Contacts of the helix formed by residues 523 - 538 (chain A) in PDB entry 2P8Q
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 ASN 523 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A ASP* 4.7 0.8 + - - -
468A SER* 4.9 0.4 - - - +
519A GLY 4.4 0.4 - - - -
520A HIS 3.9 7.2 + - - -
521A GLN 3.1 2.2 + - - -
522A ASN* 1.3 77.9 - - - +
524A LEU* 1.3 60.1 + - - +
525A ARG 3.6 1.1 - - - -
526A SER* 3.4 27.7 + - - -
527A SER* 2.8 39.3 + - - +
34B LYS* 5.1 5.1 - - - +
36B SER* 6.3 1.6 - - - -
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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
----------------------------------------------------------
464A PRO* 4.3 22.0 - - + +
467A ALA* 4.4 7.4 - - + -
468A SER* 4.5 4.9 - - - +
471A CYS* 4.4 11.9 - - - -
513A THR* 3.4 28.9 - - + +
516A ARG* 3.6 42.2 - - + +
518A ASP* 3.9 9.4 - - - +
519A GLY* 3.3 18.3 + - - +
521A GLN 3.0 12.8 + - - +
522A ASN 3.1 3.0 + - - -
523A ASN* 1.3 73.6 - - - +
525A ARG* 1.3 56.0 + - - +
527A SER* 3.0 6.7 + - - -
528A ALA* 2.7 32.6 + - + +
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Residues in contact with ARG 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A THR 5.1 1.1 - - - -
514A THR* 3.6 25.8 - - - +
519A GLY* 2.8 28.8 + - - +
520A HIS* 5.5 1.9 + - - +
523A ASN 3.6 0.4 - - - -
524A LEU* 1.3 72.9 - - - +
526A SER* 1.3 63.6 + - - +
528A ALA* 3.1 8.9 + - - +
529A TYR* 2.9 43.0 + - + -
576A GLN* 3.1 37.9 + - - +
579A ASP* 3.9 12.7 - - - +
580A LEU* 4.1 23.8 - - - +
583A LEU* 3.7 17.1 - - + +
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Residues in contact with SER 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ASN* 3.4 29.7 + - - -
524A LEU 3.3 0.6 - - - -
525A ARG* 1.3 79.0 + - - +
527A SER* 1.3 58.7 + - - +
529A TYR* 3.1 2.6 + - - +
530A GLU* 2.8 31.7 + - - +
583A LEU* 4.1 28.3 - - - +
38B LEU* 4.6 10.3 - - - +
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Residues in contact with SER 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A SER* 3.2 24.8 + - - -
471A CYS* 3.8 17.1 - - - +
472A TRP* 5.4 1.3 + - - -
523A ASN* 2.8 25.8 + - - +
524A LEU* 3.0 10.2 + - - -
526A SER* 1.3 75.1 - - - +
528A ALA* 1.3 58.8 + - - +
530A GLU* 3.6 7.6 - - - +
531A SER* 2.9 31.2 + - - -
34B LYS* 3.6 9.4 + - - +
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Residues in contact with ALA 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A CYS* 3.8 11.5 - - - -
510A LEU* 4.3 9.8 - - + +
513A THR* 4.0 18.8 - - + -
514A THR* 3.9 30.1 - - - +
524A LEU 2.7 15.8 + - - +
525A ARG* 3.4 8.7 - - - +
527A SER* 1.3 73.5 - - - +
529A TYR* 1.3 57.3 + - - +
531A SER* 3.3 3.8 + - - -
532A LEU* 2.9 29.0 + - - +
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Residues in contact with TYR 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A THR* 2.6 25.7 + - - -
515A ASP* 5.5 0.5 + - - -
525A ARG* 2.9 41.7 + - + +
526A SER 3.8 2.9 - - - +
528A ALA* 1.3 73.2 - - - +
530A GLU* 1.3 60.5 + - - +
532A LEU* 3.7 18.0 - - + +
533A MET* 2.9 36.6 + - + +
554A ILE* 5.7 2.7 - - + -
557A ARG* 2.8 33.9 + - - -
580A LEU* 3.7 24.0 - - + +
583A LEU* 3.9 26.5 - - + -
584A LEU* 3.6 22.7 - - + +
587A THR* 3.6 22.3 + - + +
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Residues in contact with GLU 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A SER* 5.5 4.7 - - - +
526A SER 2.8 21.3 + - - +
527A SER* 3.6 8.5 - - - +
529A TYR* 1.3 72.2 - - - +
531A SER* 1.3 60.6 + - - +
533A MET* 3.3 5.3 - - - +
534A GLU* 2.8 55.9 + - + +
35B TYR* 4.0 15.4 - - - +
36B SER* 3.5 13.1 - - - +
37B SER* 2.7 32.0 + - - -
38B LEU* 2.3 44.0 - - + +
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Residues in contact with SER 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A CYS* 3.0 33.4 + - - -
