Contacts of the helix formed by residues 499 - 516 (chain A) in PDB entry 7EHH
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 499 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A MET* 5.2 2.9 - - - +
452A LYS* 3.0 35.1 + - - +
476A GLU 3.7 7.3 - - - +
477A TYR* 3.2 29.1 + - - +
478A GLY* 4.5 2.4 - - - +
497A LEU 4.0 0.6 + - - -
498A GLN* 1.3 68.6 - - - +
500A HIS* 1.3 62.3 + - - +
501A ASP* 3.2 4.2 + - - +
502A LEU* 3.0 28.8 + - + +
503A TYR* 3.1 18.5 + - - +
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Residues in contact with HIS 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A TYR* 4.8 4.9 - - - -
495A PRO* 2.9 37.3 + - + +
498A GLN* 3.4 37.4 + - + +
499A ASP* 1.3 70.3 + - - +
501A ASP* 1.3 60.1 + - - +
503A TYR* 3.2 10.1 + - + +
504A ASP* 2.9 30.7 + - - +
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Residues in contact with ASP 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A LYS* 2.4 34.7 + - - +
456A LYS* 2.8 29.5 + - - -
499A ASP* 3.2 1.3 + - - +
500A HIS* 1.3 78.7 - - - +
502A LEU* 1.3 54.6 + - - +
504A ASP* 3.3 10.5 + - - +
505A PHE* 3.0 26.2 + - - +
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Residues in contact with LEU 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A MET* 3.7 25.8 - - + -
452A LYS* 4.4 7.2 - - + +
455A ALA* 5.5 1.1 - - + -
456A LYS* 4.0 31.6 - - + +
459A LEU* 4.9 11.4 - - + -
475A THR* 3.3 24.0 - - + +
476A GLU 3.6 4.9 - - - +
478A GLY* 3.6 15.3 - - - +
499A ASP* 3.0 25.3 + - + +
501A ASP* 1.3 77.8 + - - +
503A TYR* 1.3 58.7 + - - +
505A PHE* 3.2 10.6 + - + +
506A MET* 2.8 39.8 + - + +
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Residues in contact with TYR 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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193A HIS* 3.4 29.3 + + - -
196A GLU* 2.6 34.7 + - - +
197A LEU* 3.6 30.3 + - + -
476A GLU* 3.1 27.4 + - + +
477A TYR* 3.6 30.7 - + + -
499A ASP 3.1 8.9 + - - +
500A HIS* 3.2 12.1 + - + +
502A LEU* 1.3 76.5 - - - +
504A ASP* 1.3 63.1 + - - +
506A MET* 3.2 5.6 + - - +
507A GLN* 3.0 47.1 + - + +
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Residues in contact with ASP 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A HIS 2.9 16.7 + - - +
501A ASP* 3.6 8.5 - - - +
503A TYR* 1.3 77.3 - - + +
505A PHE* 1.3 64.3 + - - +
507A GLN* 3.3 20.1 + - - +
508A LYS* 3.2 52.8 + - - +
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Residues in contact with PHE 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A LYS* 3.7 51.8 - - + +
459A LEU* 5.0 1.1 - - + -
460A THR* 3.2 27.4 - - - -
501A ASP* 3.0 13.0 + - - +
502A LEU* 3.5 10.8 - - + +
504A ASP* 1.3 77.3 + - - +
506A MET* 1.3 66.2 + - - +
508A LYS* 3.1 10.2 + - + +
509A LEU* 2.8 45.2 + - + +
567A LEU* 3.5 35.2 - - + -
568A LYS 5.7 2.0 - - - -
569A THR* 5.0 3.1 - - + -
581A PHE* 3.6 16.6 - + - -
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Residues in contact with MET 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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197A LEU* 3.9 14.4 - - + -
459A LEU* 3.7 32.1 - - + -
463A PHE* 4.5 13.0 - - + -
471A ILE* 3.6 39.5 - - + -
475A THR* 5.4 1.3 - - + -
476A GLU* 3.8 23.3 - - + -
502A LEU* 2.8 21.0 + - + +
503A TYR 3.5 9.2 - - - +
505A PHE* 1.3 83.4 - - - +
507A GLN* 1.3 53.4 + - - +
509A LEU* 3.1 12.9 + - + +
510A VAL* 2.8 40.9 + - + +
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Residues in contact with GLN 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLU* 2.9 49.0 + - - +
197A LEU* 4.0 16.6 - - + +
503A TYR* 3.0 37.6 + - + +
504A ASP* 3.4 20.7 - - - +
505A PHE 3.2 0.2 - - - -
506A MET* 1.3 75.4 - - - +
508A LYS* 1.3 58.6 + - + +
510A VAL* 3.4 2.4 + - - +
511A GLN* 3.0 36.3 + - + +
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Residues in contact with LYS 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ASP* 3.2 42.2 + - - +
505A PHE* 3.1 11.7 + - + +
507A GLN* 1.3 77.7 - - + +
509A LEU* 1.3 59.9 + - - +
