Contacts of the helix formed by residues 1256 - 1271 (chain A) in PDB entry 5O9Z
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 PHE1256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1254A THR 3.9 0.4 + - - -
1255A THR* 1.3 74.1 - - - +
1257A THR* 1.3 57.7 + - - +
1259A ILE* 3.3 7.1 + - - +
1260A VAL* 2.9 32.6 + - - +
1299A ILE* 5.8 8.5 - - + -
1325A LEU* 5.8 7.4 - - + -
1531A ASN* 5.7 4.5 - - + +
1534A PHE* 5.8 8.5 - - + -
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Residues in contact with THR1257 (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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1255A THR* 3.1 7.6 - - - -
1256A PHE* 1.3 77.6 - - - +
1258A LYS* 1.3 58.0 + - - +
1260A VAL* 3.9 4.7 - - - +
1261A ASN* 2.9 30.5 + - - +
1325A LEU* 6.4 0.4 - - - -
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Residues in contact with LYS1258 (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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1254A THR* 4.1 17.3 - - - -
1255A THR* 3.1 14.4 + - - +
1257A THR* 1.3 78.3 - - - +
1259A ILE* 1.3 59.5 + - - +
1261A ASN* 3.3 5.7 + - - +
1262A LYS* 2.9 29.5 + - - +
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Residues in contact with ILE1259 (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 ILE 5.9 1.3 - - - +
1251A SER* 5.5 12.1 - - - -
1254A THR* 5.3 2.4 - - - -
1255A THR 3.5 6.9 + - - +
1256A PHE* 3.3 10.6 + - - +
1258A LYS* 1.3 76.5 - - - +
1260A VAL* 1.3 59.3 + - - +
1262A LYS* 3.2 5.7 + - - +
1263A TRP* 2.9 30.7 + - - +
1295A ILE* 6.4 2.5 - - + -
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Residues in contact with VAL1260 (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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1256A PHE 2.9 17.5 + - - +
1257A THR* 4.2 4.5 - - - +
1259A ILE* 1.3 77.1 - - - +
1261A ASN* 1.3 56.8 + - - +
1263A TRP* 4.6 4.9 - - - +
1264A ASN* 2.9 33.3 + - - +
1325A LEU* 4.0 35.2 - - + +
1326A GLY 5.6 0.2 - - - -
1327A MET* 5.1 12.7 - - + -
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Residues in contact with ASN1261 (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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1257A THR 2.9 21.7 + - - +
1258A LYS* 3.6 7.4 - - - +
1259A ILE 3.2 0.2 - - - -
1260A VAL* 1.3 76.4 - - - +
1262A LYS* 1.3 60.1 + - - +
1264A ASN* 3.9 3.2 - - - +
1265A THR* 2.9 31.9 + - - -
390H GLU* 3.6 30.8 - - + +
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Residues in contact with LYS1262 (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 ILE* 4.8 18.6 - - + -
1258A LYS 2.9 17.8 + - - +
1259A ILE* 3.8 5.2 - - - +
1261A ASN* 1.3 74.6 - - - +
1263A TRP* 1.3 60.3 + - - +
1265A THR* 3.4 4.4 + - - -
1266A ALA* 2.9 30.1 + - - +
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Residues in contact with TRP1263 (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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1259A ILE 2.9 16.8 + - - +
1260A VAL* 4.2 5.2 - - - +
1262A LYS* 1.3 77.4 - - - +
1264A ASN* 1.3 57.5 + - - +
1266A ALA* 3.3 5.3 + - - +
1267A LEU* 2.9 31.6 + - - +
1295A ILE* 4.8 18.4 - - + -
1327A MET* 5.9 5.8 - - + -
1328A LEU 5.5 1.3 - - - -
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Residues in contact with ASN1264 (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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1260A VAL 2.9 21.6 + - - +
1261A ASN* 4.2 3.1 - - - +
1263A TRP* 1.3 76.2 - - - +
1265A THR* 1.3 58.2 + - - +
1267A LEU* 4.2 4.2 - - - +
1268A ILE* 2.9 32.6 + - - +
1326A GLY 4.7 8.5 - - - +
1327A MET* 5.1 1.1 - - - +
1328A LEU* 4.6 25.3 - - + +
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Residues in contact with THR1265 (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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1261A ASN 2.9 20.8 + - - -
1262A LYS* 3.8 5.6 - - - -
1264A ASN* 1.3 74.1 - - - +
1266A ALA* 1.3 59.4 + - - +
1268A ILE* 3.9 4.0 - - - +
1269A GLY* 2.9 25.6 + - - -
1452A PRO* 4.0 15.4 - - - +
389H GLN* 4.9 19.5 - - - -
390H GLU* 5.5 4.0 - - - -
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Residues in contact with ALA1266 (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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1243A ARG* 6.1 5.4 - - + -
1262A LYS 2.9 19.2 + - - +
1263A TRP* 3.8 4.9 - - - +
1265A THR* 1.3 77.5 - - - +
1267A LEU* 1.3 58.0 + - - +
1269A GLY* 3.3 1.0 + - - -
1270A LEU* 2.9 31.5 + - - +
1452A PRO* 4.6 10.2 - - + +
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Residues in contact with LEU1267 (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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1263A TRP 2.9 17.2 + - - +
1264A ASN* 4.2 2.5 - - - +
1266A ALA* 1.3 76.2 - - - +
1268A ILE* 1.3 58.2 + - - +
1270A LEU* 3.7 4.6 - - - +
1271A MET* 2.9 33.0 + - - +
1328A LEU* 3.8 23.3 - - + +
1329A SER* 5.7 0.7 - - - -
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Residues in contact with ILE1268 (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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1264A ASN 2.9 20.6 + - - +
1265A THR* 4.0 4.5 - - - +
1267A LEU* 1.3 77.8 - - - +
1269A GLY* 1.3 62.2 + - - +
1271A MET* 3.6 10.1 + - - +
1272A THR* 3.7 14.7 + - - -
1328A LEU* 6.1 0.4 - - - +
1465A TRP* 5.3 8.6 - - + +
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Residues in contact with GLY1269 (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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1265A THR 2.9 18.3 + - - -
1266A ALA 3.8 0.7 - - - -
1267A LEU 3.2 0.2 - - - -
1268A ILE* 1.3 78.6 - - - +
1270A LEU* 1.3 59.8 + - - +
1271A MET 3.5 0.5 + - - -
1272A THR* 3.6 12.2 + - - -
1273A TYR* 4.3 5.7 + - - +
1452A PRO* 4.1 22.4 - - - -
1455A TRP* 4.4 13.7 - - - +
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Residues in contact with LEU1270 (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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1240A PHE* 6.1 4.7 - - + -
1266A ALA 2.9 18.2 + - - +
1267A LEU* 4.1 4.5 - - - +
1269A GLY* 1.3 75.9 - - - +
1271A MET* 1.3 58.5 + - - +
1272A THR 3.4 0.4 - - - -
1273A TYR* 4.3 2.5 - - - +
1274A PHE* 3.5 27.8 + - + +
1275A ARG* 4.1 1.9 + - - -
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Residues in contact with MET1271 (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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1267A LEU 2.9 19.9 + - - +
1268A ILE* 4.1 6.5 - - - +
1269A GLY 3.3 0.6 - - - -
1270A LEU* 1.3 77.6 - - - +
1272A THR* 1.3 57.6 + - - +
1273A TYR 3.4 1.1 - - - -
1275A ARG* 3.2 28.4 - - + +
1368A LEU* 5.0 17.0 - - + -
1372A ILE* 4.8 9.4 - - - +
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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