Contacts of the helix formed by residues 1494 - 1510 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1488B VAL* 5.3 1.6 - - - +
1489B ASN* 4.9 7.2 + - - +
1492B GLU* 3.9 13.3 + - - -
1493B GLU* 1.3 83.7 - - - +
1495B ASP* 1.3 66.3 + - - +
1496B ALA* 3.6 9.8 + - - +
1497B LEU* 3.2 23.2 + - - +
1498B ALA* 2.9 23.5 + - - +
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Residues in contact with ASP1495 (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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1494B SER* 1.3 75.0 - - - +
1496B ALA* 1.3 57.9 + - - +
1498B ALA* 3.2 8.3 + - - +
1499B LYS* 2.9 30.1 + - - +
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Residues in contact with ALA1496 (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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1454B LEU* 5.8 2.9 - - + -
1486B HIS* 4.4 5.0 + - + +
1487B PHE 3.7 22.7 - - - +
1488B VAL* 4.0 9.0 - - + +
1494B SER* 3.2 8.4 + - - +
1495B ASP* 1.3 78.5 - - - +
1497B LEU* 1.3 61.4 + - - +
1499B LYS* 3.4 6.3 + - - +
1500B LEU* 3.1 21.5 + - - +
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Residues in contact with LEU1497 (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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1350B LEU* 3.6 30.5 - - + -
1353B GLN* 3.5 32.5 - - + +
1354B LEU* 4.0 12.2 - - + +
1488B VAL* 4.1 19.7 - - + +
1489B ASN 4.9 4.7 - - - +
1490B ALA* 5.0 0.7 - - - -
1492B GLU 4.1 4.7 - - - +
1493B GLU* 3.8 6.7 - - - +
1494B SER* 3.2 24.0 + - - +
1496B ALA* 1.3 75.9 - - - +
1498B ALA* 1.3 58.4 + - - +
1500B LEU* 3.2 5.5 + - + +
1501B ARG* 3.0 57.6 + - - +
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Residues in contact with ALA1498 (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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1493B GLU* 4.1 10.2 + - - +
1494B SER 2.9 13.2 + - - +
1495B ASP* 3.2 12.8 + - - +
1497B LEU* 1.3 78.7 - - - +
1499B LYS* 1.3 61.5 + - - +
1501B ARG* 3.3 15.6 + - - +
1502B LYS* 3.0 21.8 + - - +
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Residues in contact with LYS1499 (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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1484B ASP* 4.6 7.2 - - - -
1486B HIS* 4.0 12.1 - - + +
1495B ASP 2.9 16.0 + - - +
1496B ALA* 3.8 7.4 - - - +
1497B LEU 3.2 0.2 - - - -
1498B ALA* 1.3 73.4 - - - +
1500B LEU* 1.3 62.6 + - - +
1502B LYS* 3.2 16.1 + - + -
1503B THR* 2.9 40.0 + - - +
1506B ASN* 6.4 0.4 - - - +
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Residues in contact with LEU1500 (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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1350B LEU* 3.8 30.1 - - + -
1354B LEU* 4.1 13.7 - - + -
1416B LEU* 4.3 1.6 - - + -
1448B ILE* 3.8 17.9 - - + -
1450B VAL* 3.9 24.7 - - + -
1486B HIS* 3.7 36.9 - - + +
1488B VAL* 4.7 3.4 - - + -
1496B ALA 3.1 13.3 + - - +
1497B LEU* 3.2 13.2 + - + +
1499B LYS* 1.3 76.8 - - - +
1501B ARG* 1.3 62.6 + - - +
1503B THR* 3.1 1.7 + - - -
1504B ILE* 2.9 36.2 + - + +
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Residues in contact with ARG1501 (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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1376A TRP* 4.2 13.6 - - + -
1378A ILE* 6.5 0.2 - - + -
1353B GLN 2.5 29.1 + - - -
1354B LEU* 2.7 36.2 + - + +
1356B LYS 3.9 12.1 + - - -
1493B GLU* 2.5 43.6 + - - -
1497B LEU* 3.0 23.0 + - - +
1498B ALA* 3.4 21.2 - - - +
1499B LYS 3.3 0.2 - - - -
1500B LEU* 1.3 74.8 - - - +
1502B LYS* 1.3 63.4 + - - +
1504B ILE* 3.1 8.0 + - - +
1505B ILE* 3.0 36.4 + - + +
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Residues in contact with LYS1502 (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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1381A ARG 5.5 0.7 - - - -
1382A ASP* 3.4 27.0 - - - +
1498B ALA 3.0 13.6 + - - +
1499B LYS* 3.2 22.9 + - + +
1501B ARG* 1.3 75.1 - - - +
1503B THR* 1.3 57.7 + - - +
1505B ILE* 3.3 19.8 + - + +
1506B ASN* 2.6 66.7 + - - +
