Contacts of the helix formed by residues 1494 - 1514 (chain A) in PDB entry 6XAF
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 SER1494 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1488A VAL* 5.3 0.9 - - - +
1489A ASN* 5.0 10.6 + - - -
1492A GLU* 3.7 6.1 + - - -
1493A GLU* 1.3 86.7 - - - +
1495A ASP* 1.3 61.8 + - - +
1496A ALA* 3.3 9.9 + - - +
1497A LEU* 3.0 23.4 + - - +
1498A ALA* 2.9 25.3 + - - +
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Residues in contact with ASP1495 (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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1494A SER* 1.3 75.3 - - - +
1496A ALA* 1.3 58.1 + - - +
1498A ALA* 3.2 8.5 + - - +
1499A LYS* 2.9 29.8 + - - +
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Residues in contact with ALA1496 (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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1454A LEU* 5.7 3.8 - - + -
1486A HIS* 4.6 5.2 - - + -
1487A PHE 3.9 22.0 - - - +
1488A VAL* 4.0 8.7 - - + +
1494A SER* 3.2 9.0 + - - +
1495A ASP* 1.3 78.5 - - - +
1497A LEU* 1.3 61.6 + - - +
1499A LYS* 3.3 7.7 + - - +
1500A LEU* 3.0 21.5 + - - +
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Residues in contact with LEU1497 (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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1350A LEU* 3.7 29.6 - - + -
1353A GLN* 3.5 32.8 - - + +
1354A LEU* 4.2 9.1 - - + +
1488A VAL* 4.0 15.3 - - + +
1489A ASN 4.4 12.8 - - - +
1490A ALA* 4.5 1.3 - - - -
1492A GLU 4.3 3.8 - - - +
1493A GLU* 3.3 24.9 - - - +
1494A SER* 3.0 22.9 + - - +
1496A ALA* 1.3 77.1 - - - +
1498A ALA* 1.3 57.6 + - - +
1500A LEU* 3.2 5.0 + - + +
1501A ARG* 2.9 44.8 + - - +
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Residues in contact with ALA1498 (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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1493A GLU* 3.7 10.4 + - - +
1494A SER 2.9 14.0 + - - +
1495A ASP* 3.5 12.6 - - - +
1497A LEU* 1.3 76.4 - - - +
1499A LYS* 1.3 57.0 + - - +
1501A ARG* 3.2 19.8 + - - +
1502A LYS* 3.0 27.4 + - - +
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Residues in contact with LYS1499 (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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1484A ASP* 4.4 9.9 + - - -
1486A HIS* 4.1 12.6 + - + +
1495A ASP 2.9 16.3 + - - +
1496A ALA* 3.7 7.4 - - - +
1497A LEU 3.2 0.2 - - - -
1498A ALA* 1.3 73.2 - - - +
1500A LEU* 1.3 61.5 + - - +
1502A LYS* 3.4 10.2 + - + +
1503A THR* 2.9 57.5 + - - +
1506A ASN* 6.0 2.0 - - - +
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Residues in contact with LEU1500 (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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1350A LEU* 3.8 31.0 - - + -
1354A LEU* 4.2 9.9 - - + -
1416A LEU* 4.7 0.2 - - + -
1448A ILE* 4.0 15.0 - - + -
1450A VAL* 3.9 26.2 - - + -
1486A HIS* 3.8 34.0 + - + +
1488A VAL* 4.6 8.1 - - + -
1496A ALA 3.0 13.9 + - - +
1497A LEU* 3.2 9.4 + - + +
1499A LYS* 1.3 75.5 - - - +
1501A ARG* 1.3 58.1 + - - +
1503A THR* 3.2 1.5 + - - -
1504A ILE* 2.9 48.4 + - + +
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Residues in contact with ARG1501 (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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1353A GLN 3.0 23.4 + - - -
1354A LEU* 2.9 29.4 + - + +
1356A LYS* 3.7 28.3 - - - +
1493A GLU* 3.0 40.8 + - - -
1497A LEU* 2.9 21.2 + - - +
1498A ALA* 3.4 29.1 - - - +
1500A LEU* 1.3 77.8 - - - +
1502A LYS* 1.3 61.8 + - - +
1504A ILE* 3.3 6.0 + - - +
1505A ILE* 3.1 39.4 + - + +
1376B TRP* 4.1 20.0 - - + -
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Residues in contact with LYS1502 (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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1498A ALA 3.0 15.6 + - - +
1499A LYS* 3.8 14.8 - - + +
1501A ARG* 1.3 76.1 - - - +
1503A THR* 1.3 57.8 + - - +
1505A ILE* 3.2 8.2 + - - +
1506A ASN* 2.8 45.9 + - - +
1381B ARG* 4.9 13.9 - - - +
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Residues in contact with THR1503 (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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1448A ILE* 3.9 18.2 - - + -
1484A ASP* 3.7 24.9 + - + +
1486A HIS* 3.5 20.6 + - + -
1499A LYS* 2.9 35.7 + - - +
1500A LEU 3.5 4.9 - - - -
1502A LYS* 1.3 76.8 - - - +
1504A ILE* 1.3 57.1 + - - +
1506A ASN* 3.9 6.1 - - - +
1507A GLU* 2.9 39.1 + - - +
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Residues in contact with ILE1504 (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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1337A LEU* 4.0 28.5 - - + -
