Contacts of the helix formed by residues 1424 - 1430 (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 GLY1424 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1420B ASP 4.0 0.4 + - - +
1421B LEU 3.0 15.8 + - - +
1422B SER 3.4 1.4 - - - -
1423B LYS* 1.3 77.2 - - - +
1425B GLN* 1.3 61.6 + - - -
1426B ALA 3.2 2.7 - - - -
1427B GLU* 2.9 26.9 + - - +
1428B VAL 4.0 0.2 + - - -
1461B GLN* 3.9 20.2 - - - -
1465B CYS* 3.8 11.1 - - - -
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Residues in contact with GLN1425 (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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1424B GLY* 1.3 68.3 - - - -
1426B ALA* 1.3 68.5 + - - +
1427B GLU 3.1 0.2 - - - -
1428B VAL* 3.0 15.4 + - - +
1429B ASP* 3.1 11.3 + - - +
1461B GLN* 5.1 0.6 + - - +
1464B ALA* 4.0 33.0 + - + +
1465B CYS* 3.8 12.6 - - - -
1468B LYS* 3.2 41.3 + - + +
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Residues in contact with ALA1426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1423B LYS 4.6 9.0 - - - +
1424B GLY 3.1 0.4 + - - -
1425B GLN* 1.3 83.5 - - - +
1427B GLU* 1.3 62.9 + - - +
1429B ASP* 3.1 16.1 + - + +
1430B ALA* 2.8 26.5 + - - +
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Residues in contact with GLU1427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342B ASN* 4.8 8.7 + - - +
1345B SER* 6.0 1.2 - - - -
1419B TYR* 4.0 21.2 - - + +
1420B ASP* 3.4 31.2 + - - +
1423B LYS* 3.4 38.7 + - + +
1424B GLY 2.9 11.5 + - - +
1426B ALA* 1.3 78.9 - - - +
1428B VAL* 1.3 65.8 + - - +
1430B ALA* 3.3 15.3 + - - +
1431B MET* 3.3 23.7 + - - +
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Residues in contact with VAL1428 (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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1419B TYR* 4.0 18.2 - - + -
1425B GLN* 3.0 8.5 + - - +
1427B GLU* 1.3 74.3 - - - +
1429B ASP* 1.3 65.6 + - - +
1431B MET* 2.9 23.3 + - + +
1432B LYS* 3.7 5.5 + - - +
1449B LEU* 5.9 0.2 - - + -
1465B CYS* 3.6 42.2 - - + +
1468B LYS* 3.8 23.3 - - + -
1469B ILE* 3.8 13.0 - - + +
1473B LEU* 3.7 29.9 - - + +
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Residues in contact with ASP1429 (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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1425B GLN* 3.1 9.6 + - - +
1426B ALA* 3.1 17.6 - - - +
1428B VAL* 1.3 76.9 - - - +
1430B ALA* 1.3 60.0 + - - +
1432B LYS* 3.0 52.4 + - - +
1433B PRO* 3.6 3.8 - - - +
1468B LYS* 3.2 29.5 + - - +
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Residues in contact with ALA1430 (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* 4.8 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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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