Contacts of the helix formed by residues 502 - 514 (chain A) in PDB entry 1PS9
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 CYS 502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501A GLY* 1.3 77.1 - - - +
503A GLY* 1.3 72.0 + - - +
506A GLY 4.2 1.0 + - - -
507A PHE* 4.0 10.3 - - + -
559A MET* 3.8 35.7 - - - -
560A LEU 3.6 26.3 + - - -
561A GLN* 3.3 30.2 - - - +
567A PRO* 4.2 14.1 - - + -
568A GLY 4.9 0.7 - - - +
623A CYS 4.3 0.9 - - - +
703A NAP 3.7 23.7 + - - -
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Residues in contact with GLY 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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502A CYS* 1.3 84.4 - - - +
504A GLY* 1.3 67.5 + - - -
505A ILE 3.6 1.1 - - - -
506A GLY 3.0 9.4 + - - -
507A PHE* 3.0 23.6 + - - -
561A GLN* 4.9 0.6 + - - -
568A GLY* 5.0 3.4 - - - +
570A GLY* 6.2 1.8 - - - -
571A LEU* 4.1 7.9 - - - -
703A NAP 3.7 13.9 + - - -
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Residues in contact with GLY 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A GLY* 1.3 69.4 - - - +
505A ILE* 1.3 62.6 + - - -
507A PHE* 3.2 4.3 + - - +
508A ASP* 3.1 27.1 + - - -
571A LEU* 3.7 5.9 - - - +
701A FAD 6.0 1.1 - - - -
703A NAP 3.5 51.0 + - - -
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Residues in contact with ILE 505 (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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483A TYR* 3.6 49.8 - - + -
487A LEU* 5.1 3.8 - - + -
503A GLY 3.3 0.4 + - - -
504A GLY* 1.3 71.5 - - - -
506A GLY* 1.3 64.0 + - - +
508A ASP* 3.1 7.6 + - - +
509A THR* 2.9 36.5 + - - +
623A CYS* 3.9 7.9 - - + -
626A GLN* 3.5 25.8 - - - +
701A FAD 4.0 23.3 - - + -
703A NAP 3.1 41.4 + - - +
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Residues in contact with GLY 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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499A ILE* 4.2 4.7 - - - +
501A GLY 3.4 25.5 + - - -
502A CYS 4.2 1.6 + - - -
503A GLY 3.0 7.6 + - - -
505A ILE* 1.3 79.4 - - - +
507A PHE* 1.3 59.7 + - - +
509A THR* 3.8 1.9 - - - -
510A ALA* 3.2 18.0 + - - +
559A MET* 3.5 14.8 - - - +
623A CYS* 3.7 16.9 - - - +
703A NAP 4.4 0.4 + - - -
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Residues in contact with PHE 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A CYS* 4.0 4.3 - - + -
503A GLY 3.0 30.5 + - - +
504A GLY 3.7 7.6 - - - +
505A ILE 3.2 0.2 - - - -
506A GLY* 1.3 74.5 - - - +
508A ASP* 1.3 63.7 + - - +
510A ALA* 3.4 3.0 + - - +
511A MET* 2.9 27.9 + - - +
559A MET* 3.6 17.3 - - + -
567A PRO* 4.0 2.9 - - + -
568A GLY* 3.5 36.8 - - - -
571A LEU* 4.0 25.1 - - + -
579A HIS* 4.4 15.9 - - + +
580A ARG* 4.3 14.1 - - + -
583A LEU* 3.5 29.2 - - + +
590A MET* 4.0 26.0 - - - -
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Residues in contact with ASP 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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418A ILE* 3.7 31.6 - - + +
421A LYS* 2.6 37.6 + - - +
504A GLY 3.1 15.3 + - - +
505A ILE 3.1 8.3 + - - +
507A PHE* 1.3 76.8 - - - +
509A THR* 1.3 60.4 + - - +
511A MET* 3.2 9.8 + - - +
