Contacts of the helix formed by residues 1506 - 1511 (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 GLU1506 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1426E GLN* 3.1 34.0 + - - +
1505E ASP* 1.3 66.8 - - - +
1507E ALA* 1.3 64.2 + - - +
1508E THR* 3.0 5.7 + - - +
1509E ALA* 3.1 10.5 + - - +
1535E ILE* 3.1 37.7 + - + +
1536E ALA* 4.2 0.4 - - - +
1537E HIS* 3.5 31.6 - - + +
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Residues in contact with ALA1507 (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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1424E ILE* 3.6 19.3 - - + -
1426E GLN 5.1 0.4 - - - -
1487E GLN* 3.3 19.3 + - - +
1491E LEU* 3.6 31.6 - - + -
1504E MET* 4.4 15.1 - - + +
1505E ASP 3.1 5.9 + - - +
1506E GLU* 1.3 76.6 - - - +
1508E THR* 1.3 59.7 + - - +
1509E ALA 3.2 1.4 + - - -
1510E SER 4.0 1.9 + - - -
1511E ILE* 3.1 19.0 - - - +
1535E ILE 4.2 2.0 + - - -
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Residues in contact with THR1508 (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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1491E LEU* 6.3 0.2 - - - -
1506E GLU* 3.0 2.0 + - - -
1507E ALA* 1.3 74.5 - - - +
1509E ALA* 1.3 63.8 + - - +
1510E SER 3.2 3.4 - - - -
1511E ILE* 2.9 34.0 + - - +
1516E GLU* 4.2 29.5 - - - +
1519E LEU* 6.5 1.1 - - - -
1536E ALA* 6.4 1.8 - - - -
1537E HIS 6.3 1.1 - - - -
1538E ARG* 4.8 11.5 + - - +
1541E THR* 4.9 8.3 - - - -
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Residues in contact with ALA1509 (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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857E SER* 3.6 33.2 + - - +
858E ALA 5.8 0.4 - - - +
888E HIS* 4.4 9.9 - - - +
1426E GLN* 3.6 17.3 - - - +
1506E GLU 3.1 15.8 + - - +
1507E ALA 3.2 0.4 - - - +
1508E THR* 1.3 77.9 - - - +
1510E SER* 1.3 62.5 + - - +
1511E ILE 3.4 3.8 + - - +
1537E HIS* 4.1 20.4 - - + +
1538E ARG* 5.0 11.3 + - - +
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Residues in contact with SER1510 (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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715E VAL* 5.0 1.0 - - - +
857E SER* 3.6 16.5 + - - -
888E HIS* 3.0 29.1 - - - -
1426E GLN 5.1 1.9 + - - -
1428E PRO* 4.9 5.9 - - - +
1483E GLN* 4.6 10.6 + - - +
1484E GLY* 4.2 19.9 + - - -
1487E GLN* 4.2 33.1 + - - +
1507E ALA 4.0 2.4 + - - -
1508E THR 3.2 0.8 - - - -
1509E ALA* 1.3 79.3 - - - +
1511E ILE* 1.3 59.0 + - - +
1512E ASP 3.8 0.3 + - - -
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Residues in contact with ILE1511 (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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715E VAL* 5.4 5.2 - - + -
888E HIS* 4.1 6.8 - - - +
1484E GLY* 4.9 2.0 - - - +
1487E GLN* 3.6 19.7 - - + -
1488E LEU* 3.5 28.7 - - + -
1491E LEU* 4.9 8.7 - - + -
1507E ALA 3.1 28.5 - - - +
1508E THR* 2.9 24.7 + - - +
1509E ALA 4.0 3.3 - - - +
1510E SER* 1.3 78.9 - - - +
1512E ASP* 1.3 83.7 + - - +
1515E THR* 3.8 10.3 - - + -
1516E GLU* 3.3 29.0 - - + +
1519E LEU* 5.2 4.7 - - + -
1538E ARG* 5.2 3.5 + - - -
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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