Contacts of the helix formed by residues 1391 - 1405 (chain A) in PDB entry 6J8H
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 ASN1391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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764A GLU 3.7 14.6 - - - +
765A HIS* 4.7 7.4 - - + +
1340A VAL* 4.0 9.7 - - - +
1389A PHE 4.2 0.6 - - - -
1390A ASP* 1.3 80.2 - - - +
1392A VAL* 1.3 65.9 + - - +
1393A GLY* 2.8 28.8 + - - -
1394A LEU* 3.1 31.5 + - - +
1395A GLY* 3.0 20.1 + - - -
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Residues in contact with VAL1392 (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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762A ALA* 2.6 44.2 - - + +
764A GLU* 4.5 2.8 + - + +
1333A LEU* 3.7 26.2 - - + -
1336A SER* 3.4 19.9 + - - +
1337A ILE* 4.8 6.7 - - + -
1340A VAL* 4.1 14.6 - - + -
1391A ASN* 1.3 74.4 - - - +
1393A GLY* 1.3 62.8 + - - +
1395A GLY 3.3 0.5 + - - -
1396A TYR* 3.2 26.0 + - + -
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Residues in contact with GLY1393 (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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1391A ASN* 2.8 15.3 + - - -
1392A VAL* 1.3 74.3 - - - +
1394A LEU* 1.3 59.9 + - - -
1396A TYR* 3.2 24.0 + - - +
1397A LEU* 3.5 5.5 + - - +
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Residues in contact with LEU1394 (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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1386A LYS 4.3 18.2 - - - +
1388A ASN* 3.2 38.6 - - - +
1390A ASP* 4.2 9.9 - - + +
1391A ASN* 3.1 34.8 + - - +
1393A GLY* 1.3 71.7 - - - +
1395A GLY* 1.3 65.7 + - - +
1397A LEU* 2.9 32.2 + - + +
1398A SER* 3.0 11.1 + - - -
1737A ILE* 6.0 3.4 - - + -
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Residues in contact with GLY1395 (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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1336A SER* 4.0 10.5 - - - -
1340A VAL* 5.1 0.4 - - - -
1388A ASN 3.5 3.3 + - - -
1389A PHE* 3.5 31.2 - - - -
1391A ASN 3.0 13.7 + - - -
1392A VAL 3.3 4.5 + - - -
1393A GLY 3.2 0.4 - - - -
1394A LEU* 1.3 75.3 - - - +
1396A TYR* 1.3 56.9 + - - +
1398A SER* 3.2 2.4 + - - -
1399A LEU* 2.9 30.5 + - - +
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Residues in contact with TYR1396 (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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1329A LEU* 2.6 57.0 + - + +
1332A TRP* 3.9 30.0 - + + -
1333A LEU* 3.6 32.9 - - + +
1336A SER* 4.0 6.7 + - - -
1392A VAL* 3.2 23.8 + - + -
1393A GLY* 3.2 13.3 + - - +
1394A LEU 3.1 0.6 - - - -
1395A GLY* 1.3 77.8 - - - +
1397A LEU* 1.3 57.1 + - - +
1399A LEU* 3.4 6.7 + - + +
1400A LEU* 3.1 25.6 + - - +
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Residues in contact with LEU1397 (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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1386A LYS 5.4 0.2 - - - +
1387A VAL* 3.9 26.9 - - + -
1393A GLY 3.5 5.1 + - - +
1394A LEU* 2.9 24.9 + - + +
1396A TYR* 1.3 77.5 - - - +
1398A SER* 1.3 64.5 + - - +
1400A LEU* 3.1 18.5 + - + +
1401A GLN* 3.2 17.9 + - - +
1700A TRP* 4.8 12.6 - - + -
1704A LEU* 4.7 11.7 - - + -
1708A LEU* 5.1 3.1 - - + -
1737A ILE* 4.2 30.3 - - + -
1741A VAL* 4.3 23.8 - - + -
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Residues in contact with SER1398 (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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1387A VAL* 3.5 12.2 - - - +
1388A ASN* 2.7 41.6 + - - -
1389A PHE* 3.8 23.8 - - - -
1394A LEU 3.0 3.9 + - - -
1395A GLY 3.2 7.2 + - - -
1397A LEU* 1.3 75.4 - - - +
1399A LEU* 1.3 64.3 + - - +
1401A GLN* 3.4 4.7 + - - +
1402A VAL* 3.3 25.2 + - - +
