Contacts of the helix formed by residues 1512 - 1527 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713H GLY 3.4 12.3 - - - +
714H GLN* 3.1 25.1 + - - +
715H VAL* 3.1 31.9 + - + +
719H LYS* 5.4 2.0 - - - +
888H HIS* 3.9 25.6 + - + +
1510H SER 3.8 2.2 + - - -
1511H ILE* 1.3 72.9 - - - +
1513H MET* 1.3 60.7 + - - +
1514H ALA 4.2 1.3 - - - -
1515H THR* 3.2 27.1 - - - -
1516H GLU* 2.9 26.8 + - - +
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Residues in contact with MET1513 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888H HIS 4.0 9.3 + - - +
889H LYS* 3.8 13.9 - - + -
890H LEU* 3.5 52.0 - - + +
891H GLN* 5.0 11.4 - - + +
925H GLU* 5.5 6.7 - - - +
926H HIS 5.6 1.6 - - - +
928H LYS* 6.6 0.2 - - + -
929H THR* 3.9 30.5 - - - -
1512H ASP* 1.3 74.1 - - - +
1514H ALA* 1.3 66.6 + - - +
1516H GLU* 3.1 15.9 + - - +
1517H ASN* 2.8 35.4 + - - +
1538H ARG* 5.0 7.4 - - - +
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Residues in contact with ALA1514 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714H GLN* 3.7 30.1 - - - +
925H GLU* 3.2 28.2 + - + +
1512H ASP* 3.5 2.2 + - - +
1513H MET* 1.3 80.4 - - - +
1515H THR* 1.3 62.9 + - - +
1517H ASN* 3.2 5.6 + - - +
1518H ILE* 3.0 36.6 + - + +
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Residues in contact with THR1515 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714H GLN* 3.8 12.0 + - - -
715H VAL* 3.8 20.5 - - + +
1458H GLN* 4.6 18.4 - - + +
1488H LEU* 4.9 8.3 - - + -
1511H ILE* 3.8 11.7 - - + -
1512H ASP* 3.2 19.9 + - - -
1514H ALA* 1.3 74.7 - - - +
1516H GLU* 1.3 58.7 + - - +
1518H ILE* 4.5 7.8 - - - +
1519H LEU* 2.8 51.3 + - + +
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Residues in contact with GLU1516 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1508H THR* 4.2 16.6 - - - -
1511H ILE* 3.3 14.9 - - + +
1512H ASP 2.9 20.5 + - - +
1513H MET* 3.2 24.2 - - - +
1515H THR* 1.3 75.4 - - - +
1517H ASN* 1.3 68.1 + - - +
1519H LEU* 3.9 2.5 - - - +
1520H GLN* 2.9 28.6 + - + +
1538H ARG* 3.1 33.4 + - - +
1540H HIS* 5.1 8.0 - - - +
1541H THR* 2.4 32.1 + - + +
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Residues in contact with ASN1517 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925H GLU* 5.3 1.0 - - - +
928H LYS* 4.9 13.6 - - - +
1513H MET* 2.8 32.7 + - - +
1514H ALA* 3.7 7.2 - - - +
1516H GLU* 1.3 75.5 - - - +
1518H ILE* 1.3 67.0 + - + +
1520H GLN* 3.9 3.1 - - - +
1521H LYS* 3.0 37.2 + - + +
1540H HIS* 3.6 30.2 + - - -
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Residues in contact with ILE1518 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714H GLN* 6.2 0.7 - - - +
1458H GLN* 4.1 24.2 - - + +
1514H ALA* 3.0 28.5 + - + +
1515H THR* 4.1 7.0 - - - +
1517H ASN* 1.3 78.1 - - + +
1519H LEU* 1.3 58.1 + - - +
1521H LYS* 3.4 9.1 + - + +
1522H VAL* 2.9 41.1 + - + +
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Residues in contact with LEU1519 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456H ILE 4.7 5.5 - - - +
1457H ALA* 4.1 4.7 - - - +
1458H GLN* 3.3 23.5 - - - +
1488H LEU* 3.4 34.5 - - + -
1491H LEU* 3.6 26.9 - - + -
1495H PHE* 5.0 6.1 - - + -
1504H MET* 6.0 3.4 - - + -
1508H THR* 6.5 1.1 - - - -
1511H ILE* 5.2 5.4 - - + -
1515H THR* 2.8 28.7 + - + +
1516H GLU* 3.9 2.9 - - - +
1518H ILE* 1.3 71.5 - - - +
