Contacts of the helix formed by residues 511 - 518 (chain A) in PDB entry 6O0T
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 ASP 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A ARG* 6.5 0.2 - - + -
485A SER* 3.1 26.2 - - - +
487A LEU* 3.8 10.8 - - - -
509A GLY 5.0 1.1 - - - +
510A LEU* 1.3 75.4 - - - +
512A ARG* 1.3 65.9 + - - +
513A SER* 3.2 16.0 + - - -
514A LEU* 3.0 41.2 + - - +
515A LEU* 3.2 16.3 + - - +
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Residues in contact with ARG 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A SER* 3.0 29.7 + - - +
486A ASN* 2.9 35.1 + - - +
487A LEU* 3.7 17.5 - - + +
489A ASP* 4.2 3.6 - - - +
490A TRP* 3.6 41.0 - - + +
511A ASP* 1.3 75.5 - - - +
513A SER* 1.3 63.5 + - - +
514A LEU 3.2 1.0 + - - -
515A LEU* 3.5 16.5 + - + +
516A HIS* 4.9 2.1 + - - -
545A MSE 4.7 22.8 - - + +
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Residues in contact with SER 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A SER* 6.0 0.3 - - - -
511A ASP* 3.2 17.5 + - - -
512A ARG* 1.3 80.0 - - - +
514A LEU* 1.3 63.8 + - - +
516A HIS* 3.0 27.2 + - - -
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Residues in contact with LEU 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A GLY 3.3 16.2 - - - +
510A LEU* 3.9 15.9 - - + +
511A ASP* 3.0 22.6 + - - +
513A SER* 1.3 85.0 - - - +
515A LEU* 1.3 64.9 + - - +
516A HIS* 3.2 4.7 - - - -
517A ARG* 3.1 40.3 + - + +
518A VAL* 3.3 11.7 - - - +
537B ARG* 3.3 46.2 - - - +
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Residues in contact with LEU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A LEU* 3.6 25.8 - - + -
490A TRP* 3.5 42.6 - - + -
505A MSE 4.2 31.0 - - + -
510A LEU* 5.0 4.5 - - + -
511A ASP 3.2 17.1 + - - +
512A ARG* 3.5 13.9 + - + +
514A LEU* 1.3 77.7 - - - +
516A HIS* 1.3 62.9 + - - +
517A ARG 3.1 1.0 + - - -
518A VAL* 3.2 26.6 + - + +
523A MSE 5.1 2.6 - - + +
538A ILE* 5.3 4.0 - - + -
539A LEU* 5.6 0.3 - - - +
542A ALA* 3.8 21.2 - - + +
545A MSE 5.2 4.9 - - - -
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Residues in contact with HIS 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A ARG 4.9 1.8 + - - -
513A SER 3.0 27.7 + - - -
514A LEU* 4.7 0.2 - - - -
515A LEU* 1.3 78.0 - - - +
517A ARG* 1.3 91.7 + - + +
518A VAL 3.4 3.1 + - - +
542A ALA* 3.7 25.5 + - - +
543A ARG* 5.0 5.9 - - - +
545A MSE 6.0 2.6 - - + -
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Residues in contact with ARG 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A LEU* 3.1 29.8 + - + +
516A HIS* 1.3 107.9 + - + +
518A VAL* 1.3 62.9 + - - +
519A SER* 3.8 1.2 + - - -
522A GLN* 3.8 10.4 + - - +
536B ALA* 5.5 3.5 - - - +
537B ARG* 5.2 10.1 - - - +
540B THR* 4.4 22.3 - - - +
544B GLU* 4.9 9.3 + - - -
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Residues in contact with VAL 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505A MSE 4.7 0.7 - - + -
510A LEU* 3.7 40.4 - - + -
514A LEU 3.3 18.2 - - - +
515A LEU* 3.2 20.8 + - + +
516A HIS 4.6 2.9 - - - +
517A ARG* 1.3 78.8 - - - +
519A SER* 1.3 72.3 + - - +
522A GLN* 3.3 18.2 - - + +
523A MSE 3.7 26.5 - - + +
527A CYS* 5.1 0.2 - - - -
539A LEU* 3.1 21.2 - - - +
533B VAL* 4.8 1.1 - - + -
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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
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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