Contacts of the helix formed by residues 1367 - 1378 (chain A) in PDB entry 6A5T
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 ASN1367 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515A PRO 4.8 1.7 + - - +
516A GLN 3.4 15.0 + - - +
517A SER* 5.3 0.9 - - - -
518A ASN* 4.8 14.6 - - - +
876A GLY* 3.6 19.6 + - - +
879A VAL* 5.1 2.9 - - - +
957A PRO* 5.5 5.7 - - - +
1365A TYR* 4.2 17.8 + - - +
1366A VAL* 1.3 91.4 - - - +
1368A TYR* 1.3 88.3 + - - +
1369A ARG* 2.7 48.7 + - - +
1370A HIS* 3.7 14.0 + - + -
1371A MET* 4.0 2.4 - - - +
203E THR* 5.5 1.0 - - - +
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Residues in contact with TYR1368 (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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870A GLY 5.1 3.6 - - - -
871A GLU* 4.0 23.2 + - + -
1348A ARG* 3.3 28.2 + - - -
1352A TYR* 2.8 46.9 - + - -
1365A TYR* 5.3 0.6 + - - -
1366A VAL 3.5 1.7 + - - -
1367A ASN* 1.3 85.6 + - - +
1369A ARG* 1.3 68.6 + - + +
1370A HIS 2.8 2.4 + - - -
1371A MET* 3.2 6.1 + - - +
1372A ALA* 2.9 40.1 + - + -
200E ARG 5.5 1.9 + - - -
201E SER* 5.7 0.2 - - - -
202E GLU* 3.1 37.2 + - + +
203E THR* 3.6 33.4 - - + -
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Residues in contact with ARG1369 (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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866A GLN* 4.7 1.0 + - - -
869A TYR* 4.0 32.2 + - + +
870A GLY* 4.2 13.8 + - - +
872A ASP* 2.5 38.3 + - - -
874A LEU* 2.7 24.3 + - - +
875A ASP 4.6 2.2 + - - -
876A GLY* 3.5 19.6 - - - +
879A VAL* 5.0 7.5 - - - +
1367A ASN* 2.7 35.3 + - - +
1368A TYR* 1.3 83.7 - - + +
1370A HIS* 1.3 72.4 + - + +
1372A ALA* 3.3 9.8 - - - +
1373A LEU* 2.9 27.7 + - - +
203E THR* 5.4 10.1 - - - +
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Residues in contact with HIS1370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A PRO* 2.9 31.9 + - + +
516A GLN* 4.6 4.7 - - - -
869A TYR* 4.5 15.6 + - - -
876A GLY* 5.8 0.6 - - - -
1066A VAL 4.7 1.3 - - - -
1069A ILE* 3.4 33.0 - - + +
1070A ALA* 3.2 32.1 + - + +
1073A SER* 5.2 4.9 - - - +
1074A ILE* 4.2 11.1 - - + +
1366A VAL* 4.2 14.4 - - + -
1367A ASN* 4.3 12.3 + - + -
1368A TYR 2.8 3.0 + - - -
1369A ARG* 1.3 88.7 - - + +
1371A MET* 1.3 66.0 + - - +
1372A ALA 3.0 1.1 - - - -
1373A LEU* 3.0 5.6 + - - +
1374A LEU* 3.0 22.7 + - - +
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Residues in contact with MET1371 (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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1074A ILE* 4.7 6.0 - - + +
1352A TYR* 3.5 28.7 - - + +
1355A ILE* 3.3 36.1 - - + +
1356A LEU* 3.5 40.8 - - + -
1359A ILE* 4.5 15.9 - - + -
1366A VAL* 3.7 33.9 - - + +
1367A ASN 4.0 6.8 + - - +
1368A TYR 3.2 2.9 + - - +
1370A HIS* 1.3 77.6 - - - +
1372A ALA* 1.3 56.4 + - - +
1374A LEU* 3.8 6.0 - - - +
1375A VAL* 2.9 35.3 + - + +
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Residues in contact with ALA1372 (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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866A GLN* 3.2 19.2 + - - +
870A GLY* 5.0 3.4 - - - -
871A GLU* 5.8 1.3 - - - +
1348A ARG* 5.2 2.5 - - - +
1352A TYR* 4.4 1.7 - - - -
1368A TYR* 2.9 41.0 + - + +
1369A ARG* 3.3 12.8 - - - +
1370A HIS 3.0 0.2 - - - -
1371A MET* 1.3 77.6 - - - +
1373A LEU* 1.3 63.4 + - - +
1375A VAL* 3.1 12.2 - - - +
1376A ASP* 2.9 22.5 + - - +
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Residues in contact with LEU1373 (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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846A LEU* 5.5 3.6 - - + -
