Contacts of the helix formed by residues 1358 - 1374 (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 PRO1358 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1292B TYR* 3.8 20.0 - - + +
1296B TYR* 3.8 24.2 - - + -
1356B GLU 3.4 7.8 - - - +
1357B PHE* 1.3 97.1 - - + +
1359B PRO* 1.3 75.3 - - + +
1360B GLN* 3.4 6.3 - - - +
1361B LEU* 3.5 27.0 + - + +
1362B ARG* 3.2 16.3 + - - +
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Residues in contact with PRO1359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1357B PHE 4.2 3.4 - - - +
1358B PRO* 1.3 83.4 - - + +
1360B GLN* 1.3 78.1 + - - +
1362B ARG* 3.1 11.1 + - + +
1363B SER* 3.0 23.7 + - - -
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Residues in contact with GLN1360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1248B ASP* 5.5 3.5 + - - +
1253B LEU* 5.6 4.3 - - + +
1292B TYR* 3.6 49.7 - - + +
1358B PRO* 3.4 3.9 - - + +
1359B PRO* 1.3 87.4 - - - +
1361B LEU* 1.3 64.3 + - - +
1363B SER* 3.3 8.6 + - - -
1364B VAL* 3.1 24.8 + - - +
1478B ILE* 6.2 2.4 - - - +
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Residues in contact with LEU1361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1288B CYS 3.4 27.6 - - - +
1289B PHE* 3.4 27.4 - - + -
1292B TYR* 3.7 13.9 - - + -
1293B GLY* 3.8 18.8 - - - -
1296B TYR* 5.0 0.4 - - + -
1357B PHE* 3.6 27.8 - - + -
1358B PRO* 3.5 26.5 + - + +
1359B PRO 3.2 0.4 - - - -
1360B GLN* 1.3 71.8 - - - +
1362B ARG* 1.3 61.4 + - - +
1363B SER 2.9 1.1 - - - -
1364B VAL* 2.4 31.6 + - + +
1365B CYS* 2.8 12.0 + - - -
1392B PHE* 4.3 15.3 - - + -
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Residues in contact with ARG1362 (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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1354B SER* 2.9 29.7 + - - +
1357B PHE* 3.4 32.3 + - + +
1358B PRO 3.2 9.9 + - - +
1359B PRO* 3.1 13.8 + - + +
1361B LEU* 1.3 78.5 - - - +
1363B SER* 1.3 60.0 + - - +
1365B CYS* 4.9 0.2 - - - -
1366B HIS* 3.3 24.3 + - - +
1460B ASP* 2.7 44.1 + - - -
1461B ILE* 3.2 28.7 - - - +
1463B SER 4.0 15.0 + - - +
1464B ASP* 4.9 11.0 - - - +
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Residues in contact with SER1363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLN 5.0 4.3 + - - -
1253B LEU* 5.5 6.7 - - - +
1254B TYR* 3.7 23.4 - - - +
1257B LEU* 5.5 0.4 - - - +
1359B PRO 3.0 12.1 + - - -
1360B GLN* 3.5 11.7 - - - -
1361B LEU 2.7 4.0 + - - -
1362B ARG* 1.3 73.3 - - - +
1364B VAL* 1.3 58.9 + - - +
1366B HIS* 4.0 4.3 - - - +
1367B CYS* 3.0 28.2 + - - +
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Residues in contact with VAL1364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253B LEU* 4.6 7.2 - - + -
1257B LEU* 3.7 30.5 - - + -
1261B PHE* 4.2 12.0 - - + -
1285B MET* 4.8 5.6 - - + -
1288B CYS* 4.0 26.2 - - + -
1289B PHE* 4.2 22.7 - - + -
1292B TYR* 5.0 2.9 - - + -
1360B GLN 3.1 15.9 + - - +
1361B LEU* 2.4 28.3 + - + +
1363B SER* 1.3 70.0 - - - +
1365B CYS* 1.3 57.3 + - - +
1367B CYS* 3.4 3.1 + - - +
1368B LEU* 2.9 28.3 + - + +
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Residues in contact with CYS1365 (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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1289B PHE* 3.9 29.4 - - - -
1357B PHE* 4.6 8.1 - - - -
1361B LEU 2.8 17.5 + - - +
1364B VAL* 1.3 73.5 - - - +
1366B HIS* 1.3 55.4 + - - +
1368B LEU* 3.2 9.6 + - - +
1369B TYR* 2.7 34.3 + - - +
1384B VAL* 3.8 24.3 - - + +
1388B MET* 4.9 4.0 - - - -
1461B ILE* 3.9 34.8 - - + +
1462B ALA* 4.2 4.0 - - - +
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Residues in contact with HIS1366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PRO* 4.2 20.0 - - + +
110A ARG* 4.7 11.8 + - - -
1254B TYR* 4.0 15.7 + - - -
1362B ARG 3.3 19.2 + - - +
1363B SER* 4.1 3.4 + - - +
1365B CYS* 1.3 76.9 - - - +
1367B CYS* 1.3 66.1 + - - +
1369B TYR* 3.0 4.9 + + - +
1370B GLN* 3.0 56.1 + - + +
1462B ALA* 2.9 33.8 + - - +
