Contacts of the helix formed by residues 1255 - 1275 (chain A) in PDB entry 6AH0
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 THR1255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253A SER 3.7 2.0 + - - -
1254A THR* 1.3 76.9 - - - +
1256A PHE* 1.3 66.3 + - - +
1257A THR 3.2 2.9 - - - -
1258A LYS* 3.1 14.9 + - - +
1259A ILE* 3.3 8.8 + - - -
1527A ASN* 4.9 15.3 - - - +
1528A GLN* 6.3 0.2 - - - +
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Residues in contact with PHE1256 (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* 1.3 71.8 - - - +
1257A THR* 1.3 58.6 + - - +
1259A ILE* 3.1 3.0 + - - +
1260A VAL* 2.8 27.0 + - - -
1531A ASN* 6.3 0.4 - - - +
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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 3.2 0.6 - - - -
1256A PHE* 1.3 75.9 - - - +
1258A LYS* 1.3 56.1 + - - +
1260A VAL* 4.5 1.3 - - - +
1261A ASN* 2.8 30.0 + - - -
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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* 6.3 0.4 - - - +
1255A THR* 3.1 10.2 + - - +
1257A THR* 1.3 75.6 - - - +
1259A ILE* 1.3 60.5 + - - +
1261A ASN* 4.2 0.8 - - - +
1262A LYS* 3.2 18.9 + - - -
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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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1255A THR 3.3 8.1 + - - -
1256A PHE* 3.1 6.7 + - - +
1258A LYS* 1.3 74.5 - - - +
1260A VAL* 1.3 65.2 + - - +
1262A LYS* 3.3 2.5 + - - +
1263A TRP* 3.0 18.5 + - - -
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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 2.8 15.2 + - - -
1257A THR* 3.9 1.3 - - - +
1259A ILE* 1.3 77.9 - - - +
1261A ASN* 1.3 50.4 + - - +
1263A TRP* 3.1 3.7 + - - +
1264A ASN* 2.7 31.5 + - - -
1325A LEU 6.1 1.3 - - - -
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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 2.8 20.2 + - - -
1258A LYS 4.2 0.4 - - - -
1260A VAL* 1.3 72.0 - - - +
1262A LYS* 1.3 61.8 + - - +
1264A ASN* 3.1 2.9 + - - +
1265A THR* 3.0 20.1 + - - -
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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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1258A LYS 3.2 15.9 + - - -
1259A ILE* 3.8 2.9 - - - +
1261A ASN* 1.3 77.0 - - - +
1263A TRP* 1.3 56.0 + - - +
1265A THR* 3.3 2.1 + - - +
1266A ALA* 2.9 25.6 + - - -
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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 3.0 14.3 + - - -
1260A VAL* 3.1 4.5 + - - +
1262A LYS* 1.3 76.6 - - - +
1264A ASN* 1.3 55.7 + - - +
1266A ALA* 3.2 1.8 + - - +
1267A LEU* 2.9 27.7 + - - -
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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 2.7 17.6 + - - -
1261A ASN* 3.1 5.1 + - - +
1263A TRP* 1.3 73.3 - - - +
1265A THR* 1.3 61.5 + - - +
1267A LEU* 3.4 0.7 + - - +
1268A ILE* 3.1 21.3 + - - -
1328A LEU 6.4 0.4 - - - +
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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 3.0 13.6 + - - -
1262A LYS* 3.8 3.1 - - - +
1264A ASN* 1.3 76.5 - - - +
1266A ALA* 1.3 64.0 + - - +
1268A ILE* 5.4 0.2 - - - +
1269A GLY* 3.0 21.7 + - - -
1452A PRO* 5.4 1.0 - - - +
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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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1262A LYS 2.9 15.3 + - - -
1263A TRP* 3.2 3.8 + - - +
1265A THR* 1.3 77.9 - - - +
1267A LEU* 1.3 60.8 + - - +
1269A GLY* 3.8 1.3 - - - -
1270A LEU* 3.2 17.3 + - - -
1452A PRO* 5.0 7.1 - - - +
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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 16.3 + - - -
1264A ASN* 3.9 0.9 - - - +
1266A ALA* 1.3 74.7 - - - +
1268A ILE* 1.3 53.7 + - - +
1270A LEU* 3.3 1.6 + - - +
1271A MET* 2.5 36.4 + - - -
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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 3.1 14.9 + - - -
1265A THR* 4.2 0.4 - - - +
1267A LEU* 1.3 72.6 - - - +
1269A GLY* 1.3 60.7 + - - +
1271A MET* 4.5 1.1 - - - +
1272A THR* 2.6 34.4 + - - +
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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 3.0 19.2 + - - -
1266A ALA 3.8 1.6 - - - -
1268A ILE* 1.3 76.5 - - - +
1270A LEU* 1.3 55.7 + - - +
1272A THR 4.0 0.3 - - - -
1273A TYR* 3.1 21.3 + - - -
1452A PRO* 2.4 36.2 - - - +
1453A PHE* 3.9 7.2 - - - -
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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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1266A ALA 3.2 12.9 + - - -
1267A LEU* 3.7 1.6 - - - +
1269A GLY* 1.3 74.3 - - - +
1271A MET* 1.3 57.9 + - - +
1273A TYR* 4.9 0.2 - - - +
1274A PHE* 2.8 28.6 + - - -
1275A ARG 4.1 0.2 + - - -
1452A PRO* 3.5 4.4 + - - +
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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 2.5 21.9 + - - -
1268A ILE* 4.4 1.6 - - - +
1270A LEU* 1.3 71.2 - - - +
1272A THR* 1.3 55.7 + - - +
1275A ARG* 3.1 28.3 + - - +
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Residues in contact with THR1272 (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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1268A ILE* 2.6 25.6 + - - +
1269A GLY 4.0 0.7 - - - -
1271A MET* 1.3 71.4 - - - +
1273A TYR* 1.3 60.0 + - - +
1275A ARG* 4.6 1.7 - - - -
1464A LEU 5.7 1.8 - - - +
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Residues in contact with TYR1273 (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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949A PRO* 6.0 1.9 - - - +
1269A GLY 3.1 19.8 + - - -
1270A LEU* 3.2 0.9 + - - +
1272A THR* 1.3 80.8 - - - +
1274A PHE* 1.3 61.9 + - - +
1452A PRO 5.1 0.9 - - - -
1453A PHE* 5.7 3.6 - - - +
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Residues in contact with PHE1274 (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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1270A LEU 2.8 11.9 + - - -
1273A TYR* 1.3 79.0 - - - +
1275A ARG* 1.3 51.8 - - - +
1276A GLU 2.7 18.0 + - - -
1277A ALA* 3.4 10.8 + - - +
1278A VAL 4.9 3.1 - - - +
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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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1270A LEU 4.1 0.6 + - - -
1271A MET* 3.1 23.8 + - - +
1272A THR* 5.2 1.8 - - - +
1273A TYR 3.7 0.6 - - - -
1274A PHE* 1.3 71.7 - - - +
1276A GLU* 1.3 62.9 + - - +
1277A ALA 3.3 0.4 + - - -
1278A VAL* 3.6 11.2 + - - +
1279A VAL 4.5 1.6 + - - -
1373A GLN 6.1 0.2 - - - -
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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