Contacts of the helix formed by residues 1512 - 1527 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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713E GLY 3.4 12.1 - - - +
714E GLN* 3.1 25.4 + - - +
715E VAL* 3.1 32.0 + - + +
719E LYS* 5.4 2.5 - - - +
888E HIS* 3.9 26.5 + - + +
1510E SER 3.8 2.6 + - - -
1511E ILE* 1.3 72.0 - - - +
1513E MET* 1.3 61.2 + - - +
1514E ALA 4.2 1.6 - - - -
1515E THR* 3.2 27.8 + - - -
1516E GLU* 2.9 26.4 + - - +
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Residues in contact with MET1513 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888E HIS 4.0 9.9 + - - +
889E LYS* 3.8 14.1 - - + -
890E LEU* 3.5 51.4 - - + +
891E GLN* 5.0 11.7 - - + +
925E GLU* 5.5 6.5 - - - +
926E HIS 5.6 1.3 - - - +
929E THR* 3.9 31.0 - - - -
1512E ASP* 1.3 74.1 - - - +
1514E ALA* 1.3 66.0 + - - +
1516E GLU* 3.1 17.6 + - - +
1517E ASN* 2.8 35.8 + - - +
1538E ARG* 5.0 7.0 - - - +
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Residues in contact with ALA1514 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714E GLN* 3.7 30.3 - - - +
925E GLU* 3.2 27.9 + - + +
1512E ASP* 3.5 2.2 + - - +
1513E MET* 1.3 79.4 - - - +
1515E THR* 1.3 63.5 + - - +
1517E ASN* 3.2 5.7 + - - +
1518E ILE* 3.0 37.1 + - + +
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Residues in contact with THR1515 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714E GLN* 3.8 11.8 + - - -
715E VAL* 3.8 19.9 - - + +
1458E GLN* 4.6 18.4 - - + +
1488E LEU* 4.9 8.7 - - + -
1511E ILE* 3.8 11.2 - - + -
1512E ASP* 3.2 20.7 + - - -
1514E ALA* 1.3 74.1 - - - +
1516E GLU* 1.3 58.6 + - - +
1518E ILE* 4.5 8.4 - - - +
1519E LEU* 2.8 51.0 + - + +
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Residues in contact with GLU1516 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1508E THR* 4.2 16.6 - - - -
1511E ILE* 3.3 14.4 - - + +
1512E ASP 2.9 21.2 + - - +
1513E MET* 3.1 25.0 + - - +
1515E THR* 1.3 77.0 - - - +
1517E ASN* 1.3 67.4 + - - +
1519E LEU* 3.9 2.7 - - - +
1520E GLN* 2.9 28.2 + - + +
1538E ARG* 3.1 35.2 + - - +
1540E HIS* 5.1 6.9 - - - +
1541E THR* 2.4 32.5 + - + +
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Residues in contact with ASN1517 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925E GLU* 5.3 1.4 - - - +
928E LYS* 4.9 13.4 - - - +
1513E MET* 2.8 30.6 + - - +
1514E ALA* 3.7 7.1 - - - +
1516E GLU* 1.3 77.8 - - - +
1518E ILE* 1.3 66.1 + - + +
1520E GLN* 3.9 2.9 - - - +
1521E LYS* 3.0 37.8 + - + +
1540E HIS* 3.6 30.6 + - - -
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Residues in contact with ILE1518 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714E GLN* 6.2 0.7 - - - +
1458E GLN* 4.1 24.7 - - + +
1514E ALA* 3.0 26.9 + - + +
1515E THR* 4.1 6.3 - - - +
1517E ASN* 1.3 77.2 - - + +
1519E LEU* 1.3 57.0 + - - +
1521E LYS* 3.6 9.1 - - + +
1522E VAL* 2.9 41.3 + - + +
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Residues in contact with LEU1519 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456E ILE 4.7 4.8 - - - +
1457E ALA* 4.1 3.6 - - - +
1458E GLN* 3.3 24.0 - - - +
1488E LEU* 3.4 34.8 - - + -
1491E LEU* 3.6 27.8 - - + -
1495E PHE* 5.0 6.1 - - + -
1504E MET* 6.0 2.9 - - + -
1508E THR* 6.5 1.3 - - - -
1511E ILE* 5.2 5.2 - - + -
1515E THR* 2.8 28.9 + - + +
1516E GLU* 3.9 2.7 - - - +
1518E ILE* 1.3 72.2 - - - +