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Residues in contact with THR1503 (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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1448B ILE* 3.9 18.4 - - + -
1484B ASP* 3.3 33.4 + - + +
1486B HIS* 3.3 19.6 + - - +
1499B LYS* 2.9 23.7 + - - +
1500B LEU* 3.1 8.9 + - - -
1502B LYS* 1.3 76.2 - - - +
1504B ILE* 1.3 56.8 + - - +
1506B ASN* 3.3 6.3 + - - +
1507B GLU* 2.9 39.4 + - + +
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Residues in contact with ILE1504 (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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1376A TRP* 4.2 17.9 - - + -
1378A ILE* 5.2 1.6 - - + -
1390A LEU* 3.7 27.1 - - + -
1337B LEU* 4.3 7.2 - - + -
1354B LEU* 3.7 33.4 - - + -
1414B LEU* 4.0 6.3 - - + +
1416B LEU* 4.0 22.9 - - + -
1448B ILE* 4.0 22.0 - - + -
1500B LEU* 2.9 25.0 + - + +
1501B ARG* 3.5 6.5 - - - +
1503B THR* 1.3 74.3 - - - +
1505B ILE* 1.3 59.3 + - - +
1508B SER* 2.7 35.3 + - - +
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Residues in contact with ILE1505 (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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1376A TRP* 6.1 0.7 - - + -
1378A ILE* 3.7 41.3 - - + -
1379A GLN 5.4 1.6 - - - +
1380A ILE* 4.1 21.3 - - + -
1382A ASP* 4.1 12.1 - - + -
1388A LEU* 4.3 9.8 - - + +
1501B ARG* 3.0 31.1 + - + +
1502B LYS* 3.5 27.8 - - + +
1504B ILE* 1.3 76.6 - - + +
1506B ASN* 1.3 58.0 + - - +
1508B SER* 3.6 1.7 - - - -
1509B LEU* 2.9 34.4 + - + +
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Residues in contact with ASN1506 (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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1382A ASP* 3.7 11.1 - - - +
1499B LYS* 6.4 0.2 - - - +
1502B LYS* 2.6 55.2 + - - +
1503B THR* 3.8 6.2 - - - +
1504B ILE 3.3 0.2 - - - -
1505B ILE* 1.3 76.2 - - - +
1507B GLU* 1.3 61.4 + - + +
1509B LEU* 3.3 6.5 + - - +
1510B ASN* 2.8 45.5 + - - +
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Residues in contact with GLU1507 (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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1414B LEU* 4.0 24.0 - - + -
1446B PRO* 4.6 5.3 - - + +
1448B ILE* 4.0 13.5 - - + -
1483B ARG* 3.2 55.6 + - + +
1484B ASP* 5.9 0.2 - - - +
1503B THR* 2.9 27.6 + - + +
1506B ASN* 1.3 79.0 - - - +
1508B SER* 1.3 56.9 + - - +
1510B ASN* 3.4 9.9 + - - +
1511B PHE* 2.9 32.4 + - - +
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Residues in contact with SER1508 (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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1388A LEU* 4.1 9.2 - - - -
1390A LEU* 3.6 33.2 - - - +
1335B MET* 3.1 36.5 - - - +
1414B LEU* 3.6 15.6 - - - +
1504B ILE 2.7 23.6 + - - -
1505B ILE 3.6 3.8 - - - -
1507B GLU* 1.3 76.5 - - - +
1509B LEU* 1.3 62.2 + - - +
1511B PHE* 3.2 9.8 + - - +
1512B LYS 5.0 0.2 + - - -
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Residues in contact with LEU1509 (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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1380A ILE* 4.3 25.6 - - + -
1382A ASP* 4.1 25.4 - - + -
1383A LYS* 4.3 19.1 - - + +
1384A ARG 5.5 0.9 - - - +
1388A LEU* 4.6 16.2 - - + -
1335B MET* 5.2 1.6 - - + -
1505B ILE* 2.9 28.7 + - + +
1506B ASN* 3.7 6.3 - - - +
1508B SER* 1.3 77.5 - - - +
1510B ASN* 1.3 64.7 + - - +
1511B PHE 3.3 0.9 + - - -
1512B LYS* 4.6 6.9 + - - +
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Residues in contact with ASN1510 (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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1506B ASN* 2.8 34.3 + - - +
1507B GLU* 3.4 12.0 + - - +
1509B LEU* 1.3 77.4 - - - +
1511B PHE* 1.3 64.1 + - - +
1512B LYS 3.2 3.1 - - - -
1513B ILE* 3.2 32.9 + - + +
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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
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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