Contacts of the helix formed by residues 495 - 504 (chain A) in PDB entry 4DK9
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 495 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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493A THR 3.8 0.4 + - - -
494A ALA* 1.3 73.0 - - - +
496A TRP* 1.3 82.1 + - - +
497A ARG* 3.0 32.3 + - - +
498A ASP* 3.1 28.3 + - + +
499A VAL* 3.3 13.6 + - - +
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Residues in contact with TRP 496 (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 ALA 3.4 3.8 + - - -
495A ASP* 1.3 83.0 + - - +
497A ARG* 1.3 76.3 + - + +
498A ASP 3.1 0.4 - - - -
499A VAL* 3.2 9.1 + - - -
500A SER* 2.8 52.8 + - - -
510A ASP* 3.4 31.6 - - + -
513A ALA* 3.5 9.5 - - + +
514A LYS* 3.8 47.0 - - + +
517A VAL* 4.2 6.7 - - + -
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Residues in contact with ARG 497 (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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495A ASP* 3.0 26.3 + - - +
496A TRP* 1.3 111.0 - - + +
498A ASP* 1.3 63.1 + - - +
500A SER* 3.5 4.3 - - - -
501A GLU* 3.2 26.7 + - - +
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Residues in contact with ASP 498 (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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484A LYS* 5.8 2.6 - - - +
485A TYR* 3.5 20.0 + - - +
495A ASP* 3.1 25.0 + - + +
496A TRP 3.1 0.4 - - - -
497A ARG* 1.3 79.7 - - - +
499A VAL* 1.3 65.9 + - - +
500A SER 3.1 1.1 - - - -
501A GLU* 3.1 29.8 + - - +
502A LEU* 3.4 11.3 + - - +
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Residues in contact with VAL 499 (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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481A PHE* 3.7 26.9 - - + -
485A TYR* 4.3 21.8 - - + +
494A ALA* 4.4 4.7 - - + -
495A ASP 3.4 15.0 - - - +
496A TRP* 3.2 1.5 + - - +
498A ASP* 1.3 75.1 - - - +
500A SER* 1.3 62.7 + - - +
502A LEU* 3.3 10.4 + - - +
503A LEU* 3.1 40.0 + - + +
513A ALA* 3.7 17.3 - - + -
516A ILE* 4.1 9.4 - - + -
517A VAL* 4.1 19.1 - - + -
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Residues in contact with SER 500 (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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496A TRP* 2.8 31.5 + - - -
497A ARG* 3.5 7.6 - - - -
499A VAL* 1.3 74.0 - - - +
501A GLU* 1.3 66.5 + - - +
503A LEU* 2.8 12.3 + - - +
504A LYS* 2.9 16.3 + - - +
509A TYR* 3.5 29.6 + - - -
510A ASP* 4.4 2.1 - - - +
513A ALA* 3.5 12.9 - - - +
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Residues in contact with GLU 501 (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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497A ARG* 3.2 15.0 + - - +
498A ASP* 3.1 24.1 + - - +
500A SER* 1.3 76.1 - - - +
502A LEU* 1.3 53.3 + - - +
504A LYS* 2.6 28.2 - - - +
505A PRO* 4.7 0.5 - - - +
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Residues in contact with LEU 502 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477A VAL* 3.7 33.3 - - + +
480A LYS* 4.5 14.1 - - + +
481A PHE* 4.0 42.8 - - + +
484A LYS* 5.4 5.8 - - + -
485A TYR* 4.9 10.5 - - + -
498A ASP 3.4 7.1 + - - +
499A VAL* 3.3 10.9 + - - +
500A SER 3.2 0.6 - - - -
501A GLU* 1.3 81.0 - - - +
503A LEU* 1.3 59.8 + - + +
504A LYS 3.1 8.4 - - - +
505A PRO* 4.1 5.5 - - - +
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Residues in contact with LEU 503 (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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465A PHE* 3.7 36.1 - - + -
477A VAL* 5.0 0.7 - - - -
499A VAL* 3.1 39.2 + - + +
500A SER 2.8 9.8 + - - +
502A LEU* 1.3 71.2 - - + +
504A LYS* 1.3 53.3 + - - +
506A LEU* 2.5 45.9 + - + +
509A TYR* 3.6 18.6 - - + +
512A ARG* 3.9 28.7 - - + +
513A ALA* 3.7 25.6 - - + +
516A ILE* 3.9 8.1 - - + -
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Residues in contact with LYS 504 (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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500A SER* 2.9 14.8 + - - +
501A GLU* 2.6 25.8 - - - +
502A LEU 3.1 1.9 - - - +
503A LEU* 1.3 70.1 - - - +
505A PRO* 1.3 66.3 - - + +
506A LEU 3.7 1.3 - - - +
509A TYR* 3.2 36.7 - - + +
7B T 5.0 5.2 - - - -
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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