Contacts of the helix formed by residues 1512 - 1527 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713G GLY 3.4 12.0 - - - +
714G GLN* 3.1 25.4 + - - +
715G VAL* 3.1 33.4 + - + +
719G LYS* 5.4 2.2 - - - +
888G HIS* 3.9 25.0 + - - +
1510G SER 3.8 2.6 + - - -
1511G ILE* 1.3 72.4 - - - +
1513G MET* 1.3 61.1 + - - +
1514G ALA 4.2 1.8 - - - -
1515G THR* 3.2 26.7 + - - -
1516G GLU* 2.9 27.3 + - - +
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Residues in contact with MET1513 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888G HIS 4.0 10.0 + - - +
889G LYS* 3.8 12.3 - - + -
890G LEU* 3.5 51.1 - - + +
891G GLN* 5.0 11.7 - - + +
925G GLU* 5.5 7.2 - - - +
926G HIS 5.6 1.3 - - - +
928G LYS* 6.6 0.2 - - + -
929G THR* 3.9 30.5 - - - -
1512G ASP* 1.3 74.2 - - - +
1514G ALA* 1.3 66.2 + - - +
1516G GLU* 3.1 17.4 + - - +
1517G ASN* 2.8 36.4 + - - +
1538G ARG* 5.0 8.1 - - - +
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Residues in contact with ALA1514 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714G GLN* 3.7 29.8 - - - +
925G GLU* 3.2 28.4 + - + +
1512G ASP* 3.5 1.6 + - - +
1513G MET* 1.3 79.7 - - - +
1515G THR* 1.3 62.5 + - - +
1517G ASN* 3.2 5.7 + - - +
1518G ILE* 3.0 37.8 + - + +
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Residues in contact with THR1515 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714G GLN* 3.8 11.8 + - - -
715G VAL* 3.8 20.2 - - + +
1458G GLN* 4.6 18.2 - - + +
1488G LEU* 4.9 8.3 - - + -
1511G ILE* 3.8 11.0 - - + -
1512G ASP* 3.2 20.5 + - - -
1514G ALA* 1.3 74.7 - - - +
1516G GLU* 1.3 60.0 + - - +
1518G ILE* 4.5 8.3 - - - +
1519G LEU* 2.8 51.0 + - + +
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Residues in contact with GLU1516 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508G THR* 4.2 17.2 - - - -
1511G ILE* 3.3 14.3 - - + +
1512G ASP 2.9 20.4 + - - +
1513G MET* 3.1 24.2 + - - +
1515G THR* 1.3 76.4 - - - +
1517G ASN* 1.3 66.7 + - - +
1519G LEU* 3.9 2.9 - - - +
1520G GLN* 2.9 27.8 + - - +
1538G ARG* 3.1 33.5 + - - +
1540G HIS* 5.1 7.9 - - - +
1541G THR* 2.4 31.3 + - + +
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Residues in contact with ASN1517 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925G GLU* 5.3 1.2 - - - +
928G LYS* 4.9 13.7 - - - +
1513G MET* 2.8 29.7 + - - +
1514G ALA* 3.7 7.7 - - - +
1516G GLU* 1.3 79.5 - - - +
1518G ILE* 1.3 67.7 + - + +
1520G GLN* 3.9 3.2 - - - +
1521G LYS* 3.0 38.0 + - + +
1540G HIS* 3.6 31.0 + - - -
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Residues in contact with ILE1518 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714G GLN* 6.2 0.4 - - - +
1458G GLN* 4.1 24.2 - - + +
1514G ALA* 3.0 26.7 + - + +
1515G THR* 4.1 6.7 - - - +
1517G ASN* 1.3 77.5 - - + +
1519G LEU* 1.3 59.0 + - - +
1521G LYS* 3.4 9.1 + - + +
1522G VAL* 2.9 41.5 + - + +
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Residues in contact with LEU1519 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456G ILE 4.7 5.3 - - - +
1457G ALA* 4.1 4.0 - - - +
1458G GLN* 3.3 23.5 - - - +
1488G LEU* 3.4 34.5 - - + -
1491G LEU* 3.6 26.9 - - + -
1495G PHE* 5.0 5.8 - - + -
1504G MET* 6.0 3.4 - - + -
1508G THR* 6.5 1.3 - - - -
1511G ILE* 5.2 5.2 - - + -
1515G THR* 2.8 29.2 + - + +
1516G GLU* 3.9 3.1 - - - +
1518G ILE* 1.3 72.0 - - - +
1520G GLN* 1.3 67.1 + - + +
1522G VAL* 3.2 2.0 + - - +
