Contacts of the helix formed by residues 1177 - 1186 (chain A) in PDB entry 6O0Z
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 ASN1177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1173A SER 3.7 7.3 + - - +
1174A PHE 3.2 5.0 + - - +
1176A LYS* 1.3 84.2 - - + +
1178A PRO* 1.3 71.0 - - - +
1179A ILE* 3.4 18.6 - - - +
1180A ASP* 3.4 28.6 - - + +
1181A PHE* 3.4 19.1 + - - +
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Residues in contact with PRO1178 (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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1174A PHE* 3.5 36.6 - - + +
1175A GLU* 5.1 3.6 - - - +
1176A LYS 4.5 2.0 - - - +
1177A ASN* 1.3 92.5 - - - +
1179A ILE* 1.3 62.5 + - + +
1181A PHE* 3.2 3.1 + - - +
1182A LEU* 3.0 37.6 + - + +
1195A ILE* 6.0 5.4 - - + -
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Residues in contact with ILE1179 (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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1177A ASN* 3.4 17.7 - - - +
1178A PRO* 1.3 80.4 - - + +
1180A ASP* 1.3 61.4 + - + +
1182A LEU* 3.5 4.9 + - - +
1183A GLU* 2.9 36.2 + - + +
1190A VAL* 3.7 32.1 - - + +
1192A LYS* 5.9 7.0 - - + -
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Residues in contact with ASP1180 (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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1177A ASN* 3.4 23.7 - - - +
1178A PRO 3.4 0.2 - - - -
1179A ILE* 1.3 83.2 - - + +
1181A PHE* 1.3 56.9 + - - +
1183A GLU* 3.5 7.4 - - - +
1184A ALA* 2.9 31.9 + - - +
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Residues in contact with PHE1181 (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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1164A LEU* 5.3 0.4 - - + -
1166A ILE* 3.9 23.8 - - + -
1170A GLU* 3.8 33.7 - - + -
1173A SER* 4.2 20.0 - - - +
1174A PHE* 3.5 28.3 - + + -
1177A ASN 3.4 20.1 + - - +
1178A PRO 3.2 3.3 + - - +
1179A ILE 3.2 0.6 - - - -
1180A ASP* 1.3 79.7 - - - +
1182A LEU* 1.3 65.0 + - + +
1184A ALA* 3.8 3.4 - - + +
1185A LYS* 3.0 59.4 + - + +
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Residues in contact with LEU1182 (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 VAL* 5.2 10.1 - - + -
1145A VAL* 4.4 20.9 - - + -
1164A LEU* 4.9 14.4 - - + -
1174A PHE* 4.7 14.8 - - + -
1178A PRO* 3.0 20.7 + - + +
1179A ILE* 4.0 4.7 - - - +
1181A PHE* 1.3 84.1 - - + +
1183A GLU* 1.3 61.8 + - - +
1185A LYS* 3.6 8.3 + - + -
1186A GLY 3.7 0.9 + - - -
1187A TYR* 3.3 45.1 + - + +
1190A VAL* 4.8 18.6 - - + -
1195A ILE* 3.8 30.3 - - + -
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Residues in contact with GLU1183 (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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1179A ILE* 2.9 26.9 + - + +
1180A ASP* 3.5 9.4 - - - +
1181A PHE 3.2 0.2 - - - -
1182A LEU* 1.3 77.6 - - - +
1184A ALA* 1.3 67.8 + - - +
1186A GLY* 3.2 12.3 + - - -
1187A TYR 3.3 23.5 + - - +
1188A LYS* 4.1 16.9 - - - +
1190A VAL* 5.8 1.1 - - - +
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Residues in contact with ALA1184 (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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1180A ASP 2.9 16.5 + - - +
1181A PHE* 4.2 3.6 - - + +
1183A GLU* 1.3 80.9 + - - +
1185A LYS* 1.3 63.0 + - - +
1186A GLY* 3.2 0.6 + - - -
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Residues in contact with LYS1185 (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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1164A LEU* 4.3 33.2 - - + +
1165A GLY 5.4 0.4 + - - -
1170A GLU* 4.1 15.5 + - - -
1181A PHE* 3.0 49.7 + - + +
1182A LEU* 3.8 12.3 - - + +
1183A GLU 3.2 0.6 - - - -
1184A ALA* 1.3 78.6 - - - +
1186A GLY* 1.3 55.8 + - - +
1187A TYR* 4.6 8.0 - - + -
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Residues in contact with GLY1186 (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 VAL* 3.4 23.9 - - - +
1150A GLU* 5.3 1.4 + - - +
1183A GLU 3.2 7.6 + - - -
1184A ALA 3.2 1.5 - - - -
1185A LYS* 1.3 79.3 - - - +
1187A TYR* 1.3 68.0 + - - +
1188A LYS* 4.1 10.9 - - - +
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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