Contacts of the helix formed by residues 1271 - 1278 (chain A) in PDB entry 2XBA
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 PHE1271 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1167A GLU* 6.2 7.7 - - + +
1170A ILE* 4.1 15.6 - - + +
1171A ILE* 3.8 31.0 - - + -
1174A PHE* 3.4 34.5 - + - -
1179A ILE* 3.7 15.7 - - + -
1240A LEU* 4.2 9.4 - - + -
1245A PHE* 3.9 10.8 - + - -
1247A HIS* 3.4 32.8 - + - -
1268A ILE* 3.5 31.9 - - + -
1269A GLY 4.2 2.7 - - - -
1270A ASP* 1.3 76.6 + - - +
1272A GLY* 1.3 58.4 + - - +
1273A MET 3.4 2.9 - - - -
1274A ALA* 3.5 8.3 + - + +
1275A ARG* 2.9 28.6 + - - +
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Residues in contact with GLY1272 (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 GLU* 6.5 0.4 - - - -
1247A HIS* 5.8 0.2 - - - -
1270A ASP* 3.0 16.9 + - - -
1271A PHE* 1.3 76.1 - - - +
1273A MET* 1.3 60.2 + - - +
1275A ARG* 3.2 21.8 + - - +
1276A ASP* 2.8 38.9 + - - +
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Residues in contact with MET1273 (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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1247A HIS* 4.3 2.9 - - + +
1248A ARG* 3.7 40.2 - - + +
1249A ASP* 3.8 27.2 + - + +
1270A ASP* 4.7 1.6 + - - -
1271A PHE 3.4 0.4 - - - -
1272A GLY* 1.3 72.0 - - - +
1274A ALA* 1.3 66.9 + - - +
1276A ASP* 3.1 13.7 + - - +
1277A ILE* 3.0 50.2 + - + +
1291A LEU* 3.8 31.4 - - + -
1292A PRO* 4.8 9.0 - - + -
1296A MET* 5.9 1.8 - - - -
1306A PHE* 5.0 7.9 - - + -
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Residues in contact with ALA1274 (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 ILE* 4.8 2.5 - - + -
1245A PHE* 3.5 35.0 - - + -
1246A ILE 3.9 7.2 - - - +
1247A HIS* 3.7 19.3 + - - +
1248A ARG* 4.8 3.4 - - - +
1271A PHE* 3.5 11.1 + - + +
1272A GLY 3.4 0.2 - - - -
1273A MET* 1.3 79.5 - - - +
1275A ARG* 1.3 57.2 + - - +
1277A ILE* 3.5 5.9 + - - +
1278A TYR* 2.9 31.1 + - - +
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Residues in contact with ARG1275 (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 ASP* 2.9 54.9 + - - +
1166A MET* 3.8 20.4 - - + +
1167A GLU* 3.3 31.5 + - - +
1170A ILE* 3.8 15.9 - - + +
1271A PHE 2.9 18.4 + - - +
1272A GLY* 3.3 17.9 + - - +
1273A MET 3.1 0.2 - - - -
1274A ALA* 1.3 77.4 - - - +
1276A ASP* 1.3 95.3 + - - +
1278A TYR* 3.4 18.1 + - - +
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Residues in contact with ASP1276 (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 ASP* 4.5 6.8 - - - +
1272A GLY 2.8 24.0 + - - +
1273A MET* 3.1 14.0 + - - +
1275A ARG* 1.3 106.0 + - - +
1277A ILE* 1.3 70.9 + - + +
1278A TYR 4.1 3.3 - - - -
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Residues in contact with ILE1277 (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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1248A ARG* 3.1 55.2 - - - +
1273A MET* 3.0 32.7 + - + +
1274A ALA* 3.9 3.6 - - - +
1276A ASP* 1.3 78.3 - - + +
1278A TYR* 1.3 66.7 + - - +
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Residues in contact with TYR1278 (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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1095A ASN 3.9 15.1 + - - -
1096A TYR* 3.5 35.9 - + - -
1097A CYS* 2.8 41.2 + - - +
1166A MET* 4.0 20.0 - - + -
1170A ILE* 5.0 2.0 - - + -
1245A PHE* 6.0 3.6 - + - -
1274A ALA 2.9 18.9 + - - +
1275A ARG* 3.5 17.9 - - - +
1276A ASP 3.3 3.8 - - - -
1277A ILE* 1.3 83.1 - - - +
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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