Contacts of the helix formed by residues 502 - 519 (chain A) in PDB entry 5E2Q
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 ILE 502 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A PHE* 3.1 34.3 + - + +
501A THR* 1.3 87.2 - - - +
503A ALA* 1.3 65.6 + - - +
504A SER 3.3 2.9 + - - -
505A SER* 3.4 7.6 + - - +
506A TYR* 2.9 34.4 + - + +
570A GLN* 5.5 5.4 - - - +
637A GLY 4.2 5.6 - - - +
638A ARG* 3.6 37.9 - - + +
641A TYR* 4.6 13.9 - - + -
642A GLU* 3.5 30.3 - - + +
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Residues in contact with ALA 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TRP* 2.9 40.6 + - - +
496A ASP* 3.6 17.3 - - - +
499A PHE* 3.6 22.2 + - + -
500A SER 3.1 20.1 + - - +
502A ILE* 1.3 80.0 - - - +
504A SER* 1.3 64.6 + - - +
507A GLU* 3.3 12.8 + - - +
802A K 4.2 1.1 - - - -
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Residues in contact with SER 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER* 3.5 6.2 + - - -
318A TYR* 3.5 35.9 - - - -
495A TRP* 5.0 0.4 - - - +
496A ASP* 5.5 0.4 - - - -
500A SER 4.6 0.8 + - - -
501A THR 5.2 1.3 + - - -
502A ILE 3.3 0.8 - - - -
503A ALA* 1.3 77.6 - - - +
505A SER* 1.3 62.9 - - - +
507A GLU* 3.2 6.4 + - - +
508A GLU* 3.0 28.8 + - - +
567A ALA* 3.9 6.1 - - - -
802A K 2.8 23.2 - - - -
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Residues in contact with SER 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A THR 5.7 1.1 + - - -
502A ILE* 3.4 8.7 + - - -
504A SER* 1.3 78.8 - - - +
506A TYR* 1.3 63.0 + - - +
508A GLU* 3.4 1.5 + - - -
509A CYS 3.0 19.2 + - - -
567A ALA* 2.8 34.9 + - - +
570A GLN* 3.2 28.7 + - - +
571A ALA* 3.7 2.3 - - - +
641A TYR* 2.5 34.9 + - - -
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Residues in contact with TYR 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TRP* 3.4 29.4 - + + -
499A PHE* 4.4 7.9 - + - -
502A ILE* 2.9 29.0 + - + +
503A ALA* 3.8 4.0 - - - +
505A SER* 1.3 76.8 - - - +
507A GLU* 1.3 57.5 + - - +
509A CYS* 3.3 5.0 + - - +
510A ARG* 3.1 24.5 + - + +
624A ARG 4.0 0.2 + - - -
625A LEU* 2.8 59.6 + - + +
628A LEU* 3.6 18.3 - - + +
629A LYS* 4.1 9.2 - - + -
637A GLY* 3.8 24.0 - - - -
640A LEU* 5.0 2.0 - - + -
641A TYR* 3.7 33.9 - + + -
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Residues in contact with GLU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ARG* 5.9 1.1 + - - -
454A GLY 4.2 0.7 - - - +
455A HIS* 3.1 33.7 + - + +
495A TRP* 4.0 13.9 - - + +
503A ALA 3.3 14.8 + - - +
504A SER* 3.2 6.1 + - - +
506A TYR* 1.3 80.4 - - - +
508A GLU* 1.3 62.4 + - - +
510A ARG* 2.7 44.1 + - - +
511A ALA* 2.8 26.0 + - - +
629A LYS* 3.2 18.9 - - - +
1B ASP* 4.1 13.1 - - - +
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Residues in contact with GLU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A TYR* 2.6 23.3 + - + -
450A HIS* 3.0 22.7 + - + -
455A HIS* 3.5 12.8 - - - -
504A SER* 3.0 20.8 + - - +
505A SER 3.8 4.3 - - - +
507A GLU* 1.3 78.0 - - - +
509A CYS* 1.3 54.0 + - - +
511A ALA* 3.6 2.7 - - - +
512A GLU* 2.7 40.0 + - + +
567A ALA* 4.4 5.2 - - + -
568A HIS* 2.9 47.7 + - + +
571A ALA* 3.9 11.4 - - + -
1B ASP* 4.2 5.2 - - - +
2B ARG 3.2 2.6 - - - +
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Residues in contact with CYS 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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505A SER 3.0 18.1 + - - +
506A TYR 3.4 5.8 - - - +
507A GLU 3.2 0.2 - - - -
508A GLU* 1.3 77.6 - - - +
510A ARG* 1.3 55.2 + - - +
512A GLU* 4.0 3.3 - - - +
513A SER* 2.7 38.5 + - - -
571A ALA* 3.4 29.8 - - + +
574A VAL* 3.7 5.2 - - - -
575A ILE* 4.0 4.5 - - - -
621A PHE* 3.7 34.3 - - - -
625A LEU* 4.3 1.8 - - + -
641A TYR* 3.5 19.5 - - + -
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Residues in contact with ARG 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A TRP* 3.8 6.0 - - + -
454A GLY 3.0 18.6 + - - -
455A HIS* 4.2 3.4 + - - +
457A SER* 3.1 36.0 + - - -
506A TYR* 3.1 15.8 + - + +
507A GLU* 2.7 47.4 + - - +
509A CYS* 1.3 75.4 - - - +
511A ALA* 1.3 58.8 + - - +
513A SER* 3.4 2.6 + - - -
514A VAL* 3.1 34.2 + - + +
622A LEU* 3.7 15.6 - - + +
625A LEU* 3.7 21.9 - - + +
626A GLN* 2.8 44.1 + - - +
629A LYS* 3.6 22.3 - - - +
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Residues in contact with ALA 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A HIS* 3.4 48.3 - - + +
454A GLY* 4.1 14.1 - - - -