472A TRP* 5.6 0.2 - - - -
474A PHE* 3.9 4.2 - - - +
475A SER* 3.8 19.2 + - - -
510A LEU* 3.8 17.9 - - - +
527A SER 2.9 18.5 + - - -
528A ALA 3.5 4.3 - - - -
530A GLU* 1.3 75.7 - - - +
532A LEU* 1.3 61.3 + - - +
534A GLU* 3.2 1.4 + - - +
535A ILE* 2.8 32.6 + - - +
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Residues in contact with LEU 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A VAL* 4.3 17.3 - - + +
510A LEU* 3.9 19.2 - - + +
511A LEU* 3.4 33.0 - - + -
514A THR* 5.9 2.0 - - + -
528A ALA 2.9 17.0 + - - +
529A TYR* 3.7 19.1 - - + +
531A SER* 1.3 73.4 - - - +
533A MET* 1.3 53.9 + - - +
535A ILE* 3.0 15.6 - - + +
536A VAL* 2.9 46.0 + - + +
550A THR* 3.8 25.6 - - + -
554A ILE* 4.5 12.1 - - + -
587A THR* 5.3 3.1 - - + -
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Residues in contact with MET 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A TYR* 2.9 29.5 + - + +
530A GLU* 3.3 6.1 - - - +
532A LEU* 1.3 77.8 - - - +
534A GLU* 1.3 63.6 + - - +
536A VAL* 3.3 5.9 + - - +
537A LYS* 3.1 22.9 + - - +
583A LEU* 4.4 3.4 - - + +
586A ALA* 3.5 17.9 - - + +
587A THR* 3.3 35.0 - - + +
590A ASN* 3.1 36.2 - - - +
591A VAL* 6.5 0.2 - - - -
37B SER* 4.0 4.5 - - - +
38B LEU* 3.1 52.5 - - + -
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Residues in contact with GLU 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A SER* 3.8 22.0 - - - -
478A ALA* 4.9 2.0 - - - +
479A GLU* 3.2 28.8 - - + +
530A GLU* 2.8 43.4 + - - +
533A MET* 1.3 74.4 - - - +
535A ILE* 1.3 57.6 + - - +
537A LYS* 3.6 27.8 + - - +
538A ASN* 2.9 41.2 + - - +
590A ASN* 5.7 1.7 + - - +
35B TYR* 5.1 3.7 - - - -
37B SER* 3.6 14.4 + - - -
46B ARG* 4.4 12.1 + - - -
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Residues in contact with ILE 535 (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 PHE* 5.6 2.0 - - + +
475A SER* 5.3 2.0 - - - -
478A ALA* 3.1 31.9 - - + -
497A TYR* 3.4 15.5 - - - +
499A LEU* 4.4 6.5 - - + -
503A PHE* 3.5 13.4 - - + -
506A ILE* 5.1 12.8 - - + -
507A VAL* 4.3 11.9 - - + -
510A LEU* 4.3 13.0 - - + -
531A SER* 2.8 19.7 + - - +
532A LEU* 3.0 30.5 - - + +
534A GLU* 1.3 71.6 - - - +
536A VAL* 1.3 66.7 + - - +
538A ASN 3.1 22.5 - - - +
539A SER* 3.5 5.2 - - - -
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Residues in contact with VAL 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A PHE* 4.5 11.2 - - + -
507A VAL* 5.2 0.9 - - + -
532A LEU* 2.9 37.0 + - + +
533A MET* 3.7 6.1 - - - +
535A ILE* 1.3 75.7 - - + +
537A LYS* 1.3 64.7 + - - +
539A SER* 2.7 25.3 + - - -
547A VAL* 4.4 22.2 - - + +
550A THR* 4.5 15.3 - - + -
554A ILE* 5.7 0.9 - - + -
587A THR* 6.4 0.7 - - + -
590A ASN* 4.6 3.8 - - + +
591A VAL* 4.2 31.9 - - + +
594A LYS* 3.3 10.9 - - + +
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Residues in contact with LYS 537 (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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482A TYR* 4.4 3.3 - - - -
533A MET 3.1 17.0 + - - +
534A GLU* 3.6 24.5 + - - +
536A VAL* 1.3 78.9 - - - +
538A ASN* 1.3 69.0 + - - +
539A SER 2.9 8.0 + - - -
590A ASN* 4.5 25.4 + - + +
593A ARG* 6.2 1.8 - - - +
594A LYS* 3.0 27.4 + - - +
46B ARG* 4.4 17.5 - - - +
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Residues in contact with ASN 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ALA* 3.8 11.2 - - + +
479A GLU* 3.5 31.4 - - - +
482A TYR* 3.6 41.3 - - + +
483A GLU* 5.8 1.0 - - - +
497A TYR* 3.3 10.4 + - - -
534A GLU* 2.9 37.4 + - - +
535A ILE* 3.1 22.3 - - - +
537A LYS* 1.3 87.6 - - - +
539A SER* 1.3 56.1 + - - +
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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
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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