Contacts of the helix formed by residues 1503 - 1527 (chain A) in PDB entry 5KHU
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 ASN1503 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1502A PRO* 3.8 29.4 - - - -
1504A ALA* 3.8 24.2 - - - +
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Residues in contact with ALA1504 (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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1503A ASN* 3.8 27.8 - - - +
1505A SER* 3.8 28.9 - - - +
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Residues in contact with SER1505 (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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1504A ALA* 3.8 26.0 - - - +
1506A VAL* 3.8 29.6 - - - +
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Residues in contact with VAL1506 (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 SER* 3.8 29.2 - - - +
1507A THR* 3.8 27.4 - - - +
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Residues in contact with THR1507 (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 VAL* 3.8 29.2 - - - +
1508A GLY* 3.8 26.9 - - - +
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Residues in contact with GLY1508 (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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1507A THR* 3.8 28.9 - - - +
1509A PRO* 3.8 29.4 - - - -
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Residues in contact with PRO1509 (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 GLY* 3.8 25.6 - - - -
1510A HIS* 3.7 29.2 - - - -
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Residues in contact with HIS1510 (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 PRO* 3.7 26.0 - - - -
1511A ASN* 3.7 30.3 - - - +
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Residues in contact with ASN1511 (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 HIS* 3.7 29.4 - - - +
1512A LEU* 3.7 27.1 - - - +
1514A THR* 4.4 17.0 - - - +
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Residues in contact with LEU1512 (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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1511A ASN* 3.7 29.6 - - - +
1513A GLU* 3.8 27.8 - - - +
1515A CYS* 4.6 14.6 - - - +
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Residues in contact with GLU1513 (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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1512A LEU* 3.8 22.9 - - - +
1514A THR* 3.7 30.3 - - - +
1516A LEU* 4.5 15.5 - - - +
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Residues in contact with THR1514 (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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1511A ASN* 4.4 18.8 - - - +
1513A GLU* 3.7 29.8 - - - +
1515A CYS* 3.8 26.2 - - - +
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Residues in contact with CYS1515 (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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1512A LEU* 4.6 12.3 - - - +
1514A THR* 3.8 29.6 - - - +
1516A LEU* 3.8 25.8 - - - +
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Residues in contact with LEU1516 (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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1513A GLU* 4.5 15.7 - - - +
1515A CYS* 3.8 26.2 - - - +
1517A SER* 3.8 29.2 - - - +
1519A VAL* 4.6 16.4 - - - +
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Residues in contact with SER1517 (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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1516A LEU* 3.8 26.2 - - - +
1518A VAL* 3.7 29.4 - - - +
1520A LEU* 4.7 13.2 - - - +
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Residues in contact with VAL1518 (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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1517A SER* 3.7 29.8 - - - +
1519A VAL* 3.7 25.6 - - - +
1521A LEU* 4.6 15.3 - - - +
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Residues in contact with VAL1519 (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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1516A LEU* 4.6 14.4 - - - +
1518A VAL* 3.7 25.6 - - - +
1520A LEU* 3.7 29.4 - - - +
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Residues in contact with LEU1520 (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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1517A SER* 4.7 15.0 - - - +
1519A VAL* 3.7 29.4 - - - +
1521A LEU* 3.8 25.6 - - - +
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Residues in contact with LEU1521 (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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1518A VAL* 4.6 15.7 - - - +
1520A LEU* 3.8 26.0 - - - +
1522A SER* 3.7 29.2 - - - +
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Residues in contact with SER1522 (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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1521A LEU* 3.7 30.1 - - - +
1523A LEU* 3.7 26.0 - - - +
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Residues in contact with LEU1523 (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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1522A SER* 3.7 27.1 - - - +
1524A ALA* 3.7 29.6 - - - +
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Residues in contact with ALA1524 (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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1523A LEU* 3.7 30.1 - - - +
1525A MET* 3.7 27.8 - - - +
1528A ALA* 4.4 15.9 - - - +
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Residues in contact with MET1525 (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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1524A ALA* 3.7 26.5 - - - +
1526A VAL* 3.7 29.2 - - - +
1528A ALA* 4.6 9.6 - - - +
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Residues in contact with VAL1526 (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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1473A GLY* 4.7 9.0 - - - +
1477A ALA* 3.7 23.8 - - - +
1478A GLY* 4.2 3.4 - - - +
1525A MET* 3.7 30.3 - - - +
1527A MET* 3.8 28.0 - - - +
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Residues in contact with MET1527 (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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1478A GLY* 3.9 11.9 - - - +
1480A GLU* 4.3 19.1 - - - +
1526A VAL* 3.8 26.0 - - - +
1528A ALA* 3.7 29.8 - - - +
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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