455A HIS* 3.6 15.0 - - + +
507A GLU* 2.8 16.4 + - - +
508A GLU 3.6 1.1 - - - +
510A ARG* 1.3 75.7 - - - +
512A GLU* 1.3 64.5 + - - +
514A VAL* 3.3 4.3 + - - +
515A GLY* 3.1 18.7 + - - -
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Residues in contact with GLU 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLN* 3.1 34.7 + - - +
450A HIS* 3.3 23.6 + - + -
508A GLU* 2.7 31.1 + - + +
509A CYS* 4.0 2.2 - - - +
511A ALA* 1.3 72.5 - - - +
513A SER* 1.3 60.8 + - - +
515A GLY 3.3 1.4 + - - -
516A LEU* 3.1 23.4 + - - +
546A MET* 3.8 7.8 - - + +
568A HIS* 4.6 8.2 - - + +
571A ALA* 4.8 4.5 - - + -
572A ARG* 2.7 47.6 + - + +
575A ILE* 3.7 19.3 - - + -
3B VAL* 5.6 1.4 - - - +
4B TYR 5.0 0.2 - - - +
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Residues in contact with SER 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A CYS 2.7 22.6 + - - -
510A ARG* 3.7 4.9 - - - -
512A GLU* 1.3 75.1 - - - +
514A VAL* 1.3 60.5 + - - +
516A LEU* 3.4 2.7 + - - -
517A TYR* 2.9 30.4 + - - +
575A ILE* 3.4 21.5 - - - +
618A LEU* 3.6 22.6 - - - +
621A PHE* 3.8 13.8 - - - -
622A LEU* 3.8 17.7 - - - -
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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
----------------------------------------------------------
357A LEU* 4.0 10.5 - - + -
359A TRP* 4.4 11.4 - - + -
449A LEU* 4.5 1.8 - - + +
453A LEU* 3.4 36.6 - - + +
454A GLY* 4.0 8.1 - - - +
457A SER* 4.7 0.9 - - - +
510A ARG* 3.1 18.8 + - + +
511A ALA 3.5 7.2 - - - +
513A SER* 1.3 77.5 - - - +
515A GLY* 1.3 56.6 + - - +
517A TYR* 4.3 1.1 - - - -
518A LEU* 2.8 51.2 + - + +
622A LEU* 3.9 24.5 - - + -
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Residues in contact with GLY 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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446A GLN* 3.4 20.7 - - - +
449A LEU* 3.3 26.5 - - - +
450A HIS 4.8 1.6 - - - -
511A ALA 3.1 13.2 + - - -
512A GLU 3.6 4.7 - - - -
513A SER 3.2 0.4 - - - -
514A VAL* 1.3 76.0 - - - +
516A LEU* 1.3 60.3 + - - +
519A SER* 3.1 25.8 + - - -
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Residues in contact with LEU 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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446A GLN* 3.8 1.7 + - - +
512A GLU 3.1 8.9 + - - +
513A SER 3.8 2.5 - - - +
515A GLY* 1.3 75.2 - - - +
517A TYR* 1.3 63.1 + - - +
519A SER* 2.5 20.1 + - - -
520A LEU* 3.8 4.5 - - - +
542A ASN* 3.7 33.7 - - - +
543A TRP* 3.5 45.5 + - + -
546A MET* 3.5 44.4 - - + -
575A ILE* 3.8 18.4 - - + -
579A LEU* 5.1 1.8 - - + -
618A LEU* 3.8 18.2 - - + -
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Residues in contact with TYR 517 (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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356A GLU* 3.6 27.3 + - + +
357A LEU* 4.5 1.6 - - + -
358A PRO* 3.8 18.7 - - + +
513A SER 2.9 18.7 + - - +
514A VAL 3.7 3.6 - - - +
516A LEU* 1.3 77.2 - - - +
518A LEU* 1.3 74.3 + - + +
519A SER 3.3 0.2 - - - -
520A LEU* 3.4 26.1 + - + +
521A HIS* 4.6 0.5 + - - +
615A LYS* 2.7 51.2 + - + -
618A LEU* 3.9 16.6 - - + -
619A GLU* 3.3 43.0 + - + -
622A LEU* 4.3 10.1 - - + -
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Residues in contact with LEU 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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353A LEU* 4.3 12.1 - - + +
356A GLU* 4.3 24.2 - - + -
357A LEU* 3.7 28.7 - - + -
449A LEU* 3.7 14.0 - - + +
453A LEU* 3.6 39.9 - - + -
514A VAL* 2.8 22.6 + - + +
517A TYR* 1.3 87.4 - - + +
519A SER* 1.3 59.5 + - - +
520A LEU 3.0 6.1 + - - -
521A HIS* 3.3 17.8 + - + +
524A VAL* 3.5 23.1 - - + +
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Residues in contact with SER 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A VAL* 5.0 5.4 - - - -
446A GLN* 4.9 0.4 - - - -
449A LEU* 4.1 8.5 - - - -
515A GLY 3.1 15.7 + - - -
516A LEU* 2.5 23.9 + - - -
517A TYR 3.3 0.2 - - - -
518A LEU* 1.3 76.5 - - - +
520A LEU* 1.3 59.5 + - - +
521A HIS 3.3 0.2 - - - -
524A VAL* 5.1 0.4 - - - -
525A LEU* 3.2 28.7 - - - +
538A VAL* 6.5 1.3 - - - -
539A ILE* 3.2 18.1 - - - +
542A ASN* 3.3 24.9 + - - -
543A TRP* 3.8 8.1 + - - -
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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
------------------------------------------------------------
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