512A TYR* 3.0 28.2 + - - +
579A HIS* 4.7 10.4 + - - -
701A FAD 3.1 26.6 + - + -
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Residues in contact with THR 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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418A ILE* 4.8 0.2 - - - +
483A TYR* 3.9 2.4 - - + +
486A VAL* 4.7 4.7 - - + -
487A LEU* 3.7 27.1 - - + +
499A ILE* 4.4 4.7 - - + -
505A ILE* 2.9 21.6 + - - +
506A GLY 3.8 4.9 - - - -
508A ASP* 1.3 75.6 - - - +
510A ALA* 1.3 59.3 + - - +
512A TYR* 3.3 7.5 + - - +
513A LEU* 2.9 48.9 + - + +
621A VAL* 4.0 22.4 - - + -
623A CYS* 3.5 15.0 - - - -
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Residues in contact with ALA 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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499A ILE* 3.7 20.4 - - + +
506A GLY 3.2 15.3 + - - +
507A PHE 3.7 4.5 - - - +
509A THR* 1.3 75.9 - - - +
511A MET* 1.3 57.7 + - - +
513A LEU* 4.5 3.1 - - - +
514A SER* 2.7 37.5 + - - -
557A ILE* 4.2 7.4 - - + +
559A MET* 3.7 21.5 - - + -
583A LEU* 3.9 11.2 - - + +
588A VAL* 5.5 2.0 - - + -
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Residues in contact with MET 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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418A ILE* 4.3 3.4 - - + -
419A PRO* 3.8 31.0 - - + +
507A PHE 2.9 13.4 + - - +
508A ASP* 3.2 15.7 + - - +
510A ALA* 1.3 76.2 - - - +
512A TYR* 1.3 62.3 + - - +
514A SER* 3.9 2.5 - - - -
515A GLN* 3.1 22.2 + - - +
579A HIS* 4.1 36.3 - - + -
582A THR* 4.0 13.5 - - + +
583A LEU* 3.7 23.5 - - + +
586A ARG* 3.1 38.4 + - - -
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Residues in contact with TYR 512 (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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417A GLN* 3.6 30.1 - - + -
418A ILE* 4.4 1.8 - - + -
419A PRO* 3.8 16.4 - - + +
486A VAL* 4.2 10.3 - - + -
487A LEU* 3.6 31.0 - - + -
490A LYS* 2.9 40.9 + - - +
508A ASP 3.0 12.9 + - - +
509A THR 3.4 7.6 - - - +
511A MET* 1.3 77.6 - - - +
513A LEU* 1.3 79.8 + - + +
515A GLN* 3.3 18.0 + - - +
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Residues in contact with LEU 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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486A VAL* 3.5 26.2 - - + -
493A VAL* 4.3 4.3 - - + -
497A VAL* 4.3 14.4 - - + -
499A ILE* 4.7 6.1 - - + -
509A THR* 2.9 39.0 + - + +
512A TYR* 1.3 84.0 - - + +
514A SER* 1.3 58.3 + - - +
515A GLN 3.4 0.4 - - - +
554A PRO* 4.7 2.6 - - - +
555A ARG* 3.0 58.2 + - - +
557A ILE* 3.7 15.6 - - + +
621A VAL* 4.2 20.2 - - + -
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Residues in contact with SER 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A ALA 2.7 23.6 + - - -
511A MET* 3.9 0.9 - - - -
513A LEU* 1.3 77.2 - - - +
515A GLN* 1.3 60.6 + - - +
516A PRO* 2.9 17.8 - - - +
553A SER* 3.1 28.6 + - - -
554A PRO* 3.3 11.0 - - - +
557A ILE* 3.9 7.9 - - - -
583A LEU* 4.0 4.2 - - - +
586A ARG* 3.0 24.3 + - - -
588A VAL* 4.0 9.9 - - - -
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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