Contacts of the helix formed by residues 1170 - 1179 (chain A) in PDB entry 1WUF
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 ASP1170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1165A ILE* 3.4 22.4 - - + +
1167A PRO* 2.5 31.2 - - - +
1168A ASN 3.7 1.9 + - - -
1169A LYS* 1.3 74.2 + - - +
1171A ILE* 1.3 94.7 + - + +
1172A GLN* 3.4 4.3 + - - +
1173A PHE* 3.2 5.8 + - - +
1174A VAL* 3.1 25.6 + - - +
1194A TYR* 3.2 25.9 + - - +
1201A LEU* 4.0 12.7 - - - +
1205A LEU* 4.3 6.6 - - + +
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Residues in contact with ILE1171 (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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1170A ASP* 1.3 91.2 - - - +
1172A GLN* 1.3 63.8 + - - +
1173A PHE 3.3 0.2 + - - -
1174A VAL* 3.4 4.5 + - - +
1175A GLU* 3.2 28.4 + - - +
1201A LEU* 3.6 16.6 - - + +
1204A GLU* 3.0 53.4 - - + +
1205A LEU* 3.2 18.6 - - + -
1208A TYR* 4.0 27.1 - - + +
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Residues in contact with GLN1172 (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* 4.3 15.5 - - + +
1168A ASN 2.7 31.3 + - - -
1169A LYS* 4.1 1.0 - - - +
1170A ASP* 4.3 4.0 + - - +
1171A ILE* 1.3 76.7 - - - +
1173A PHE* 1.3 84.5 + - + +
1175A GLU* 4.0 13.5 - - - +
1176A ALA* 3.5 20.6 + - - +
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Residues in contact with PHE1173 (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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1139A LEU* 6.5 0.2 - - + -
1140A GLN* 3.1 36.8 - - + -
1141A GLN 4.2 9.4 - - - -
1142A ASN 3.6 17.0 - - - -
1143A VAL* 4.3 11.7 - - + -
1146A LEU* 3.4 30.3 - - + -
1163A LEU* 4.9 3.1 - - + -
1164A LYS 6.1 0.9 - - - +
1165A ILE* 5.2 4.0 - - + -
1169A LYS* 3.5 46.2 - - + +
1170A ASP* 3.2 5.7 + - - +
1172A GLN* 1.3 95.4 - - + +
1174A VAL* 1.3 69.2 + - + +
1176A ALA* 3.3 8.1 - - - +
1177A VAL* 3.0 26.4 + - - +
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Residues in contact with VAL1174 (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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1163A LEU* 4.5 12.3 - - + -
1165A ILE* 3.9 17.3 - - + -
1170A ASP 3.1 21.7 + - - +
1171A ILE 3.8 4.5 - - - +
1173A PHE* 1.3 75.8 - - - +
1175A GLU* 1.3 51.2 + - - +
1177A VAL* 3.1 3.8 + - - +
1178A ARG* 2.7 38.5 + - + +
1186A LEU* 4.6 3.7 - - + +
1188A ALA* 5.4 0.9 - - + -
1205A LEU* 4.3 15.3 - - + -
1208A TYR* 3.7 26.7 - - + -
1210A LEU* 3.6 33.4 - - + -
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Residues in contact with GLU1175 (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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1171A ILE* 3.2 18.1 + - - +
1172A GLN* 4.0 13.2 - - - +
1174A VAL* 1.3 75.0 - - - +
1176A ALA* 1.3 55.9 + - - +
1178A ARG* 2.5 9.2 + - - -
1179A LYS* 2.5 68.6 + - + +
1208A TYR* 2.9 43.7 + - + +
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Residues in contact with ALA1176 (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* 3.3 34.8 - - + +
1146A LEU* 5.4 1.1 - - + -
1147A LEU* 3.3 14.7 - - + +
1172A GLN 3.5 6.6 + - - +
1173A PHE 3.3 9.8 + - - +
1175A GLU* 1.3 80.7 - - - +
1177A VAL* 1.3 59.4 + - + +
1179A LYS* 3.4 5.9 - - - +
1180A SER* 3.1 24.8 - - - -
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Residues in contact with VAL1177 (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 LEU* 3.6 24.7 - - + -
1147A LEU* 4.0 8.7 - - + -
1150A VAL* 3.8 35.7 - - + -
1163A LEU* 3.9 8.7 - - + -
1173A PHE 3.0 13.2 + - - +
1174A VAL 3.7 5.2 - - - +
1175A GLU 2.7 4.2 + - - -
1176A ALA* 1.3 73.5 - - + +
1178A ARG* 1.3 58.2 + - - +
1181A PHE* 3.0 32.7 + - + +
1184A LEU* 4.5 3.8 - - + -
1186A LEU* 3.3 33.9 - - + -
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Residues in contact with ARG1178 (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 VAL* 2.7 17.3 + - + +
1175A GLU 2.5 8.3 + - - +
1177A VAL* 1.3 72.9 - - - +
1179A LYS* 1.3 58.5 + - + +
1180A SER 2.9 7.2 + - - -
1181A PHE 3.0 16.8 + - - -
1182A PRO* 3.2 43.3 + - - +
1183A LYS 4.3 0.4 - - - -
1184A LEU 2.8 30.8 + - - +
1185A SER* 4.5 0.4 - - - +
1186A LEU* 3.1 33.9 + - + +
1208A TYR* 3.0 48.9 + - + +
1209A ASP* 3.7 25.4 + - - +
1210A LEU* 4.9 0.4 - - - +
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Residues in contact with LYS1179 (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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1175A GLU* 2.5 50.7 + - + +
1176A ALA* 3.4 5.4 - - - +
1178A ARG* 1.3 72.9 - - + +
1180A SER* 1.3 65.2 + - - +
1182A PRO* 5.5 1.1 - - - -
1208A TYR* 4.5 13.0 + - + -
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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