Contacts of the helix formed by residues 1434 - 1440 (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 THR1434 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1433E GLY* 1.3 73.2 - - - -
1435E ILE* 1.3 59.4 + - - +
1436E ARG* 3.8 13.9 - - + -
1437E PHE* 2.8 24.6 + - + +
1438E ASN* 2.4 43.0 + - - +
1470E LEU 3.2 1.7 + - - -
1471E ASP* 3.0 26.3 - - - +
1472E ALA 3.0 19.1 + - - -
1473E ILE* 5.7 1.8 - - - -
1474E ILE 5.0 0.2 - - - +
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Residues in contact with ILE1435 (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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1434E THR* 1.3 78.3 + - - +
1436E ARG* 1.3 59.9 + - - +
1438E ASN* 3.8 5.8 - - + +
1439E LEU* 2.9 49.0 + - + +
1450E LEU* 5.8 0.4 - - + -
1454E LEU* 4.7 10.5 - - + -
1463E VAL* 5.8 5.2 - - + -
1466E LEU* 6.5 1.6 - - + -
1470E LEU* 3.2 50.5 - - + +
1471E ASP 4.6 0.2 - - - +
1472E ALA* 5.1 7.9 - - + +
1474E ILE* 4.0 28.0 - - + -
1481E PHE* 6.0 1.3 - - + -
1489E PHE* 4.1 22.9 - - + -
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Residues in contact with ARG1436 (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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1434E THR* 3.8 11.7 - - + -
1435E ILE* 1.3 77.2 - - - +
1437E PHE* 1.3 57.2 + - - +
1440E ASP* 2.7 39.0 + - + +
1447E ASP* 2.7 44.1 + - - -
1450E LEU* 3.8 13.0 - - - -
1469E GLY 5.3 0.6 + - - -
1470E LEU* 3.2 23.2 + - + +
1471E ASP* 3.9 24.4 + - - +
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Residues in contact with PHE1437 (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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501E GLU* 5.9 0.9 - - - -
517E ILE* 5.8 0.7 - - + -
518E PHE* 3.5 33.9 - + - -
521E ARG* 3.3 54.1 - - - -
1431E PHE* 4.3 20.9 - + + +
1432E SER 4.1 17.9 - - - -
1433E GLY* 4.4 5.6 - - - -
1434E THR* 2.8 24.5 + - + +
1436E ARG* 1.3 75.6 - - - +
1438E ASN* 1.3 65.1 + - - +
1439E LEU 3.5 0.2 + - - -
1440E ASP 3.5 19.1 - - - +
1441E PRO* 3.9 15.1 - - + +
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Residues in contact with ASN1438 (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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514E TRP* 4.6 3.1 - - - -
1430E LEU* 5.1 0.8 - - + +
1431E PHE* 2.3 58.4 + - + +
1433E GLY* 3.6 4.4 - - - +
1434E THR* 2.4 48.8 + - - +
1435E ILE* 3.5 8.0 + - + +
1437E PHE* 1.3 72.2 - - - +
1439E LEU* 1.3 63.4 + - + +
1474E ILE* 3.1 29.6 - - + +
1489E PHE* 6.5 0.2 - - + -
1493E ARG* 3.4 23.8 + - - +
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Residues in contact with LEU1439 (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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514E TRP* 3.9 11.4 - - - -
1435E ILE* 2.9 37.9 + - + +
1438E ASN* 1.3 80.4 - - + +
1440E ASP* 1.3 65.9 + - - +
1441E PRO* 3.1 12.6 - - - +
1450E LEU* 3.9 33.0 - - + +
1453E ALA* 5.5 1.8 - - + -
1454E LEU* 4.7 13.0 - - + -
1489E PHE* 4.3 9.6 - - + +
1492E ALA* 4.2 6.3 - - + -
1493E ARG* 3.5 41.3 - - + +
1496E VAL* 4.0 18.7 - - + +
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Residues in contact with ASP1440 (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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1436E ARG* 2.7 28.1 + - + +
1437E PHE* 3.5 12.0 - - - -
1439E LEU* 1.3 74.8 - - - +
1441E PRO* 1.3 65.6 - - - +
1442E GLU* 2.9 21.4 - - + +
1443E ARG* 4.8 3.3 - - - -
1445E CYS* 3.2 37.0 - - - +
1450E LEU* 3.2 31.6 - - - +
1496E VAL* 3.8 12.0 - - - +
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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