1520E GLN* 1.3 66.6 + - + +
1522E VAL* 3.2 1.8 + - - +
1523E VAL* 2.9 42.7 + - + +
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Residues in contact with GLN1520 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1504E MET* 5.4 7.5 - - - -
1516E GLU* 2.9 19.4 + - + +
1517E ASN* 4.0 3.4 - - - +
1519E LEU* 1.3 81.2 - - + +
1521E LYS* 1.3 63.4 + - + +
1523E VAL* 3.1 16.0 - - - +
1524E MET* 2.9 57.4 + - + +
1534E THR* 4.9 11.0 - - - +
1541E THR* 3.2 35.9 - - + +
1544E SER* 4.6 7.4 - - - +
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Residues in contact with LYS1521 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1517E ASN* 3.0 32.2 + - + +
1518E ILE* 3.6 7.2 - - + +
1520E GLN* 1.3 78.2 - - + +
1522E VAL* 1.3 64.6 + - + +
1524E MET* 3.3 4.9 + - - +
1525E THR* 3.0 32.5 + - + +
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Residues in contact with VAL1522 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456E ILE* 3.4 43.7 - - + +
1458E GLN* 3.8 14.1 - - - +
1518E ILE* 2.9 28.8 + - + +
1519E LEU 3.2 3.3 + - - +
1521E LYS* 1.3 77.2 - - + +
1523E VAL* 1.3 57.3 + - - +
1525E THR* 2.6 21.8 + - - +
1526E ALA* 2.9 16.4 + - + +
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Residues in contact with VAL1523 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1456E ILE* 5.5 7.0 - - + +
1495E PHE* 4.3 12.6 - - + -
1504E MET* 4.2 22.7 - - + -
1519E LEU* 2.9 24.9 + - + +
1520E GLN* 3.1 36.8 - - - +
1522E VAL* 1.3 75.6 - - - +
1524E MET* 1.3 59.8 + - - +
1526E ALA* 4.6 2.9 - - - +
1527E PHE* 2.8 65.3 + - + +
1532E VAL* 5.6 2.2 - - + -
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Residues in contact with MET1524 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1373E LYS* 3.4 36.1 - - + -
1520E GLN* 2.9 53.6 + - + +
1521E LYS* 3.6 5.4 - - - +
1523E VAL* 1.3 77.0 - - - +
1525E THR* 1.3 59.7 + - + +
1527E PHE* 3.2 5.6 - - - +
1528E ALA* 2.9 27.4 + - - +
1532E VAL* 6.2 2.9 - - + -
1534E THR* 4.6 13.5 - - + +
1541E THR 5.5 1.1 - - - +
1544E SER* 4.1 19.7 - - - +
1545E ALA* 5.1 5.2 - - + -
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Residues in contact with THR1525 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521E LYS* 3.0 17.2 + - + +
1522E VAL* 2.6 27.1 + - - +
1524E MET* 1.3 77.0 - - + +
1526E ALA* 1.3 60.3 + - - +
1528E ALA* 2.8 29.7 + - - +
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Residues in contact with ALA1526 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456E ILE* 4.6 22.4 - - + -
1522E VAL* 2.9 16.4 + - + +
1523E VAL* 4.5 2.7 - - - +
1525E THR* 1.3 79.3 + - - +
1527E PHE* 1.3 74.4 + - + +
1528E ALA 3.4 1.3 + - - -
1529E ASP 5.3 0.5 + - - -
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Residues in contact with PHE1527 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372E GLN* 4.7 3.3 - - - +
1456E ILE* 5.5 5.2 - - + -
1495E PHE* 3.9 32.8 - + + -
1497E ARG 5.0 7.4 - - - -
1498E LYS* 6.3 2.0 - - - -
1499E THR 5.2 4.0 - - - -
1502E PHE* 3.5 36.6 - + - -
1523E VAL* 2.8 39.0 + - + +
1524E MET* 3.2 8.6 - - - +
1526E ALA* 1.3 95.0 - - + +
1528E ALA* 1.3 63.6 + - - +
1529E ASP 3.2 2.7 - - - +
1530E ARG* 3.2 35.0 + - + +
1532E 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
------------------------------------------------------------
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