Contacts of the helix formed by residues 1256 - 1272 (chain A) in PDB entry 5LUQ
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 TRP1256 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119A LYS* 3.0 40.3 - - + +
1163A LEU* 2.8 81.0 - - + +
1164A CYS* 4.9 4.9 - - + -
1166A LEU* 3.7 16.8 - - + -
1251A GLN 4.3 6.7 - - - -
1252A ALA 2.9 8.3 + - - +
1253A THR 3.5 0.8 + - - -
1255A CYS* 1.3 106.9 + - + +
1257A LEU* 1.3 59.1 + - - +
1258A ASP 3.0 2.2 - - - +
1259A LEU* 2.6 20.7 + - + +
1260A LEU* 2.2 47.1 + - + +
1336A THR* 6.3 4.3 - - + -
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Residues in contact with LEU1257 (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 LEU* 5.2 4.7 - - + -
1252A ALA* 2.9 21.9 + - + +
1253A THR* 3.5 37.0 - - + +
1256A TRP* 1.3 73.5 - - - +
1258A ASP* 1.3 63.0 + - - +
1260A LEU* 4.5 16.2 - - + +
1261A LEU* 3.3 29.5 + - - +
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Residues in contact with ASP1258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1236A LEU* 5.5 2.8 - - - -
1237A ALA* 4.9 9.5 - - - +
1253A THR* 3.1 10.9 + - - +
1254A LEU* 3.2 33.2 - - - +
1256A TRP 3.0 0.2 - - - -
1257A LEU* 1.3 77.6 - - - +
1259A LEU* 1.3 61.1 + - + +
1261A LEU* 3.5 10.1 + - - +
1262A ALA* 3.0 24.0 + - - +
1298A LEU* 4.4 25.4 - - - +
1337A VAL* 4.8 17.0 - - + +
1341A ILE* 6.1 2.0 - - + -
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Residues in contact with LEU1259 (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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1166A LEU* 5.3 1.6 - - + -
1255A CYS 3.7 17.5 - - - +
1256A TRP* 2.6 20.7 + - + +
1258A ASP* 1.3 75.0 - - - +
1260A LEU* 1.3 56.7 + - - +
1261A LEU 3.1 1.3 - - - -
1262A ALA* 3.4 14.7 - - + +
1263A ALA* 2.7 36.6 + - - +
1336A THR* 3.3 30.1 - - + +
1337A VAL* 3.5 40.2 - - + +
1340A ARG* 3.5 32.3 - - + +
1341A ILE* 4.6 3.6 - - + -
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Residues in contact with LEU1260 (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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1161A ALA* 3.0 30.1 - - + +
1163A LEU* 3.5 43.7 - - + +
1166A LEU* 3.5 35.0 - - + -
1256A TRP* 2.2 41.5 + - + +
1257A LEU* 4.2 14.1 - - + +
1259A LEU* 1.3 66.1 - - - +
1261A LEU* 1.3 62.1 + - + +
1263A ALA* 3.7 3.6 - - - +
1264A LEU* 3.0 34.2 + - + +
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Residues in contact with LEU1261 (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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1232A PRO* 5.1 3.1 - - + -
1233A SER* 3.1 52.0 - - - +
1234A GLY* 5.1 5.6 - - - -
1236A LEU 5.8 3.8 - - - +
1257A LEU 3.3 17.8 + - - +
1258A ASP* 3.5 12.5 + - - +
1259A LEU 3.1 0.4 - - - -
1260A LEU* 1.3 77.3 - - + +
1262A ALA* 1.3 67.5 + - - +
1263A ALA 3.2 0.2 + - - -
1264A LEU* 3.4 8.7 + - + +
1265A GLU* 3.0 35.7 + - - +
1291A LEU* 5.5 13.5 - - + -
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Residues in contact with ALA1262 (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 ASP 3.0 16.0 + - - +
1259A LEU* 3.2 24.2 + - + +
1261A LEU* 1.3 75.6 - - - +
1263A ALA* 1.3 56.0 + - - +
1265A GLU* 3.2 18.7 + - - +
1266A CYS* 2.9 34.5 + - - -
1340A ARG* 5.7 2.5 - - + +
1341A ILE* 5.3 8.7 - - + -
1344A PHE* 3.9 12.9 - - + -
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Residues in contact with ALA1263 (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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1166A LEU* 3.8 30.7 - - + -
1170A LYS* 4.3 8.5 - - - +
1259A LEU 2.7 20.6 + - - +
1260A LEU 3.7 3.6 - - - +
1261A LEU 3.2 0.2 - - - -
1262A ALA* 1.3 70.1 - - - +
1264A LEU* 1.3 69.8 + - - +
1266A CYS* 2.9 19.8 + - - -
1267A TYR* 3.0 25.5 + - + -
1340A ARG* 4.8 7.6 - - - +
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Residues in contact with LEU1264 (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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1158A PRO* 3.0 54.3 - - + +
1159A PRO* 5.0 1.3 - - + -
