Contacts of the helix formed by residues 500 - 513 (chain A) in PDB entry 4OT9
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 GLN 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A ALA* 2.9 22.9 + - - +
498A HIS* 2.7 28.7 + - + +
499A GLY* 1.3 67.3 - - - +
501A THR* 1.3 54.7 + - - +
502A SER* 3.1 10.3 - - - -
503A VAL* 2.8 42.3 + - + +
504A ILE* 3.2 11.3 + - - +
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Residues in contact with THR 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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499A GLY 2.4 25.2 + - - +
500A GLN* 1.3 69.6 - - - +
502A SER* 1.3 67.6 + - - +
504A ILE* 3.4 15.1 + - - +
505A GLU* 2.9 40.5 + - - +
539A GLN* 5.6 2.9 - - - -
542A VAL* 5.5 8.1 - - - +
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Residues in contact with SER 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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500A GLN* 3.1 8.9 - - - -
501A THR* 1.3 84.2 - - - +
503A VAL* 1.3 63.4 + - - +
505A GLU* 3.1 23.7 - - - +
506A GLN* 2.9 17.2 + - - +
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Residues in contact with VAL 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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474A LEU* 6.3 1.8 - - + -
495A ALA* 4.0 11.2 - - + -
500A GLN* 2.8 34.0 + - + +
502A SER* 1.3 68.5 - - - +
504A ILE* 1.3 67.1 + - - +
505A GLU 2.6 6.1 + - - -
506A GLN* 2.6 28.3 + - + +
507A ILE* 3.0 38.6 + - + -
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Residues in contact with ILE 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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492A LEU* 3.8 22.4 - - + -
495A ALA* 3.6 22.7 - - + +
496A ILE* 3.3 37.0 - - + +
500A GLN 3.2 8.0 + - - +
501A THR* 3.4 12.5 + - - +
503A VAL* 1.3 74.5 - - - +
505A GLU* 1.3 65.6 + - - +
507A ILE* 4.1 2.7 - - - -
508A VAL* 3.2 29.8 + - + +
539A GLN* 4.9 2.5 - - - +
542A VAL* 4.0 34.8 - - + -
545A PHE* 3.7 9.0 - - + -
546A LEU* 4.9 1.8 - - + -
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Residues in contact with GLU 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A ARG* 5.9 0.2 - - - -
501A THR* 2.9 35.8 + - - +
502A SER* 3.1 13.9 - - - +
503A VAL 2.6 4.0 + - - -
504A ILE* 1.3 77.1 - - - +
506A GLN* 1.3 64.5 + - + +
508A VAL* 3.8 3.5 - - - +
509A TYR* 3.3 17.0 + - - +
545A PHE* 4.0 25.4 - - - -
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Residues in contact with GLN 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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470A ALA* 3.0 39.6 + - - +
471A ARG* 3.5 33.8 - - + +
474A LEU* 5.1 8.2 - - + +
502A SER* 2.9 27.1 + - - +
503A VAL* 2.6 27.8 + - + +
505A GLU* 1.3 70.0 - - + +
507A ILE* 1.3 67.7 + - + +
509A TYR* 2.7 23.2 + - - +
510A VAL* 3.0 11.7 + - - +
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Residues in contact with ILE 507 (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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474A LEU* 4.4 19.5 - - + +
481A LEU* 4.8 11.4 - - + -
491A PRO* 4.0 13.2 - - + -
492A LEU* 3.4 63.5 - - + +
495A ALA* 4.7 0.7 - - + -
503A VAL* 3.0 35.8 + - + +
504A ILE 4.1 2.5 - - - +
506A GLN* 1.3 80.1 - - + +
508A VAL* 1.3 65.7 + - - +
510A VAL* 3.1 9.8 + - - +
511A ILE* 3.0 33.1 + - + +
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Residues in contact with VAL 508 (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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492A LEU* 4.6 10.3 - - + -
504A ILE* 3.2 27.3 + - + +
505A GLU 3.8 0.2 - - - +
507A ILE* 1.3 80.3 - - - +
509A TYR* 1.3 58.3 + - - +
511A ILE* 3.3 7.4 + - + +
512A HIS* 2.8 29.4 + - + +
520A VAL* 5.6 3.4 - - + -
545A PHE* 3.5 33.9 - - + -
546A LEU* 4.3 17.5 - - + -
549A VAL* 3.4 33.9 - - + -
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Residues in contact with TYR 509 (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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471A ARG* 3.0 58.5 + - + -
505A GLU 3.3 9.3 + - - +
506A GLN* 2.7 19.5 + - - +
508A VAL* 1.3 76.0 - - - +
510A VAL* 1.3 58.2 + - + +
512A HIS* 3.3 8.4 + - + +
513A HIS* 2.9 64.8 + + + +
545A PHE* 5.3 0.9 - - - -
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Residues in contact with VAL 510 (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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471A ARG* 4.3 17.3 - - + +
474A LEU* 3.6 24.2 - - + -
475A ALA* 3.7 27.8 - - + +
478A ARG* 3.8 25.1 - - + +
481A LEU* 4.3 8.1 - - + -
506A GLN* 3.3 15.7 - - - +
507A ILE 3.4 4.9 - - - +
509A TYR* 1.3 80.7 - - + +
511A ILE* 1.3 63.7 + - - +
513A HIS* 3.5 3.7 + - - -
514A ALA* 3.1 24.9 + - - +
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Residues in contact with ILE 511 (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 LEU* 3.8 32.3 - - + -
492A LEU* 5.5 0.4 - - + -
507A ILE* 3.0 23.7 + - + +
508A VAL* 3.6 8.5 - - + +
510A VAL* 1.3 78.7 - - + +
512A HIS* 1.3 62.6 + - - +
514A ALA* 3.3 9.1 + - - -
515A GLN* 3.3 0.3 + - - -
516A ASP* 3.1 55.8 + - + +
517A LEU* 3.7 10.4 + - + -
519A VAL* 3.2 27.8 - - + -
520A VAL* 3.6 21.5 - - + -
549A VAL* 6.4 0.2 - - + -
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Residues in contact with HIS 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A VAL* 2.8 21.9 + - + +
509A TYR* 3.7 9.7 - - + +
511A ILE* 1.3 74.3 - - - +
513A HIS* 1.3 59.8 + - - +
514A ALA 3.0 5.5 + - - -
515A GLN* 3.4 10.7 + - - +
517A LEU* 4.0 16.9 - - + +
549A VAL* 3.5 34.0 - - + +
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Residues in contact with HIS 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A TYR* 2.9 51.7 + + + +
510A VAL* 3.6 3.8 - - - +
512A HIS* 1.3 76.8 - - + +
514A ALA* 1.3 58.1 + - - +
515A GLN* 3.8 6.7 - - - +
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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