1520H GLN* 1.3 66.9 + - + +
1522H VAL* 3.2 2.2 + - - +
1523H VAL* 2.9 42.1 + - + +
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Residues in contact with GLN1520 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1504H MET* 5.4 7.7 - - - -
1516H GLU* 2.9 19.4 + - + +
1517H ASN* 4.0 3.1 - - - +
1519H LEU* 1.3 81.0 - - + +
1521H LYS* 1.3 64.5 + - + +
1523H VAL* 3.1 16.9 - - - +
1524H MET* 2.9 59.3 + - + +
1534H THR* 4.9 11.3 - - - +
1541H THR* 3.2 36.9 + - + +
1544H SER* 4.6 7.4 - - - +
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Residues in contact with LYS1521 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517H ASN* 3.0 31.5 + - + +
1518H ILE* 3.6 8.3 - - + +
1520H GLN* 1.3 77.4 - - + +
1522H VAL* 1.3 64.4 + - + +
1524H MET* 3.6 4.6 - - - +
1525H THR* 3.0 32.8 + - + +
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Residues in contact with VAL1522 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456H ILE* 3.4 43.7 - - + +
1458H GLN* 3.8 15.0 - - - +
1518H ILE* 2.9 29.9 + - + +
1519H LEU 3.9 3.6 - - - +
1521H LYS* 1.3 77.7 - - + +
1523H VAL* 1.3 57.3 + - - +
1525H THR* 2.6 22.4 + - - +
1526H ALA* 2.9 15.5 + - + +
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Residues in contact with VAL1523 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456H ILE* 5.5 6.5 - - + +
1495H PHE* 4.3 12.1 - - + -
1502H PHE* 5.1 0.2 - - + -
1504H MET* 4.2 22.2 - - + -
1519H LEU* 2.9 25.5 + - + +
1520H GLN* 3.1 37.0 - - - +
1522H VAL* 1.3 75.4 - - - +
1524H MET* 1.3 60.8 + - - +
1526H ALA* 4.8 2.9 - - - -
1527H PHE* 2.8 65.2 + - + +
1532H VAL* 5.6 2.7 - - + -
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Residues in contact with MET1524 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373H LYS* 3.4 35.9 - - + -
1520H GLN* 2.9 52.9 + - + +
1521H LYS* 3.6 5.6 - - - +
1523H VAL* 1.3 77.2 - - - +
1525H THR* 1.3 59.1 + - + +
1527H PHE* 3.2 5.1 - - - +
1528H ALA* 2.9 28.2 + - - +
1532H VAL* 6.2 3.1 - - + -
1534H THR* 4.6 13.2 - - + -
1541H THR 5.5 0.4 - - - +
1544H SER* 4.1 19.3 - - - +
1545H ALA* 5.1 4.7 - - + -
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Residues in contact with THR1525 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521H LYS* 3.0 17.7 + - + +
1522H VAL* 2.6 26.7 + - - +
1524H MET* 1.3 76.7 - - + +
1526H ALA* 1.3 58.8 + - - +
1528H ALA* 2.8 29.9 + - - +
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Residues in contact with ALA1526 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456H ILE* 4.6 21.5 - - + -
1522H VAL* 2.9 16.7 + - + +
1523H VAL* 4.5 2.7 - - - +
1525H THR* 1.3 79.4 + - - +
1527H PHE* 1.3 74.0 + - + +
1528H ALA 3.4 1.0 + - - -
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Residues in contact with PHE1527 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372H GLN* 4.7 3.3 - - - +
1456H ILE* 5.5 5.6 - - + -
1495H PHE* 3.9 31.2 - + + -
1497H ARG 5.0 7.2 - - - -
1498H LYS* 6.3 1.6 - - - -
1499H THR 5.2 4.3 - - - -
1502H PHE* 3.5 37.0 - + - -
1523H VAL* 2.8 39.9 + - + +
1524H MET* 3.2 8.4 - - - +
1526H ALA* 1.3 94.2 - - + +
1528H ALA* 1.3 63.0 + - - +
1529H ASP* 3.2 2.7 - - - +
1530H ARG* 3.2 35.9 + - + +
1532H VAL* 4.4 6.8 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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