1161A ALA* 4.1 15.5 - - + -
1166A LEU* 4.3 10.1 - - + -
1169A VAL* 4.7 7.0 - - + -
1170A LYS* 5.1 7.6 - - + +
1173A LEU* 5.9 0.9 - - + -
1231A GLN 5.7 4.3 - - - +
1233A SER* 5.1 8.3 - - - +
1260A LEU* 3.0 24.2 + - + +
1261A LEU* 4.0 7.6 - - + +
1263A ALA* 1.3 75.1 - - - +
1265A GLU* 1.3 63.8 + - - +
1267A TYR* 4.7 2.2 - - - +
1268A ASN* 2.8 41.5 + - - +
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Residues in contact with GLU1265 (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 LEU* 3.0 23.2 + - + +
1262A ALA* 3.2 17.3 + - - +
1264A LEU* 1.3 78.2 - - + +
1266A CYS* 1.3 62.2 + - - +
1268A ASN* 3.3 5.1 + - - +
1269A THR* 3.0 28.0 + - + +
1275A THR* 4.9 0.3 - - - +
1291A LEU* 4.5 17.8 - - - +
1292A LYS* 4.8 13.6 - - - +
1344A PHE* 3.3 30.5 - - + -
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Residues in contact with CYS1266 (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 ALA* 2.9 30.8 + - - -
1263A ALA* 2.9 11.0 + - - +
1265A GLU* 1.3 73.7 - - - +
1267A TYR* 1.3 73.1 + - + +
1269A THR* 2.2 27.4 + - - -
1270A PHE* 3.3 12.6 - - + -
1340A ARG* 4.9 14.6 - - - -
1343A GLU* 5.8 1.8 - - - -
1344A PHE* 3.2 43.5 - - + -
1347A THR* 4.4 9.4 - - + -
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Residues in contact with TYR1267 (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 ASP* 4.6 6.8 + - - -
1170A LYS* 3.4 53.7 + - + -
1263A ALA* 3.0 19.3 + - + +
1264A LEU* 4.7 2.0 - - - +
1266A CYS* 1.3 84.5 - - + +
1268A ASN* 1.3 60.7 + - - +
1269A THR 3.4 0.3 + - - -
1270A PHE* 3.8 14.3 + + - +
1271A ILE* 2.9 30.0 + - + +
1340A ARG* 3.6 28.9 + - - -
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Residues in contact with ASN1268 (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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1158A PRO* 5.6 6.6 - - - +
1173A LEU* 5.0 10.9 - - - +
1220A LEU* 5.2 8.0 - - + +
1231A GLN* 5.0 17.8 + - - +
1264A LEU* 2.8 39.2 + - - +
1265A GLU* 3.7 6.0 - - - +
1267A TYR* 1.3 77.8 - - - +
1269A THR* 1.3 64.8 + - - +
1271A ILE* 3.6 29.6 - - + +
1272A GLY 3.7 7.3 + - - +
1274A ARG* 5.8 0.5 - - - +
1275A THR* 4.3 10.1 - - + +
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Residues in contact with THR1269 (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 GLU* 3.0 22.4 + - + +
1266A CYS* 2.2 27.5 + - - -
1268A ASN* 1.3 73.6 - - - +
1270A PHE* 1.3 70.3 + - - +
1271A ILE 2.9 11.8 + - - +
1272A GLY 3.1 18.2 - - - +
1273A GLU* 5.1 0.5 - - - -
1275A THR* 3.5 34.9 + - + +
1344A PHE* 4.3 5.6 - - + -
1347A THR* 4.7 2.6 + - - +
1348A LEU* 4.0 22.2 - - + -
1351A THR* 5.5 0.7 - - - -
1352A SER* 4.1 12.3 - - - +
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Residues in contact with PHE1270 (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 CYS* 3.3 27.8 + - + -
1267A TYR* 3.8 14.3 + + - +
1268A ASN 3.6 0.2 - - - -
1269A THR* 1.3 82.2 + - - +
1271A ILE* 1.3 65.0 + - - +
1347A THR* 3.3 42.2 - - + -
1351A THR* 3.3 38.1 - - + -
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Residues in contact with ILE1271 (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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1173A LEU* 6.0 6.1 - - + -
1174A ALA* 6.4 2.0 - - + -
1215A GLU* 3.1 30.7 - - + +
1216A GLY* 3.2 14.8 - - - -
1217A VAL* 5.5 1.5 - - - +
1220A LEU* 5.1 4.7 - - + -
1267A TYR* 2.9 22.4 - - + +
1268A ASN* 3.6 27.6 - - - +
1269A THR 2.9 1.6 + - - +
1270A PHE* 1.3 84.0 - - + +
1272A GLY* 1.3 64.4 + - - +
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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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1216A GLY* 4.6 0.4 - - - -
1217A VAL* 4.4 24.2 - - - -
1220A LEU* 4.6 7.4 - - - +
1268A ASN 3.7 7.0 + - - +
1269A THR 3.1 15.0 - - - +
1271A ILE* 1.3 88.0 - - - +
1273A GLU* 1.3 54.3 + - - -
1274A ARG* 2.8 20.6 + - - +
1275A THR* 4.2 2.8 + - - -
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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