849A ILE* 4.5 13.9 - - + -
857A THR* 3.8 26.9 - - + -
865A ILE* 5.0 4.3 - - + -
866A GLN* 3.3 18.3 - - + +
869A TYR* 4.6 9.0 - - + +
1066A VAL* 3.9 19.1 - - + -
1067A GLY* 3.5 32.1 - - - +
1070A ALA* 3.9 14.4 - - + -
1369A ARG 2.9 14.6 + - - +
1370A HIS* 3.0 7.8 + - - +
1372A ALA* 1.3 74.1 - - - +
1374A LEU* 1.3 62.8 + - - +
1376A ASP* 3.2 1.7 + - - -
1377A VAL* 3.1 22.2 + - - +
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Residues in contact with LEU1374 (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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842A LEU* 4.7 15.9 - - + -
846A LEU* 3.9 29.2 - - + -
1070A ALA* 5.2 1.2 - - + +
1071A ALA* 6.2 0.2 - - - -
1074A ILE* 3.9 27.8 - - + -
1107A LEU* 4.2 20.9 - - + -
1355A ILE* 3.8 26.9 - - + -
1370A HIS 3.0 14.1 + - - +
1371A MET* 3.8 4.7 - - - +
1373A LEU* 1.3 76.9 - - - +
1375A VAL* 1.3 64.4 + - + +
1376A ASP 3.0 1.0 + - - -
1377A VAL* 3.1 14.0 + - + +
1378A MET* 3.2 17.5 + - + +
1387A ILE* 5.3 10.8 - - + -
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Residues in contact with VAL1375 (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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1348A ARG* 4.2 30.1 - - + +
1351A LEU* 3.5 40.7 - - + +
1352A TYR* 4.0 26.5 - - + -
1355A ILE* 4.4 12.8 - - + -
1371A MET* 2.9 28.9 + - + +
1372A ALA* 3.1 15.9 - - - +
1374A LEU* 1.3 72.5 - - - +
1376A ASP* 1.3 60.7 + - - +
1378A MET 3.7 5.2 + - - +
1379A THR* 3.3 18.5 + - - -
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Residues in contact with ASP1376 (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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865A ILE* 3.2 34.2 - - + +
866A GLN* 2.7 33.4 + - - +
871A GLU* 5.2 2.1 - - - +
1348A ARG* 3.8 30.3 + - - +
1372A ALA 2.9 14.1 + - - +
1373A LEU 3.8 2.5 - - - +
1374A LEU 3.0 0.4 - - - -
1375A VAL* 1.3 80.1 - - - +
1377A VAL* 1.3 65.7 + - - +
1378A MET 3.2 0.7 - - - -
1379A THR* 3.6 7.5 + - - +
1380A SER* 3.5 14.9 + - - -
199E ARG* 4.7 5.2 + - - -
207E TYR* 5.8 1.4 - - - -
211E ARG* 5.6 2.4 + - - -
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Residues in contact with VAL1377 (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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845A ALA* 5.4 4.3 - - + +
846A LEU* 3.7 18.8 - - + -
849A ILE* 3.5 31.9 - - + -
859A ASN* 6.1 2.0 - - - +
865A ILE* 4.0 17.9 - - + -
1373A LEU 3.1 13.3 + - - +
1374A LEU* 3.1 8.2 + - + +
1376A ASP* 1.3 78.4 - - - +
1378A MET* 1.3 62.2 + - + +
1379A THR 3.0 6.1 + - - -
1380A SER* 3.2 14.8 + - - -
1385A MET* 4.0 29.0 - - + +
1387A ILE* 4.8 14.4 - - + -
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Residues in contact with MET1378 (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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1106A ILE* 4.3 3.8 - - - +
1107A LEU* 4.2 22.7 - - - -
1109A VAL* 3.5 31.0 - - + -
1335A PHE* 4.9 0.4 - - + -
1351A LEU* 3.8 40.8 - - + -
1355A ILE* 5.6 0.4 - - - -
1374A LEU* 3.2 23.8 + - + +
1375A VAL 3.7 0.8 + - - +
1376A ASP 3.2 0.4 - - - -
1377A VAL* 1.3 76.7 - - + +
1379A THR* 1.3 65.5 + - - +
1380A SER 3.8 0.2 - - - -
1384A LEU* 3.4 15.3 - - + +
1385A MET* 3.4 38.8 + - - +
1386A ALA* 5.1 2.7 - - - -
1387A ILE* 4.3 16.6 - - + -
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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
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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