Contacts of the helix formed by residues 1512 - 1527 (chain F) in PDB entry 6C3P
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 ASP1512 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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713F GLY 3.4 12.4 - - - +
714F GLN* 3.1 25.2 + - - +
715F VAL* 3.1 32.2 + - + +
719F LYS* 5.4 1.8 - - - +
888F HIS* 3.9 25.6 + - + +
1510F SER 3.8 2.2 + - - -
1511F ILE* 1.3 73.6 - - - +
1513F MET* 1.3 60.2 + - - +
1514F ALA 4.2 2.0 + - - -
1515F THR* 3.2 26.3 + - - -
1516F GLU* 2.9 26.1 + - - +
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Residues in contact with MET1513 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888F HIS 4.0 10.6 + - - +
889F LYS* 3.8 13.7 - - + -
890F LEU* 3.5 51.4 - - + +
891F GLN* 5.0 11.9 - - + +
925F GLU* 5.5 6.5 - - - +
926F HIS 5.6 0.9 - - - +
929F THR* 3.9 31.4 - - - -
1512F ASP* 1.3 74.3 - - - +
1514F ALA* 1.3 67.5 + - - +
1516F GLU* 3.1 15.2 + - - +
1517F ASN* 2.8 35.8 + - - +
1538F ARG* 5.0 7.6 - - - +
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Residues in contact with ALA1514 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714F GLN* 3.7 29.8 - - - +
925F GLU* 3.2 26.8 + - + +
1512F ASP* 3.5 2.4 + - - +
1513F MET* 1.3 79.9 - - - +
1515F THR* 1.3 63.3 + - - +
1517F ASN* 3.2 6.0 + - - +
1518F ILE* 3.0 36.0 + - + +
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Residues in contact with THR1515 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714F GLN* 3.8 11.8 + - - +
715F VAL* 3.8 19.0 - - + +
1458F GLN* 4.6 17.9 - - + +
1488F LEU* 4.9 8.7 - - + -
1511F ILE* 3.8 12.3 - - + -
1512F ASP* 3.2 20.0 + - - -
1514F ALA* 1.3 74.3 - - - +
1516F GLU* 1.3 58.3 + - - +
1518F ILE* 4.5 8.0 - - - +
1519F LEU* 2.8 51.7 + - + +
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Residues in contact with GLU1516 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508F THR* 4.2 16.6 - - - -
1511F ILE* 3.3 15.7 - - + +
1512F ASP 2.9 20.0 + - - +
1513F MET* 3.1 24.8 + - - +
1515F THR* 1.3 75.6 - - - +
1517F ASN* 1.3 67.0 + - - +
1519F LEU* 3.9 2.8 - - - +
1520F GLN* 2.9 28.2 + - + +
1538F ARG* 3.1 33.5 + - - +
1540F HIS* 5.1 7.1 - - - +
1541F THR* 2.4 33.1 + - + +
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Residues in contact with ASN1517 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925F GLU* 5.3 1.0 - - - +
928F LYS* 4.9 13.6 - - - +
1513F MET* 2.8 29.9 + - - +
1514F ALA* 3.7 7.2 - - - +
1516F GLU* 1.3 78.3 - - - +
1518F ILE* 1.3 66.6 + - + +
1520F GLN* 3.9 3.1 - - - +
1521F LYS* 3.0 36.7 + - + +
1540F HIS* 3.6 30.6 + - - -
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Residues in contact with ILE1518 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714F GLN* 6.2 0.9 - - - +
1458F GLN* 4.1 24.5 - - + +
1514F ALA* 3.0 26.9 + - + +
1515F THR* 4.1 6.1 - - - +
1517F ASN* 1.3 79.6 - - + +
1519F LEU* 1.3 57.6 + - - +
1521F LYS* 3.6 9.6 - - + +
1522F VAL* 2.9 41.0 + - + +
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Residues in contact with LEU1519 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456F ILE 4.7 5.2 - - - +
1457F ALA* 4.1 4.3 - - - +
1458F GLN* 3.3 23.3 - - - +
1488F LEU* 3.4 35.0 - - + -
1491F LEU* 3.6 27.6 - - + -
1495F PHE* 5.0 5.6 - - + -
1504F MET* 6.0 2.9 - - + -
1508F THR* 6.5 1.1 - - - -
1511F ILE* 5.2 5.2 - - + -
