 5.5 7.6 - - - -
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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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1156A ASP* 3.2 37.2 + - - +
1157A ILE* 3.0 15.2 + - + +
1159A CYS* 1.3 75.7 - - - +
1161A LEU* 1.3 62.3 + - - +
1162A GLU 4.2 0.4 - - - -
1299A GLN* 3.9 13.1 - - + +
1300A GLY* 3.8 15.1 + - - -
1345A ARG* 5.6 2.9 + - - -
1349A GLU* 3.5 36.6 + - + +
1350A LYS* 6.0 7.3 - - - +
5E GLU* 4.5 20.4 + - - -
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Residues in contact with LEU1161 (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 VAL* 4.3 17.3 - - + -
1157A ILE* 2.8 18.9 + - + +
1158A LEU* 3.8 6.5 - - + +
1160A ARG* 1.3 77.2 - - + +
1162A GLU* 1.3 69.1 + - - +
1300A GLY* 4.0 5.5 - - - -
1304A ILE* 3.1 17.2 - - + +
1307A VAL* 3.1 37.7 - - + +
1308A TYR* 5.5 2.0 - - + -
1336A LEU* 4.4 18.2 - - + -
1338A THR* 3.8 17.0 - - + -
1345A ARG* 5.5 4.2 + - - +
1346A VAL* 4.3 29.6 - - + -
1349A GLU* 5.9 7.2 - - + -
1352A VAL* 4.8 9.4 - - + -
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Residues in contact with GLU1162 (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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1158A LEU* 2.9 30.8 + - + +
1159A CYS* 3.5 18.2 + - - +
1160A ARG 3.5 0.2 - - - -
1161A LEU* 1.3 83.1 - - - +
1163A HIS* 1.3 61.9 + - - +
1164A THR* 4.1 1.1 - - + +
1224A ARG* 3.4 36.8 + - - +
1299A GLN* 3.8 7.7 - - + +
1300A GLY 3.0 18.0 + - - -
1306A LYS 4.5 3.8 - - - +
1307A VAL* 3.5 11.4 - - + -
1308A TYR* 2.7 63.5 + - + -
245U ILE* 5.0 0.2 - - - +
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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