Contacts of the helix formed by residues 495 - 506 (chain A) in PDB entry 5DO7
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 GLU 495 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488A TRP* 4.7 1.5 - - - -
493A HIS* 3.4 13.9 + - + +
494A PRO* 1.3 77.2 - - - +
496A VAL* 1.3 103.3 + - - +
497A ALA* 4.1 13.9 - - + +
498A ARG* 2.8 26.9 + - + -
499A PHE* 3.0 9.6 + - - +
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Residues in contact with VAL 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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488A TRP* 4.1 22.6 - - + -
494A PRO 4.1 0.6 - - - -
495A GLU* 1.3 91.4 + - - +
497A ALA* 1.3 67.4 + - - +
499A PHE* 2.8 20.3 + - + +
500A GLY* 2.6 22.0 + - - +
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Residues in contact with ALA 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 GLU* 3.1 12.2 + - + +
496A VAL* 1.3 79.7 - - - +
498A ARG* 1.3 63.8 + - + +
500A GLY* 2.8 6.9 + - - +
501A TYR* 2.8 40.2 + - + -
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Residues in contact with ARG 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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487A TYR* 4.0 3.9 + - - +
493A HIS* 3.5 35.5 - - + +
495A GLU* 2.8 18.5 + - + +
497A ALA* 1.3 74.9 - - + +
499A PHE* 1.3 63.8 + - - +
501A TYR* 3.3 34.0 + - - -
502A PHE* 3.1 9.7 + - - +
578A ASN* 2.5 51.4 + - - +
581A TYR* 3.2 48.5 + - - -
620A PHE* 4.5 10.3 - - - -
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Residues in contact with PHE 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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480A MET* 4.8 8.3 - - - -
483A SER* 3.2 31.9 - - - -
484A SER* 3.4 35.2 - - - -
487A TYR* 3.6 35.4 + + + -
488A TRP* 3.3 26.2 - + + +
495A GLU 3.0 5.2 + - - +
496A VAL* 2.8 23.6 + - + +
498A ARG* 1.3 72.9 - - - +
500A GLY* 1.3 59.4 + - - +
502A PHE* 2.8 24.0 + - - +
503A SER* 2.8 27.2 + - - -
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Residues in contact with GLY 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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480A MET* 5.7 1.9 - - - +
496A VAL* 2.6 17.0 + - - -
497A ALA* 2.8 8.7 + - - -
499A PHE* 1.3 81.0 - - - +
501A TYR* 1.3 60.4 - - - -
503A SER* 3.3 6.2 + - - -
504A ALA* 3.2 20.3 + - - +
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Residues in contact with TYR 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 ALA* 2.8 28.9 + - + -
498A ARG* 3.3 40.9 + - - +
500A GLY* 1.3 70.5 - - - +
502A PHE* 1.3 52.6 + - - +
504A ALA* 2.8 8.7 + - + +
505A ALA* 2.8 35.5 + - - +
578A ASN* 3.4 15.7 - - + +
620A PHE* 4.0 22.8 - + + -
624A PHE* 3.7 28.2 - + + -
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Residues in contact with PHE 502 (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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423A LEU* 4.6 7.4 - - + -
426A PHE* 3.6 36.6 - + - -
482A PHE* 4.1 11.2 - + - -
483A SER* 4.2 11.2 - - - -
486A CYS* 6.3 0.2 - - + -
487A TYR* 3.6 50.0 - + + -
492A LEU* 4.2 11.7 - - + -
498A ARG 3.1 13.2 + - - +
499A PHE* 2.8 12.9 + + - +
501A TYR* 1.3 74.5 - - - +
503A SER* 1.3 62.6 + - - +
505A ALA* 3.8 0.6 - - - +
506A LEU* 3.4 43.3 + - + +
574A ILE* 6.3 0.2 - - - -
575A LEU* 3.6 26.7 - - + -
578A ASN* 3.7 9.3 - - - +
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Residues in contact with SER 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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479A THR* 3.4 25.3 - - - +
480A MET* 3.8 30.0 - - - +
483A SER* 2.7 34.5 + - - -
499A PHE* 2.8 22.3 + - - -
500A GLY* 3.7 9.9 - - - -
501A TYR 3.1 0.2 - - - -
502A PHE* 1.3 75.8 - - - +
504A ALA* 1.3 61.1 - - - +
506A LEU* 4.1 0.9 - - - -
507A LEU* 3.7 5.9 - - - +
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Residues in contact with ALA 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 GLY 3.2 10.9 + - - +
501A TYR* 2.8 11.2 + - + +
503A SER* 1.3 76.5 - - - +
505A ALA* 1.3 62.7 + - - +
506A LEU 3.3 1.0 + - - -
507A LEU* 3.5 5.9 + - - -
508A ALA 3.7 0.7 + - - -
624A PHE* 3.6 19.5 - - + -
628A TYR* 2.3 41.6 + - + +
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Residues in contact with ALA 505 (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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501A TYR 2.8 13.9 + - - +
502A PHE 3.6 0.9 + - - +
503A SER 3.4 0.2 - - - -
504A ALA* 1.3 79.9 - - - +
506A LEU* 1.3 58.9 + - - +
509A PRO* 2.9 23.4 - - - +
571A CYS* 3.6 12.4 - - - -
574A ILE* 4.0 19.1 - - + -
575A LEU* 3.7 32.8 - - + -
624A PHE* 4.1 5.1 - - + -
627A LEU* 3.8 10.7 - - + +
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Residues in contact with LEU 506 (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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393A ASN* 4.5 0.3 + - - -
426A PHE* 3.9 26.5 - - + -
427A VAL* 4.5 1.1 - - + +
430A THR* 3.9 26.4 - - + +
479A THR* 3.3 18.6 - - + +
482A PHE* 3.6 28.9 - - + -
502A PHE* 3.4 38.0 + - + +
503A SER 4.1 0.4 + - - -
505A ALA* 1.3 79.0 - - - +
507A LEU* 1.3 61.4 + - - +
508A ALA 3.4 0.9 - - - -
509A PRO* 3.7 5.2 - - + -
510A HIS* 3.7 16.1 + - - +
571A CYS* 4.6 4.5 - - - -
575A LEU* 3.7 26.5 - - + -
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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