1354A LEU* 3.6 24.0 - - + -
1414A LEU* 3.8 2.3 - - + +
1416A LEU* 3.6 39.0 - - + -
1448A ILE* 4.0 10.8 - - + -
1500A LEU* 2.9 36.2 + - + +
1501A ARG* 3.7 4.9 - - - +
1502A LYS 3.3 0.2 - - - -
1503A THR* 1.3 75.7 - - - +
1505A ILE* 1.3 58.7 + - + +
1508A SER* 2.7 34.8 + - - +
1376B TRP* 4.2 8.7 - - + -
1390B LEU* 4.1 14.6 - - + -
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Residues in contact with ILE1505 (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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1501A ARG* 3.1 40.1 + - + +
1502A LYS* 3.7 7.0 - - - +
1504A ILE* 1.3 77.9 - - + +
1506A ASN* 1.3 74.2 + - - +
1508A SER* 3.3 5.8 + - - -
1509A LEU* 3.1 28.9 + - + +
1376B TRP* 5.3 1.1 - - + -
1378B ILE* 3.5 43.1 - - + -
1379B GLN 5.2 2.0 - - - +
1380B ILE* 3.8 27.4 - - + -
1381B ARG* 5.4 4.3 - - - +
1387B ASP* 5.4 2.2 - - - +
1390B LEU* 5.6 0.7 - - - -
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Residues in contact with ASN1506 (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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1499A LYS* 6.0 2.0 - - - +
1502A LYS* 2.8 31.3 + - - +
1503A THR* 4.0 5.9 - - - +
1505A ILE* 1.3 79.0 - - - +
1507A GLU* 1.3 59.4 + - - +
1509A LEU* 3.4 10.1 + - - +
1510A ASN* 2.9 43.9 + - - +
1381B ARG* 3.3 27.6 + - - +
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Residues in contact with GLU1507 (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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1414A LEU* 4.3 22.9 - - + -
1446A PRO* 4.8 6.9 - - + +
1448A ILE* 4.5 7.5 - - + +
1483A ARG* 3.4 50.8 - - + +
1484A ASP* 5.3 0.2 - - - +
1503A THR* 2.9 26.3 + - - +
1506A ASN* 1.3 75.2 - - - +
1508A SER* 1.3 59.8 + - - +
1510A ASN* 3.6 21.6 + - - +
1511A PHE* 2.8 32.8 + - + +
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Residues in contact with SER1508 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1335A MET* 5.3 4.7 - - - -
1414A LEU* 3.3 20.0 - - - +
1504A ILE 2.7 23.8 + - - -
1505A ILE* 3.6 6.3 - - - -
1507A GLU* 1.3 77.6 - - - +
1509A LEU* 1.3 63.2 + - - +
1511A PHE* 3.5 6.7 + - - +
1512A LYS* 3.4 21.5 + - - +
1387B ASP* 5.9 2.7 - - - -
1390B LEU* 3.6 32.4 - - - +
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Residues in contact with LEU1509 (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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1505A ILE* 3.1 26.4 + - + +
1506A ASN* 3.7 9.9 - - - +
1508A SER* 1.3 78.7 - - - +
1510A ASN* 1.3 66.1 + - - +
1512A LYS* 3.6 11.1 + - + +
1513A ILE* 3.2 29.5 + - + +
1380B ILE* 4.2 28.5 - - + -
1385B LYS* 5.7 8.1 - - + +
1387B ASP* 3.6 33.7 - - + +
1388B LEU* 6.3 0.9 - - + -
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Residues in contact with ASN1510 (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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1506A ASN* 2.9 33.3 + - - +
1507A GLU* 3.6 20.9 + - - +
1509A LEU* 1.3 77.4 - - - +
1511A PHE* 1.3 61.6 + - - +
1513A ILE* 3.1 16.8 + - - +
1514A ARG* 2.9 32.1 + - - +
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Residues in contact with PHE1511 (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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1335A MET* 5.8 7.2 - - + -
1411A GLN 3.2 26.5 - - - -
1412A ARG* 3.9 18.4 - - + -
1413A ALA 4.1 12.1 - - - -
1414A LEU* 5.7 3.1 - - + -
1444A SER* 3.9 19.5 - - - -
1445A SER* 4.5 0.7 - - - -
1446A PRO* 3.5 38.1 - - + -
1507A GLU* 2.8 24.0 + - + +
1508A SER* 3.8 7.6 - - - +
1509A LEU 3.4 0.2 - - - -
1510A ASN* 1.3 73.3 - - - +
1512A LYS* 1.3 66.5 + - + +
1514A ARG* 3.2 22.3 + - + +
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Residues in contact with LYS1512 (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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1508A SER 3.4 10.2 + - - +
1509A LEU* 3.7 14.4 - - + +
1510A ASN 3.3 0.6 - - - -
1511A PHE* 1.3 84.3 - - + +
1513A ILE* 1.3 62.1 + - + +
1514A ARG 4.2 2.1 - - - +
1388B LEU* 3.6 30.4 - - + +
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Residues in contact with ILE1513 (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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1509A LEU* 3.2 24.5 - - + +
1510A ASN* 3.1 19.5 + - - +
1512A LYS* 1.3 79.9 - - + +
1514A ARG* 1.3 68.4 + - - +
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Residues in contact with ARG1514 (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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1510A ASN 2.9 15.5 + - - +
1511A PHE* 3.2 18.7 - - + +
1512A LYS 4.2 2.6 - - - +
1513A ILE* 1.3 83.6 - - - +
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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