Contacts of the helix formed by residues 1430 - 1442 (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 ALA1430 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1398A HIS* 4.8 0.2 + - - -
1342B ASN* 3.9 21.6 + - - +
1426B ALA 2.8 13.1 + - - +
1427B GLU* 3.6 18.8 - - - +
1428B VAL 3.1 0.6 - - - -
1429B ASP* 1.3 76.1 - - - +
1431B MET* 1.3 64.3 + - + +
1432B LYS 3.2 0.4 - - - -
1433B PRO* 3.3 20.9 - - - +
1434B TRP* 3.6 12.0 - - - -
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Residues in contact with MET1431 (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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1341B GLY* 4.1 8.1 - - - -
1342B ASN* 4.8 5.4 - - - +
1417B ALA* 4.0 14.4 - - + -
1418B VAL 3.2 27.8 - - - +
1419B TYR* 3.9 17.0 - - + -
1427B GLU 3.3 13.6 + - - +
1428B VAL* 2.9 15.6 + - + +
1430B ALA* 1.3 79.7 - - + +
1432B LYS* 1.3 63.1 + - - +
1434B TRP* 3.2 28.8 + - + +
1435B LEU* 2.9 29.9 + - + +
1449B LEU* 3.7 28.3 - - + -
1473B LEU* 4.5 12.1 - - + -
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Residues in contact with LYS1432 (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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1428B VAL 3.7 2.0 + - - +
1429B ASP* 3.0 39.6 + - - +
1431B MET* 1.3 77.3 - - - +
1433B PRO* 1.3 69.4 - - + +
1435B LEU* 3.0 6.5 + - - +
1436B PHE* 2.9 35.3 + - + -
1468B LYS* 5.4 1.3 - - - +
1472B GLU* 3.1 45.8 + - - -
1473B LEU* 3.8 19.5 - - + -
1479B PHE* 4.0 18.6 - - + -
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Residues in contact with PRO1433 (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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1398A HIS* 4.3 16.6 - - + +
1429B ASP 3.6 7.0 - - - +
1430B ALA* 3.3 21.3 - - - +
1432B LYS* 1.3 93.4 - - + +
1434B TRP* 1.3 55.1 + - - +
1436B PHE* 3.8 10.8 - - + +
1437B ASN* 3.0 38.0 + - - +
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Residues in contact with TRP1434 (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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1395A PHE* 5.3 0.9 - - + -
1397A GLY* 3.5 18.8 - - - -
1398A HIS* 3.0 47.5 + + - -
1401A PHE* 3.6 34.1 - + + -
1340B VAL* 3.5 30.1 - - + -
1341B GLY 3.1 35.7 - - - -
1342B ASN* 3.0 20.2 + - - -
1417B ALA* 5.6 2.5 - - + -
1430B ALA 3.6 17.3 - - - -
1431B MET* 3.2 28.0 + - + +
1432B LYS 3.1 0.6 - - - -
1433B PRO* 1.3 79.8 - - - +
1435B LEU* 1.3 59.1 + - + +
1437B ASN* 3.2 6.4 + - - +
1438B ILE* 2.8 41.4 + - + +
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Residues in contact with LEU1435 (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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1417B ALA* 5.1 6.1 - - + -
1431B MET* 2.9 22.7 + - + +
1432B LYS 3.0 3.3 + - - +
1434B TRP* 1.3 72.4 - - + +
1436B PHE* 1.3 61.7 + - - +
1438B ILE* 3.3 5.1 + - + -
1439B LYS* 2.9 25.6 + - - +
1447B VAL* 4.1 24.9 - - + -
1449B LEU* 5.5 3.1 - - + -
1473B LEU* 4.0 32.8 - - + -
1479B PHE* 3.6 26.5 - - + -
1480B PRO* 3.3 31.4 - - + +
1482B ILE* 4.0 22.7 - - + -
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Residues in contact with PHE1436 (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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1432B LYS* 2.9 34.9 + - + +
1433B PRO* 3.8 8.5 - - + +
1435B LEU* 1.3 74.1 - - - +
1437B ASN* 1.3 64.5 + - - +
1439B LYS* 3.4 7.1 + - + +
1440B ALA* 3.1 22.3 + - - +
1478B GLY* 4.0 17.0 - - - -
1479B PHE* 3.4 32.8 - + - -
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Residues in contact with ASN1437 (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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1398A HIS* 3.6 28.1 + - - -
1401A PHE* 4.3 19.7 - - + -
1433B PRO* 3.0 24.4 + - - +
1434B TRP* 3.5 7.9 - - + +
1436B PHE* 1.3 76.8 - - - +
1438B ILE* 1.3 61.8 + - - +
1440B ALA* 3.3 15.5 + - - +
1441B ARG* 3.4 18.5 + - - +
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Residues in contact with ILE1438 (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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1401A PHE* 4.8 6.5 - - + -
1340B VAL* 4.0 18.6 - - + -
1415B TYR* 3.8 44.9 - - + -
1417B ALA* 5.1 1.8 - - + -
1434B TRP* 2.8 28.6 + - + +
1435B LEU* 3.3 11.2 + - + +
1437B ASN* 1.3 75.5 - - - +
1439B LYS* 1.3 65.0 + - - +
1441B ARG* 3.0 18.6 + - - +
1442B ALA 3.3 10.9 + - - +
1445B SER* 3.5 26.6 + - - -
1447B VAL* 4.0 13.2 - - + -
1480B PRO* 3.7 11.7 - - + -
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Residues in contact with LYS1439 (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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1435B LEU 2.9 16.9 + - - +
1436B PHE* 3.6 6.3 - - + +
1438B ILE* 1.3 77.6 - - - +
1440B ALA* 1.3 61.7 + - - +
1442B ALA* 3.2 22.4 - - - +
1443B SER* 2.8 51.7 + - - +
1478B GLY* 3.5 31.7 - - - +
1479B PHE 3.5 26.1 + - - +
1480B PRO* 3.9 7.9 - - + +
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Residues in contact with ALA1440 (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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1436B PHE 3.1 14.0 + - - +
1437B ASN* 3.6 12.1 - - - +
1438B ILE 3.2 0.4 - - - -
1439B LYS* 1.3 76.4 - - - +
1441B ARG* 1.3 62.1 + - + +
1442B ALA* 4.7 0.3 - - - -
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Residues in contact with ARG1441 (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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1401A PHE* 2.8 61.8 + - + -
1402A TYR* 4.0 6.1 - - - +
1404A THR* 3.1 28.3 + - - -
1405A HIS* 3.4 32.9 - - - +
1406A PRO* 4.5 8.2 - - - +
1409B MET* 5.9 5.4 + - - +
1410B THR* 3.6 38.0 - - + +
1411B GLN* 3.7 5.5 + - - -
1415B TYR* 4.1 13.6 + - - +
1437B ASN 3.6 12.9 + - - +
1438B ILE* 3.0 8.5 + - - +
1440B ALA* 1.3 80.3 - - + +
1442B ALA* 1.3 63.7 + - + +
1445B SER* 5.0 0.4 - - - +
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Residues in contact with ALA1442 (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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1410B THR 3.2 26.0 - - - +
1411B GLN* 3.6 21.3 - - - +
1438B ILE 3.3 4.8 + - - +
1439B LYS* 3.2 12.6 - - - +
1440B ALA 4.7 0.2 - - - -
1441B ARG* 1.3 78.5 - - - +
1443B SER* 1.3 64.9 + - - +
1444B SER* 4.1 8.5 - - - +
1445B SER* 2.6 30.2 + - - +
1480B PRO* 5.5 0.2 - - - +
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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