Contacts of the helix formed by residues 508 - 524 (chain A) in PDB entry 6V3O
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 THR 508 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506A PRO 4.3 1.1 + - - +
507A GLN* 1.3 76.3 - - - +
509A GLU* 1.3 60.5 + - - +
510A GLU* 3.4 8.2 + - - +
511A ILE* 3.2 35.6 + - + +
512A ALA* 2.9 27.8 + - - +
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Residues in contact with GLU 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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508A THR* 1.3 75.5 - - - +
510A GLU* 1.3 58.6 + - + +
512A ALA* 3.6 6.9 + - - +
513A ASP* 3.0 27.5 + - - +
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Residues in contact with GLU 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ARG* 2.7 60.1 + - - +
464A ASP* 4.5 7.6 - - - +
508A THR* 3.2 7.4 + - - +
509A GLU* 1.3 77.0 - - + +
511A ILE* 1.3 65.6 + - + +
513A ASP* 3.2 8.2 + - - -
514A VAL* 3.2 6.6 + - - +
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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
----------------------------------------------------------
461A ARG 5.6 0.7 - - - +
464A ASP* 3.7 21.5 - - + +
465A VAL* 4.2 26.4 - - + +
468A ALA* 3.6 28.3 - - + -
505A LEU* 4.8 4.7 - - + -
506A PRO 5.0 0.9 - - - +
507A GLN* 3.9 22.9 - - + -
508A THR* 3.2 32.1 + - + +
510A GLU* 1.3 77.5 - - + +
512A ALA* 1.3 63.5 + - - +
514A VAL* 3.1 4.3 + - - +
515A ILE* 3.0 34.2 + - + +
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Residues in contact with ALA 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PRO* 5.3 0.3 - - - +
507A GLN* 3.2 27.6 + - + +
508A THR 2.9 17.3 + - - +
509A GLU* 3.8 7.9 - - - +
511A ILE* 1.3 77.6 - - - +
513A ASP* 1.3 53.0 + - - +
515A ILE* 4.0 1.2 - - - +
516A GLY* 2.7 32.2 + - - -
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Residues in contact with ASP 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 4.2 12.0 + - - +
297A PRO* 5.0 8.4 - - - +
299A VAL 4.1 9.8 - - - +
300A THR* 4.6 10.2 - - - +
301A PRO* 3.8 26.9 - - - +
457A GLN* 5.1 1.7 + - - -
461A ARG* 3.8 11.1 + - - +
509A GLU 3.0 15.1 + - - +
510A GLU* 3.4 10.5 - - - +
511A ILE 3.1 0.6 - - - -
512A ALA* 1.3 74.8 - - - +
514A VAL* 1.3 59.8 + - - +
517A ALA* 3.0 27.9 + - - +
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Residues in contact with VAL 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 6.3 0.9 - - - +
457A GLN* 3.9 17.5 - - + +
461A ARG* 3.6 33.9 - - + +
462A HIS* 4.0 17.3 - - + +
465A VAL* 4.0 17.3 - - + -
510A GLU 3.2 12.5 + - - +
511A ILE 3.1 6.5 + - - +
513A ASP* 1.3 75.8 - - - +
515A ILE* 1.3 66.4 + - + +
517A ALA* 3.3 6.8 + - - +
518A PHE* 3.1 50.2 + - + -
532A TYR* 4.7 2.9 - - - +
549A LEU* 5.0 1.6 - - + -
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Residues in contact with ILE 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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465A VAL* 4.3 15.3 - - + -
501A LEU* 4.0 26.7 - - + -
505A LEU* 4.2 5.2 - - + -
507A GLN* 3.7 35.7 - - - +
511A ILE* 3.0 26.8 + - + +
512A ALA 4.0 2.9 - - - +
514A VAL* 1.3 75.5 - - + +
516A GLY* 1.3 61.7 + - - +
518A PHE* 3.2 6.7 + - - +
519A HIS* 3.1 41.9 + - + +
549A LEU* 6.1 0.2 - - + -
553A CYS* 4.2 19.5 - - - -
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Residues in contact with GLY 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PRO* 3.6 13.1 - - - +
512A ALA 2.7 22.7 + - - -
513A ASP 4.0 0.7 - - - -
515A ILE* 1.3 73.8 - - - +
517A ALA* 1.3 61.9 - - - +
519A HIS* 3.2 12.9 + - - +
520A VAL* 3.1 25.1 + - - +
