Contacts of the helix formed by residues 1168 - 1173 (chain A) in PDB entry 1MWH
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 ASN1168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1105A TYR* 4.9 8.5 + - - -
1108A GLN* 4.1 11.7 + - - +
1109A THR* 3.5 21.6 - - - +
1166A ASP 3.6 4.1 + - - +
1167A VAL* 1.3 75.1 - - - +
1169A THR* 1.3 65.1 + - - +
1170A VAL* 4.2 4.1 - - - +
1171A GLN* 2.9 31.4 + - - +
1172A LEU* 3.1 17.0 + - - +
1194A LYS* 5.9 5.8 - - - +
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Residues in contact with THR1169 (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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1167A VAL 3.9 0.4 + - - -
1168A ASN* 1.3 72.1 - - - +
1170A VAL* 1.3 58.2 + - - +
1172A LEU 3.6 0.2 + - - -
1173A ALA* 3.0 29.1 + - - +
1193A PHE* 4.0 32.0 - - + +
1194A LYS* 5.7 4.7 - - - +
1220A ALA* 3.8 31.7 - - - +
1223A ARG* 3.1 37.2 + - + +
1224A PHE* 4.1 9.2 - - + -
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Residues in contact with VAL1170 (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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1105A TYR* 3.8 21.3 - - + +
1106A PHE* 3.9 20.9 - - + -
1109A THR* 3.6 26.7 - - + -
1168A ASN* 3.4 2.7 + - - +
1169A THR* 1.3 79.3 - - - +
1171A GLN* 1.3 64.7 + - - +
1173A ALA* 3.4 12.6 + - - +
1174A ARG* 3.8 15.8 + - - +
1178A LEU 4.7 2.5 - - - +
1179A ALA* 6.5 0.2 - - - -
1180A VAL* 3.7 26.0 - - + +
1189A PHE* 4.3 2.0 - - + -
1193A PHE* 4.0 18.6 - - + -
1224A PHE* 4.2 8.7 - - + -
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Residues in contact with GLN1171 (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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1108A GLN 4.1 5.4 - - - +
1109A THR* 2.9 32.2 + - - +
1110A LEU* 3.4 8.0 + - - +
1111A PHE* 3.5 22.5 - - - +
1125A ASP* 3.0 33.6 + - - +
1129A LEU* 3.6 8.8 - - + +
1165A GLN* 4.7 8.0 - - - +
1167A VAL* 3.4 19.9 - - + +
1168A ASN* 2.9 20.6 + - - +
1170A VAL* 1.3 79.1 - - - +
1172A LEU* 1.3 61.0 + - - +
1174A ARG* 3.4 28.4 + - - +
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Residues in contact with LEU1172 (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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1129A LEU* 3.7 28.0 - - + -
1132A ARG* 4.3 11.4 - - - +
1133A THR* 4.7 4.3 - - - +
1167A VAL* 3.4 29.7 - - + +
1168A ASN 3.1 12.6 + - - +
1171A GLN* 1.3 72.6 - - - +
1173A ALA* 1.3 59.4 + - - +
1174A ARG 2.9 11.2 + - - -
1175A VAL* 3.0 41.1 + - + +
1216A GLY 5.3 0.7 - - - +
1217A TRP* 3.6 39.3 - - + +
1220A ALA* 4.0 15.9 - - + -
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Residues in contact with ALA1173 (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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1169A THR 3.0 20.6 + - - +
1170A VAL 3.6 5.4 - - - +
1171A GLN 3.3 0.4 - - - -
1172A LEU* 1.3 76.9 - - - +
1174A ARG* 1.3 60.4 + - - +
1175A VAL* 3.1 4.0 + - - -
1176A VAL* 3.3 13.0 + - - +
1178A LEU* 3.2 28.4 + - + +
1220A ALA* 4.2 10.5 - - - +
1221A ILE* 4.9 4.5 - - - -
1224A PHE* 3.4 32.5 - - + -
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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