1523G VAL* 2.9 42.5 + - + +
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Residues in contact with GLN1520 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1504G MET* 5.4 7.7 - - - -
1516G GLU* 2.9 19.0 + - + +
1517G ASN* 4.0 3.4 - - - +
1519G LEU* 1.3 81.5 - - + +
1521G LYS* 1.3 63.4 + - + +
1523G VAL* 3.1 17.5 - - - +
1524G MET* 2.9 58.0 + - + +
1534G THR* 4.9 11.1 - - - +
1541G THR* 3.2 35.8 - - + +
1544G SER* 4.6 8.1 - - - +
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Residues in contact with LYS1521 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517G ASN* 3.0 31.5 + - + +
1518G ILE* 3.6 7.9 - - + +
1520G GLN* 1.3 78.0 - - + +
1522G VAL* 1.3 64.9 + - + +
1524G MET* 3.3 5.1 + - - +
1525G THR* 3.0 31.4 + - + +
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Residues in contact with VAL1522 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456G ILE* 3.4 43.5 - - + +
1458G GLN* 3.8 14.6 - - - +
1518G ILE* 2.9 28.8 + - + +
1519G LEU 3.2 3.3 + - - +
1521G LYS* 1.3 77.7 - - + +
1523G VAL* 1.3 57.3 + - - +
1525G THR* 2.6 22.7 + - - +
1526G ALA* 2.9 15.7 + - + +
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Residues in contact with VAL1523 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456G ILE* 5.5 7.2 - - + +
1495G PHE* 4.3 12.3 - - + -
1504G MET* 4.2 22.7 - - + -
1519G LEU* 2.9 23.6 + - + +
1520G GLN* 3.1 37.2 - - - +
1522G VAL* 1.3 76.1 - - - +
1524G MET* 1.3 60.0 + - - +
1526G ALA* 4.6 3.1 - - - +
1527G PHE* 2.8 65.8 + - + +
1532G VAL* 5.6 2.2 - - + -
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Residues in contact with MET1524 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373G LYS* 3.4 35.0 - - + -
1520G GLN* 2.9 54.9 + - + +
1521G LYS* 3.6 6.5 - - - +
1523G VAL* 1.3 78.1 - - - +
1525G THR* 1.3 58.2 + - + +
1527G PHE* 3.2 6.2 - - - +
1528G ALA* 2.9 27.4 + - - +
1532G VAL* 6.2 2.9 - - + -
1534G THR* 4.6 13.2 - - + -
1541G THR 5.5 0.9 - - - +
1544G SER* 4.1 20.4 - - - +
1545G ALA* 5.1 4.9 - - + -
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Residues in contact with THR1525 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521G LYS* 3.0 17.5 + - + +
1522G VAL* 2.6 26.7 + - - +
1524G MET* 1.3 75.6 - - + +
1526G ALA* 1.3 57.1 + - - +
1528G ALA* 2.8 29.4 + - - +
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Residues in contact with ALA1526 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456G ILE* 4.6 21.5 - - + -
1522G VAL* 2.9 17.6 + - + +
1523G VAL* 4.5 2.7 - - - +
1525G THR* 1.3 79.1 + - - +
1527G PHE* 1.3 75.5 + - + +
1528G ALA 3.4 1.3 + - - -
1529G ASP 5.3 0.3 + - - -
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Residues in contact with PHE1527 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372G GLN* 4.7 3.1 - - - +
1456G ILE* 5.5 5.6 - - + -
1495G PHE* 3.9 32.1 - + + -
1497G ARG 5.0 7.4 - - - -
1498G LYS* 6.3 1.6 - - - -
1499G THR 5.2 4.7 - - - -
1502G PHE* 3.5 36.6 - + - -
1523G VAL* 2.8 39.7 + - + +
1524G MET* 3.2 8.6 - - - +
1526G ALA* 1.3 94.1 - - + +
1528G ALA* 1.3 62.7 + - - +
1529G ASP 3.2 2.5 - - - +
1530G ARG* 3.2 37.1 + - + +
1532G VAL* 4.4 7.2 - - + +
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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
------------------------------------------------------------
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