Contacts of the helix formed by residues 513 - 523 (chain A) in PDB entry 5C8H
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 PHE 513 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A SER* 1.3 73.7 - - - +
514A GLN* 1.3 73.4 + - + +
516A PHE* 3.7 1.6 - + - +
517A TYR* 2.7 51.5 + + + +
529A ASP* 3.7 34.1 - - - -
532A LEU* 3.7 31.6 - - + -
533A ARG* 3.6 40.4 - - + +
536A LEU* 3.7 22.2 - - + -
554A VAL* 5.4 0.4 - - - +
555A GLU* 4.0 7.9 + - + +
557A LEU* 4.4 12.0 - - + +
601A UNX 4.0 14.8 - - - -
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Residues in contact with GLN 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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512A SER* 3.3 7.2 + - - +
513A PHE* 1.3 99.4 - - + +
515A ASP* 1.3 64.2 + - - +
517A TYR* 3.4 17.9 + - - +
518A GLN* 3.2 22.2 + - - +
529A ASP* 4.4 7.5 + - - -
533A ARG* 4.6 4.6 - - - +
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Residues in contact with ASP 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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511A LEU* 3.7 21.6 - - + +
512A SER* 3.1 26.3 + - - +
514A GLN* 1.3 78.7 - - - +
516A PHE* 1.3 64.3 + - - +
517A TYR 3.2 0.5 + - - -
518A GLN* 3.2 4.8 + - - +
519A GLN* 3.0 37.5 + - - +
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Residues in contact with PHE 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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491A ILE* 3.5 40.8 - - + -
494A LEU* 4.1 11.2 - - + -
495A LEU* 3.9 37.7 - - + -
498A TYR* 4.7 5.2 - + - -
511A LEU* 3.8 25.6 - - + -
512A SER 2.9 17.3 + - - +
513A PHE* 3.9 2.2 - - - +
515A ASP* 1.3 76.5 - - - +
517A TYR* 1.3 58.0 + - - +
519A GLN* 3.2 4.4 + - + +
520A CYS* 2.8 49.9 + - - -
532A LEU* 4.1 15.0 - - + -
536A LEU* 4.2 12.1 - - + -
557A LEU* 4.1 21.3 - - + -
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Residues in contact with TYR 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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513A PHE* 2.7 35.8 + + + +
514A GLN* 3.7 20.6 - - - +
516A PHE* 1.3 74.0 - - - +
518A GLN* 1.3 59.0 + - - +
520A CYS* 3.2 2.6 + - - +
521A ARG* 2.9 51.0 + - + +
526A VAL* 3.6 21.5 - - + -
527A ASN 3.3 7.6 + - - -
528A SER* 3.3 27.8 - - - -
529A ASP* 3.0 27.3 + - + +
532A LEU* 3.4 22.6 - - + +
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Residues in contact with GLN 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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514A GLN 3.2 11.0 + - - +
515A ASP* 3.5 9.9 - - - +
517A TYR* 1.3 77.7 - - - +
519A GLN* 1.3 67.0 + - - +
521A ARG* 2.8 38.4 + - - +
522A GLU* 2.9 66.7 + - - +
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Residues in contact with GLN 519 (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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494A LEU* 4.0 14.5 - - + +
498A TYR* 3.2 34.4 + - + +
511A LEU* 4.4 3.8 - - + -
515A ASP* 3.0 34.0 + - - +
516A PHE* 3.5 7.6 - - + +
518A GLN* 1.3 89.2 - - - +
520A CYS* 1.3 61.2 + - - +
522A GLU* 3.4 22.4 + - - +
523A ALA* 3.3 21.5 + - - +
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Residues in contact with CYS 520 (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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491A ILE* 4.1 17.7 - - - -
494A LEU* 4.1 11.2 - - - -
516A PHE* 2.8 60.0 + - - +
517A TYR* 3.5 5.4 - - - +
519A GLN* 1.3 73.6 - - - +
521A ARG* 1.3 60.7 + - - +
523A ALA 3.2 1.7 + - - -
524A PHE 3.2 3.8 + - - -
525A LEU* 3.0 36.1 + - + +
526A VAL* 3.8 17.9 - - + -
532A LEU* 4.2 5.4 - - + -
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Residues in contact with ARG 521 (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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517A TYR* 2.9 62.3 + - + +
518A GLN* 2.8 50.0 + - - +
520A CYS* 1.3 75.1 - - - +
522A GLU* 1.3 64.2 + - - +
524A PHE* 3.1 23.9 + - - -
526A VAL* 3.7 18.8 - - + +
527A ASN* 4.6 12.5 + - - +
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Residues in contact with GLU 522 (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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518A GLN* 2.9 45.9 + - - +
519A GLN* 3.5 25.2 + - - +
520A CYS 3.3 0.2 - - - -
521A ARG* 1.3 78.5 - - + +
523A ALA* 1.3 55.1 + - - +
524A PHE* 3.4 23.0 - - - -
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Residues in contact with ALA 523 (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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494A LEU* 4.7 8.7 - - + -
519A GLN 3.3 13.2 + - - +
520A CYS 3.2 5.2 + - - +
521A ARG 3.1 0.8 - - - -
522A GLU* 1.3 74.9 - - - +
524A PHE* 1.3 76.9 - - - +
525A LEU* 3.1 25.5 + - + +
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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