1411A ILE* 3.8 11.7 - - - +
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Residues in contact with LEU1399 (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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1332A TRP* 3.7 25.4 - - + +
1335A PHE* 4.1 6.7 - - + -
1336A SER* 3.6 36.6 - - - +
1389A PHE* 3.5 29.6 - - + -
1395A GLY 2.9 11.4 + - - +
1396A TYR* 3.6 6.7 - - + +
1398A SER* 1.3 75.8 - - - +
1400A LEU* 1.3 65.1 + - - +
1402A VAL* 3.2 7.9 + - + +
1403A ALA* 2.9 24.4 + - - +
1436A TYR* 4.2 11.9 - - + +
1437A PHE* 6.0 1.3 - - + -
1440A PHE* 3.6 33.6 - - + -
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Residues in contact with LEU1400 (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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1332A TRP* 4.0 24.2 - - + -
1396A TYR 3.1 14.4 + - - +
1397A LEU* 3.1 15.7 + - + +
1399A LEU* 1.3 77.8 - - - +
1401A GLN* 1.3 61.5 + - - +
1403A ALA* 3.3 2.2 + - + +
1404A THR* 3.0 37.1 + - + -
1700A TRP* 4.1 22.9 - - + -
1741A VAL* 4.2 29.4 - - + -
1744A ILE* 5.7 9.4 - - + -
1745A ILE* 6.0 4.0 - - + -
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Residues in contact with GLN1401 (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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1387A VAL* 3.6 39.4 - - - +
1397A LEU* 3.2 7.9 + - - +
1398A SER 3.8 7.6 - - - +
1399A LEU 3.2 0.6 - - - -
1400A LEU* 1.3 80.8 - - - +
1402A VAL* 1.3 56.9 + - - +
1404A THR* 3.3 4.9 + - - -
1405A PHE* 2.9 23.9 + - - -
1406A LYS 3.2 29.3 + - - +
1407A GLY* 3.9 9.2 - - - +
1408A TRP* 3.9 1.9 - - - +
1411A ILE* 3.6 13.5 - - + +
1700A TRP* 3.7 25.9 - - + -
1701A ASP* 4.1 17.6 + - + +
1704A LEU* 4.4 10.5 - - - +
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Residues in contact with VAL1402 (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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1389A PHE* 6.1 0.4 - - + -
1398A SER 3.3 14.3 + - - +
1399A LEU* 3.2 11.9 + - + +
1401A GLN* 1.3 75.0 - - - +
1403A ALA* 1.3 65.3 + - - +
1405A PHE* 3.2 22.9 + - - -
1408A TRP* 3.6 28.8 - - + +
1411A ILE* 4.6 7.6 - - + -
1412A MET* 5.4 0.2 - - + -
1437A PHE* 4.1 33.0 - - + +
1440A PHE* 3.8 23.6 - - + -
1441A ILE* 3.9 20.7 - - + +
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Residues in contact with ALA1403 (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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1332A TRP* 3.6 29.4 - - + -
1399A LEU 2.9 17.7 + - - +
1400A LEU* 3.5 7.9 - - + +
1401A GLN 3.2 0.2 - - - -
1402A VAL* 1.3 79.3 - - - +
1404A THR* 1.3 61.2 + - + +
1405A PHE* 3.8 14.7 - - - -
1440A PHE* 4.1 9.4 - - + -
1441A ILE* 5.9 0.7 - - - -
1445A SER* 3.9 23.1 + - - -
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Residues in contact with THR1404 (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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1400A LEU* 3.0 29.4 + - + +
1401A GLN* 3.3 7.4 + - - -
1403A ALA* 1.3 77.4 - - + +
1405A PHE* 1.3 74.8 + - - +
1406A LYS* 3.1 22.8 + - - +
1697A SER* 4.8 9.1 + - - +
1700A TRP* 3.4 26.8 + - - +
1744A ILE* 5.1 11.0 - - + -
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Residues in contact with PHE1405 (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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925A CYS* 3.7 35.9 - - + -
926A GLY 5.7 1.3 - - - -
927A GLU* 3.6 15.0 - - + +
1401A GLN 2.9 8.3 + - - -
1402A VAL 3.2 12.7 + - - -
1403A ALA* 3.8 12.1 - - - -
1404A THR* 1.3 87.1 - - - +
1406A LYS* 1.3 66.1 + - - +
1408A TRP* 3.3 42.2 - + + -
1441A ILE* 3.6 36.6 - - + -
1445A SER* 4.1 10.3 - - - -
2007A 9SL 3.6 12.0 + - - +
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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