1515F THR* 2.8 29.2 + - + +
1516F GLU* 3.9 2.9 - - - +
1518F ILE* 1.3 72.4 - - - +
1520F GLN* 1.3 66.0 + - + +
1522F VAL* 3.2 2.4 + - - +
1523F VAL* 2.9 42.0 + - + +
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Residues in contact with GLN1520 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1504F MET* 5.4 7.5 - - - -
1516F GLU* 2.9 19.6 + - + +
1517F ASN* 4.0 3.4 - - - +
1519F LEU* 1.3 80.6 - - + +
1521F LYS* 1.3 63.6 + - + +
1523F VAL* 3.1 16.9 - - - +
1524F MET* 2.9 58.4 + - + +
1534F THR* 4.9 11.2 - - - +
1541F THR* 3.2 36.3 + - + +
1544F SER* 4.6 7.6 - - - +
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Residues in contact with LYS1521 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517F ASN* 3.0 29.8 + - + +
1518F ILE* 3.6 8.7 - - + +
1520F GLN* 1.3 78.8 - - + +
1522F VAL* 1.3 64.4 + - + +
1524F MET* 3.6 4.8 - - - +
1525F THR* 3.0 31.8 + - + +
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Residues in contact with VAL1522 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456F ILE* 3.4 44.2 - - + +
1458F GLN* 3.8 14.1 - - - +
1518F ILE* 2.9 30.5 + - + +
1519F LEU 3.9 2.9 - - - +
1521F LYS* 1.3 76.8 - - + +
1523F VAL* 1.3 57.5 + - - +
1525F THR* 2.6 22.3 + - - +
1526F ALA* 2.9 16.2 + - + +
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Residues in contact with VAL1523 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456F ILE* 5.1 7.2 + - + +
1495F PHE* 4.3 11.9 - - + -
1504F MET* 4.2 23.6 - - + -
1519F LEU* 2.9 25.0 + - + +
1520F GLN* 3.1 36.8 - - - +
1522F VAL* 1.3 75.7 - - - +
1524F MET* 1.3 60.5 + - - +
1526F ALA* 4.8 3.1 - - - -
1527F PHE* 2.8 64.6 + - + +
1532F VAL* 5.6 2.5 - - + -
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Residues in contact with MET1524 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1373F LYS* 3.4 35.4 - - + -
1520F GLN* 2.9 54.4 + - + +
1521F LYS* 3.6 6.3 - - - +
1523F VAL* 1.3 76.2 - - - +
1525F THR* 1.3 58.4 + - + +
1527F PHE 3.2 4.9 - - - +
1528F ALA* 2.9 28.2 + - - +
1532F VAL* 6.2 3.1 - - + -
1534F THR* 4.6 13.0 - - + -
1541F THR 5.5 1.1 - - - +
1544F SER* 4.1 20.2 - - - +
1545F ALA* 5.1 5.2 - - + -
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Residues in contact with THR1525 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521F LYS* 3.0 17.6 + - + +
1522F VAL* 2.6 27.6 + - - +
1524F MET* 1.3 76.5 - - + +
1526F ALA* 1.3 56.7 + - - +
1528F ALA* 2.8 29.8 + - - +
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Residues in contact with ALA1526 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456F ILE* 4.6 22.2 - - + -
1522F VAL* 2.9 17.0 + - + +
1523F VAL* 4.5 2.5 - - - +
1525F THR* 1.3 78.5 + - - +
1527F PHE* 1.3 73.6 + - + +
1528F ALA 3.4 1.5 + - - -
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Residues in contact with PHE1527 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372F GLN* 4.7 3.6 - - - +
1456F ILE* 5.5 5.6 - - + -
1495F PHE* 3.9 33.4 - + + -
1497F ARG 5.0 6.7 - - - -
1498F LYS* 6.3 1.8 - - - -
1499F THR 5.2 4.7 - - - -
1502F PHE* 3.5 36.1 - + - -
1523F VAL* 2.8 40.1 + - + +
1524F MET* 3.2 8.4 - - - +
1526F ALA* 1.3 94.5 - - + +
1528F ALA* 1.3 63.7 + - - +
1529F ASP 3.2 2.5 - - - +
1530F ARG* 3.2 36.5 + - + +
1532F VAL* 4.4 7.1 - - + +
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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