1463B SER* 4.2 8.1 - - - +
1464B ASP* 4.2 26.9 + - + +
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Residues in contact with CYS1367 (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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1254B TYR* 3.6 36.6 - - + -
1257B LEU* 3.7 31.6 - - + -
1258B TRP* 3.9 22.1 - - - -
1261B PHE* 4.0 6.3 - - - -
1363B SER 3.0 20.4 + - - +
1364B VAL* 3.7 6.3 - - - +
1366B HIS* 1.3 77.1 + - - +
1368B LEU* 1.3 61.9 + - - +
1370B GLN* 3.6 2.0 + - - +
1371B VAL* 3.2 24.3 + - - +
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Residues in contact with LEU1368 (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* 4.0 13.6 - - + -
1275B PHE* 4.0 24.5 - - + -
1285B MET* 3.6 38.1 - - + -
1289B PHE* 5.6 4.3 - - + -
1364B VAL* 2.9 19.8 + - + +
1365B CYS* 3.5 6.1 - - - +
1367B CYS* 1.3 75.8 - - - +
1369B TYR* 1.3 63.4 + - - +
1371B VAL* 3.2 15.9 - - + +
1372B VAL* 3.1 24.2 - - + +
1383B ALA* 4.7 6.5 - - + +
1384B VAL* 3.7 36.3 - - + +
1387B ALA* 4.9 2.2 - - + -
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Residues in contact with TYR1369 (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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1365B CYS 2.7 20.4 + - - +
1366B HIS* 3.0 9.4 + + - +
1368B LEU* 1.3 74.7 - - - +
1370B GLN* 1.3 72.6 + - - +
1372B VAL* 3.3 8.9 - - - +
1373B SER* 2.5 32.2 + - - -
1380B SER* 3.1 27.7 + - - -
1381B ILE* 3.6 33.3 + - + +
1384B VAL* 3.8 6.7 - - + -
1459B LEU* 4.1 17.3 - - + +
1462B ALA* 3.7 31.9 - - + -
1463B SER* 5.4 4.5 - - - -
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Residues in contact with GLN1370 (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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106A PRO* 6.0 1.3 - - + -
110A ARG* 5.6 5.6 - - - +
1254B TYR* 4.9 4.5 - - - +
1258B TRP* 4.6 15.9 - - + -
1366B HIS* 3.0 48.3 + - + +
1367B CYS 4.3 2.7 - - - +
1369B TYR* 1.3 89.0 - - - +
1371B VAL* 1.3 65.9 + - - +
1373B SER* 3.2 18.6 + - - -
1374B GLN* 3.4 11.6 + - - +
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Residues in contact with VAL1371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258B TRP* 4.8 17.2 - - + +
1261B PHE* 3.8 20.9 - - + +
1262B SER* 3.5 44.2 - - - +
1265B VAL* 4.3 13.2 - - + +
1367B CYS* 3.2 20.9 + - - +
1368B LEU* 3.2 19.7 - - + +
1370B GLN* 1.3 79.4 - - - +
1372B VAL* 1.3 64.3 + - - +
1374B GLN* 3.4 19.0 + - - +
1375B ARG* 4.3 1.4 + - - +
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Residues in contact with VAL1372 (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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1265B VAL* 4.1 19.3 - - + -
1271B MET* 5.0 3.8 - - + -
1274B LEU* 5.8 5.2 - - + -
1368B LEU* 3.1 23.3 - - + +
1369B TYR* 3.3 9.6 - - - +
1371B VAL* 1.3 77.3 - - + +
1373B SER* 1.3 64.0 + - - +
1374B GLN 3.1 2.0 - - - -
1375B ARG* 3.0 4.3 + - - +
1376B PHE* 2.8 53.3 + - + -
1380B SER* 3.9 25.1 - - - +
1383B ALA* 4.8 17.5 - - + -
1384B VAL* 5.2 2.2 - - + -
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Residues in contact with SER1373 (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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1369B TYR* 2.5 31.2 + - - -
1370B GLN* 3.2 16.6 + - - -
1372B VAL* 1.3 77.9 - - - +
1374B GLN* 1.3 60.6 + - - +
1376B PHE 3.9 11.0 - - - -
1377B PRO* 3.4 26.8 - - - +
1380B SER* 2.9 19.1 + - - -
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Residues in contact with GLN1374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1258B TRP* 6.5 1.3 - - + -
1370B GLN 3.4 8.3 + - - +
1371B VAL* 3.6 13.2 - - - +
1372B VAL 3.1 1.0 + - - -
1373B SER* 1.3 80.1 - - - +
1375B ARG* 1.3 61.6 + - + +
1377B PRO* 4.9 2.6 - - - +
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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
------------------------------------------------------------
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