Contacts of the helix formed by residues 1264 - 1268 (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 LEU1264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102A ALA* 4.4 1.6 - - - -
1106A LEU* 3.8 29.2 - - + -
1262A LEU* 4.2 3.0 + - - +
1263A LYS* 1.3 68.6 - - - +
1265A ALA* 1.3 63.7 + - - +
1267A VAL* 3.1 11.4 - - - +
1269A GLY 3.1 53.8 + - - +
1270A MET* 3.9 12.3 - - + -
1273A ALA* 3.4 18.6 - - + -
1294A GLU* 6.0 1.6 - - - +
1298A GLY 5.5 0.2 - - - +
1301A HIS* 3.9 31.9 - - + +
1302A ASN* 4.2 10.9 + - + +
1305A LEU* 3.6 21.9 - - + +
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Residues in contact with ALA1265 (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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1047A GLU 5.7 1.1 - - - +
1049A GLU* 3.8 35.2 - - + +
1098A GLU 3.3 19.6 - - - +
1099A MET* 3.4 17.9 - - + +
1102A ALA* 3.6 13.5 - - + -
1106A LEU* 5.4 1.1 - - - +
1263A LYS* 3.1 1.2 + - - +
1264A LEU* 1.3 77.9 - - - +
1266A ARG* 1.3 63.2 + - - +
1267A VAL 3.0 1.6 + - - -
1268A GLY 3.1 10.0 + - - -
1292A MET* 4.1 10.5 - - + -
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Residues in contact with ARG1266 (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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1056A TYR* 3.6 17.3 - - - +
1057A THR* 4.4 5.8 - - + -
1098A GLU* 3.5 9.0 - - - +
1099A MET* 4.0 24.1 - - + +
1239A ASP* 2.9 34.2 + - - -
1240A GLU* 3.7 11.4 - - - +
1242A ILE* 2.7 45.1 + - - +
1243A ARG* 3.1 31.6 - - - +
1261A ASN 2.8 31.1 + - - -
1262A LEU* 4.1 7.1 - - - +
1263A LYS* 3.1 38.6 + - + +
1265A ALA* 1.3 77.9 - - - +
1267A VAL* 1.3 60.8 + - - +
1268A GLY 3.5 0.2 - - - -
1292A MET* 4.8 0.2 - - - -
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Residues in contact with VAL1267 (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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1098A GLU* 4.1 3.0 - - - +
1242A ILE 4.6 4.3 - - - +
1243A ARG* 3.2 23.2 - - - +
1262A LEU* 3.6 19.3 - - + -
1263A LYS 3.1 10.9 + - - +
1264A LEU* 3.1 18.8 - - - +
1265A ALA 3.0 1.4 - - - -
1266A ARG* 1.3 78.5 - - - +
1268A GLY* 1.3 56.2 + - - +
1269A GLY 3.6 16.8 - - - +
1272A SER* 2.6 34.1 + - - +
1273A ALA* 4.0 3.4 - - + -
1276A ILE* 3.0 37.2 - - + -
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Residues in contact with GLY1268 (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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1088A GLN* 5.7 4.9 + - - +
1098A GLU* 3.3 29.0 - - - +
1101A LYS* 4.1 13.0 - - - +
1102A ALA* 3.8 14.4 + - - -
1105A GLU* 4.3 9.2 - - - +
1265A ALA 3.1 7.4 + - - -
1266A ARG 3.5 1.2 - - - -
1267A VAL* 1.3 79.3 - - - +
1269A GLY* 1.3 57.4 + - - +
1272A SER* 4.5 4.4 - - - -
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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