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Residues in contact with ALA 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 3.7 32.3 - - - +
301A PRO* 3.5 10.4 - - - +
455A ILE* 5.9 3.8 - - + -
513A ASP 3.0 19.6 + - - +
514A VAL* 3.5 7.4 - - - +
516A GLY* 1.3 76.1 - - - +
518A PHE* 1.3 64.2 + - + +
520A VAL* 3.1 7.1 + - - +
521A LEU* 3.0 27.4 + - + +
532A TYR* 5.9 5.6 - - + +
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Residues in contact with PHE 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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462A HIS* 4.5 1.6 - + - -
514A VAL* 3.1 43.2 + - + -
515A ILE* 3.2 4.3 + - - +
517A ALA* 1.3 80.3 - - + +
519A HIS* 1.3 64.0 + - - +
521A LEU* 3.2 19.8 + - + +
522A ALA* 2.9 18.0 + - - +
532A TYR* 3.4 37.9 - + - -
546A VAL* 3.6 24.0 - - + -
549A LEU* 3.9 22.4 - - + -
550A GLN* 4.2 23.8 - - + -
553A CYS* 3.5 31.9 - - + -
555A VAL* 3.6 11.5 - - + +
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Residues in contact with HIS 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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501A LEU* 4.9 6.9 - - + +
515A ILE* 3.1 29.5 + - + +
516A GLY* 3.2 12.7 + - - +
518A PHE* 1.3 75.4 - - - +
520A VAL* 1.3 63.4 + - + +
522A ALA* 3.1 14.8 + - - +
523A GLU* 3.2 22.2 + - - +
553A CYS* 3.1 42.1 + - + +
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Residues in contact with VAL 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PRO* 3.6 37.9 - - + +
302A GLU* 4.8 0.9 - - - +
304A THR* 4.4 9.9 - - + -
305A ARG* 4.0 17.3 - - + +
516A GLY 3.1 13.2 + - - +
517A ALA* 3.1 9.5 + - - +
519A HIS* 1.3 73.2 - - + +
521A LEU* 1.3 67.3 + - + +
523A GLU* 3.2 30.6 + - - +
524A LEU* 3.4 29.8 + - + +
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Residues in contact with LEU 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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304A THR* 5.0 5.4 - - + -
455A ILE* 3.9 19.5 - - + -
517A ALA* 3.0 18.9 + - + +
518A PHE* 3.2 23.5 + - + +
520A VAL* 1.3 77.1 - - + +
522A ALA* 1.3 62.4 + - - +
523A GLU 3.3 0.9 + - - -
524A LEU 3.5 14.4 + - - +
529A PHE* 3.5 47.1 - - + -
532A TYR* 4.2 24.7 - - + -
550A GLN* 5.1 1.1 - - - +
555A VAL* 4.4 11.1 - - + +
559A LEU* 3.9 28.4 - - + +
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Residues in contact with ALA 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 PHE 2.9 12.4 + - - +
519A HIS* 3.1 10.5 + - - +
521A LEU* 1.3 78.6 - - - +
523A GLU* 1.3 58.3 + - - +
524A LEU 3.4 3.7 + - - +
553A CYS 4.1 6.7 - - - +
554A GLY 3.2 35.0 - - - +
555A VAL* 3.9 11.0 - - + +
556A ARG* 5.4 2.3 + - - +
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Residues in contact with GLU 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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305A ARG* 4.1 20.2 - - + -
519A HIS* 3.2 17.0 + - - +
520A VAL* 3.4 27.2 - - + +
522A ALA* 1.3 77.4 - - - +
524A LEU* 1.3 67.2 + - + +
525A PRO* 4.7 0.9 - - - +
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Residues in contact with LEU 524 (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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304A THR 4.7 0.4 - - - +
305A ARG* 4.2 20.9 - - + -
308A CYS* 4.1 26.7 - - + -
309A LEU* 4.8 15.0 - - + -
312A ARG* 5.0 2.5 - - - +
520A VAL* 3.4 29.0 + - + +
521A LEU 3.5 9.9 + - - +
522A ALA 3.4 4.3 - - - +
523A GLU* 1.3 86.1 - - + +
525A PRO* 1.3 78.5 - - + +
526A PRO* 3.5 4.7 - - - +
528A SER* 4.9 1.1 - - - +
529A PHE* 3.5 35.7 - - + -
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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