511A GLN* 3.3 7.3 + - - +
512A VAL* 2.9 35.3 + - + +
567A LEU* 4.0 22.9 - - + -
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Residues in contact with LEU 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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459A LEU* 3.8 26.7 - - + +
460A THR* 3.9 24.5 - - + +
463A PHE* 3.7 47.6 - - + -
464A MET* 6.2 0.7 - - + -
505A PHE* 2.8 23.5 + - + +
506A MET* 3.1 16.6 + - + +
508A LYS* 1.3 73.8 - - - +
510A VAL* 1.3 60.3 + - - +
512A VAL* 3.2 12.6 + - + +
513A ARG* 2.9 26.7 + - + +
517A ILE* 6.6 0.2 - - + -
567A LEU* 4.1 15.8 - - + +
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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
----------------------------------------------------------
144A VAL* 4.2 11.2 - - + -
197A LEU* 3.8 15.5 - - + +
198A GLY* 3.4 34.1 - - - +
199A ILE* 5.1 0.7 - - + -
463A PHE* 4.2 12.8 - - + -
471A ILE* 4.0 26.5 - - + -
506A MET* 2.8 25.3 + - + +
507A GLN 3.8 4.3 - - - +
509A LEU* 1.3 71.7 - - - +
511A GLN* 1.3 60.3 + - - +
513A ARG* 3.2 6.5 + - - +
514A ARG* 2.9 39.0 + - + +
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Residues in contact with GLN 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU 4.9 1.0 + - - -
198A GLY* 4.3 22.2 + - - -
507A GLN* 3.0 21.1 + - + +
508A LYS* 3.6 7.6 - - - +
509A LEU 3.2 0.2 - - - -
510A VAL* 1.3 82.5 + - - +
512A VAL* 1.3 57.9 + - + +
514A ARG* 4.9 9.1 - - - +
515A GLN* 2.8 74.3 + - - +
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Residues in contact with VAL 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A LYS* 2.9 21.3 + - + +
509A LEU* 3.2 15.5 + - + +
511A GLN* 1.3 76.2 - - + +
513A ARG* 1.3 62.6 + - - +
516A VAL* 3.1 29.0 + - + +
517A ILE* 3.2 19.4 + - + -
546A ILE* 4.4 3.8 - - + -
566A LEU* 4.4 47.8 - - + +
567A LEU* 4.7 10.8 - - + -
583A ILE* 5.2 6.1 - - + -
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Residues in contact with ARG 513 (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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141A THR* 4.5 16.8 + - - +
143A THR 5.0 2.0 + - - +
144A VAL* 3.8 21.1 - - + -
430A ARG 5.5 0.4 + - - -
462A THR 4.9 0.2 + - - -
463A PHE* 2.9 43.8 + - + +
465A GLN 2.9 24.7 + - - -
466A PRO 3.8 8.1 + - - -
467A GLY 2.9 25.8 + - - -
468A VAL* 3.9 3.8 - - - +
469A PRO* 3.6 19.6 - - + +
509A LEU* 2.9 13.3 + - - +
510A VAL 3.2 7.8 + - - +
512A VAL* 1.3 78.7 - - - +
514A ARG* 1.3 57.5 + - + +
517A ILE* 4.2 24.3 - - + +
518A ALA* 2.8 35.5 + - + +
539A ARG* 5.1 2.2 - - - +
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Residues in contact with ARG 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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142A ASP* 3.4 25.1 + - + +
144A VAL* 3.7 21.8 - - + -
198A GLY* 2.9 33.5 + - - -
199A ILE 4.4 1.2 + - - -
200A SER* 3.5 29.0 + - - -
245A GLY 5.3 1.2 + - - -
510A VAL* 2.9 24.5 + - - +
511A GLN* 4.4 10.3 - - - +
513A ARG* 1.3 78.2 - - + +
515A GLN* 1.3 64.9 + - + +
516A VAL 3.5 0.2 - - - -
518A ALA* 3.7 18.3 - - - +
519A LYS* 4.1 9.4 - - - +
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Residues in contact with GLN 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 GLN* 2.8 46.9 + - - +
514A ARG* 1.3 77.5 - - + +
516A VAL* 1.3 68.4 + - + +
519A LYS* 2.6 39.1 + - - +
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Residues in contact with VAL 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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512A VAL* 3.1 19.7 + - + +
514A ARG 3.5 0.6 - - - -
515A GLN* 1.3 91.8 - - + +
517A ILE* 1.3 70.2 + - - +
518A ALA 3.2 0.9 - - - -
519A LYS* 3.2 13.4 + - - +
520A LEU* 3.6 14.7 + - + +
546A ILE* 3.9 29.4 - - + -
566A LEU* 4.1 27.4 - - + -
585A THR* 5.4 5.6 - - - +
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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
------------------------------------------------------------
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