Contacts of the helix formed by residues 1252 - 1268 (chain B) in PDB entry 6V65
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 LEU1252 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 4.7 1.8 - - + -
22A MET* 4.0 18.2 - - + -
33A PRO* 5.2 6.5 - - + -
102A THR* 3.3 31.4 - - + +
1213B THR* 4.1 35.2 - - + +
1215B MET* 4.9 7.6 - - - -
1247B PHE* 2.8 27.4 + - + +
1250B ARG* 3.4 21.5 - - + +
1251B HIS* 1.3 87.6 - - - +
1253B LEU* 1.3 65.0 + - - +
1254B TYR 3.3 3.4 - - - +
1255B GLN* 3.1 23.3 + - + +
1256B LEU 3.2 9.0 + - - -
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Residues in contact with LEU1253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244B VAL* 4.8 12.1 - - + +
1247B PHE* 3.5 11.7 + - + -
1248B ASP* 3.5 29.8 - - + +
1251B HIS* 3.6 3.0 - - - -
1252B LEU* 1.3 78.9 - - - +
1254B TYR* 1.3 65.7 + - - +
1256B LEU* 3.2 6.7 + - + +
1257B LEU* 3.0 48.1 + - + +
1288B CYS* 4.9 3.4 - - - -
1292B TYR* 3.2 36.3 - - + +
1360B GLN* 5.6 4.0 - - + +
1363B SER* 5.5 7.0 - - - +
1364B VAL* 4.6 9.0 - - + -
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Residues in contact with TYR1254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PRO* 5.1 2.7 - - + -
88A THR* 3.6 30.1 - - + +
103A PHE 4.8 5.4 - - - +
104A GLN* 4.6 16.8 - - - +
105A SER* 5.2 0.7 - - - -
106A PRO* 3.4 31.5 - - + +
1252B LEU* 3.3 1.0 - - - -
1253B LEU* 1.3 81.2 - - - +
1255B GLN* 1.3 62.2 + - + +
1257B LEU* 3.4 5.6 + - + +
1258B TRP* 2.8 56.3 + + + +
1363B SER* 3.7 23.8 - - - +
1366B HIS* 4.0 10.1 + - - -
1367B CYS* 3.6 43.0 - - + -
1370B GLN* 4.9 4.0 - - - +
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Residues in contact with GLN1255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A THR* 4.2 5.5 + - - -
87A PRO 4.1 3.4 + - - -
88A THR* 2.2 44.9 + - - +
89A PHE* 3.9 11.1 - - - +
102A THR* 4.7 4.0 - - - -
103A PHE 4.1 4.3 - - - +
1215B MET* 3.3 41.9 - - + +
1219B GLY* 5.5 0.8 - - - -
1221B LEU* 4.1 6.7 - - + -
1247B PHE* 5.2 1.6 - - + -
1252B LEU* 3.1 26.4 + - + +
1254B TYR* 1.3 78.9 - - + +
1256B LEU* 1.3 61.1 + - - +
1258B TRP* 3.9 9.3 - - - +
1259B ASN* 3.1 30.3 + - - +
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Residues in contact with LEU1256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221B LEU* 3.8 18.3 - - + +
1224B ALA* 4.9 3.4 - - + -
1243B LEU* 3.5 53.6 - - + +
1244B VAL* 3.9 16.6 - - + +
1247B PHE* 3.7 27.8 - - + -
1252B LEU 3.2 3.4 + - - -
1253B LEU* 3.2 9.2 + - + +
1255B GLN* 1.3 80.1 - - - +
1257B LEU* 1.3 67.6 + - + +
1259B ASN* 3.3 1.4 + - - +
1260B MET* 3.0 42.1 + - + +
1284B ILE* 5.0 5.8 - - + -
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Residues in contact with LEU1257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244B VAL* 5.4 0.9 - - + -
1253B LEU* 3.0 40.6 + - + +
1254B TYR* 3.9 3.8 - - + +
1256B LEU* 1.3 81.6 - - + +
1258B TRP* 1.3 58.4 + - - +
1260B MET* 4.7 1.1 - - + +
1261B PHE* 2.9 55.5 + - + +
1284B ILE* 3.7 30.1 - - + -
1288B CYS* 4.4 9.4 - - - -
1363B SER* 5.2 0.9 - - - +
1364B VAL* 3.7 37.7 - - + -
1367B CYS* 3.7 17.9 - - + -
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Residues in contact with TRP1258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A THR* 4.0 25.7 - - + +
87A PRO* 3.6 39.5 - - + -
1219B GLY 5.7 0.4 - - - -
1254B TYR* 2.8 48.8 + + + +
1255B GLN* 3.9 11.4 - - - +
1257B LEU* 1.3 72.9 - - - +
1259B ASN* 1.3 72.9 + - - +
1261B PHE* 4.6 1.5 - - - +
1262B SER* 2.5 45.0 + - - -
1367B CYS* 3.9 10.5 - - - -
1370B GLN* 4.6 20.9 - - + -
1371B VAL* 4.8 17.3 - - + -
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Residues in contact with ASN1259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B MET* 5.3 1.4 - - - +
1218B GLN 5.2 0.2 + - - -
1219B GLY 2.9 28.6 + - - +
1220B GLU* 4.1 10.4 + - - +
1221B LEU* 3.3 32.5 - - + +
1225B MET* 4.8 8.7 - - - +
1255B GLN* 3.1 17.3 + - - +
1256B LEU 3.9 2.5 - - - +
1258B TRP* 1.3 86.5 - - - +
1260B MET* 1.3 71.3 + - + +
1262B SER* 3.4 6.3 + - - -
1263B LYS* 3.3 20.4 + - - +
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Residues in contact with MET1260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1221B LEU* 6.4 0.2 - - - -
1224B ALA* 5.5 3.6 - - - +
1225B MET* 3.5 31.2 - - - +
1228B ALA* 4.3 21.1 - - + -
1243B LEU* 6.1 2.9 - - - -
1256B LEU* 3.0 32.4 + - + +
1257B LEU* 4.5 1.8 - - - +
1259B ASN* 1.3 73.8 - - - +
1261B PHE* 1.3 71.3 + - + +
1263B LYS* 3.3 16.1 + - + +
1264B GLU* 3.4 9.2 + - - +
1280B LEU* 4.6 13.0 - - + -
1281B ALA* 3.9 24.6 - - + +
1284B ILE* 3.8 26.2 - - + -
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Residues in contact with PHE1261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1257B LEU* 2.9 58.8 + - + +
1258B TRP* 4.6 1.1 - - - +
1260B MET* 1.3 79.5 - - + +
1262B SER* 1.3 62.7 + - - +
1264B GLU* 3.2 11.6 + - - +
1265B VAL* 3.3 18.5 + - - +
1275B PHE* 3.5 27.5 - + + -
1281B ALA* 4.1 21.1 - - + -
1284B ILE* 4.9 2.9 - - + -
1285B MET* 4.3 22.0 - - + -
1364B VAL* 4.2 11.0 - - + -
1367B CYS* 4.0 12.3 - - - -
1368B LEU* 4.0 29.2 - - + -
1371B VAL* 3.8 17.9 - - + -
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Residues in contact with SER1262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258B TRP* 2.5 39.2 + - - -
1259B ASN* 3.7 7.2 - - - -
1260B MET 3.2 1.0 - - - -
1261B PHE* 1.3 79.4 - - - +
1263B LYS* 1.3 56.4 + - - +
1265B VAL* 3.6 1.6 + - - +
1266B GLU* 3.0 32.5 + - - +
1371B VAL* 3.5 20.3 - - - +
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Residues in contact with LYS1263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1225B MET* 4.8 13.5 - - - -
1259B ASN 3.3 9.1 + - - +
1260B MET* 3.3 16.2 + - + +
1261B PHE 3.3 0.6 - - - -
1262B SER* 1.3 79.1 - - - +
1264B GLU* 1.3 62.8 + - - +
1266B GLU* 3.5 14.5 + - - +
1267B LEU* 3.2 35.4 + - + +
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Residues in contact with GLU1264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1260B MET 3.4 2.1 + - - +
1261B PHE 3.2 9.7 + - - +
1263B LYS* 1.3 75.7 - - - +
1265B VAL* 1.3 61.6 + - - +
1266B GLU 3.3 0.2 + - - -
1267B LEU* 3.3 27.3 + - - +
1268B ALA* 2.8 31.5 + - - +
1273B THR 5.6 0.2 - - - +
1274B LEU* 6.4 0.4 - - - -
1275B PHE* 3.6 38.3 + - + +
1279B SER* 4.1 23.1 + - - -
1281B ALA* 3.5 29.2 - - + -
1282B SER* 4.3 9.8 + - - -
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Residues in contact with VAL1265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1261B PHE 3.3 15.0 + - - +
1262B SER 4.3 2.5 - - - +
1264B GLU* 1.3 74.6 - - - +
1266B GLU* 1.3 54.3 + - - +
1268B ALA* 3.3 15.5 + - - +
1274B LEU* 5.8 7.0 - - + -
1275B PHE* 4.4 15.3 - - + -
1368B LEU* 6.0 0.4 - - + -
1371B VAL* 4.3 14.4 - - + +
1372B VAL* 4.1 28.0 - - + +
1375B ARG* 2.7 45.9 + - + -
1376B PHE* 3.7 29.3 - - + -
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Residues in contact with GLU1266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1262B SER* 3.0 19.1 + - - +
1263B LYS* 3.6 16.7 - - - +
1264B GLU 3.1 0.2 - - - -
1265B VAL* 1.3 77.9 - - - +
1267B LEU* 1.3 61.9 + - + +
1375B ARG* 2.7 26.0 + - - +
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Residues in contact with LEU1267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1263B LYS* 3.2 23.6 - - + +
1264B GLU* 3.6 24.9 - - - +
1266B GLU* 1.3 80.2 - - + +
1268B ALA* 1.3 70.7 + - + +
1269B ASP* 3.2 12.8 - - - +
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Residues in contact with ALA1268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264B GLU* 2.8 18.9 + - - +
1265B VAL* 3.3 12.6 + - + +
1266B GLU 4.2 0.2 - - - +
1267B LEU* 1.3 82.5 - - + +
1269B ASP* 1.3 66.6 + - - +
1270B SER* 3.5 13.1 - - - +
1273B THR* 4.7 8.1 - - + +
1274B LEU* 4.4 19.7 - - + +
1275B PHE 5.6 0.2 - - - +
1375B ARG* 3.6 19.4 + - - -
1376B PHE* 5.2 3.9 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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