Contacts of the helix formed by residues 519 - 539 (chain A) in PDB entry 2PA5
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 519 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A VAL* 3.9 31.9 - - + -
515A CYS* 3.6 0.6 - - - -
517A ALA* 3.9 18.2 - - + +
518A GLY* 1.3 85.5 - - - +
520A GLY* 1.3 62.8 + - - +
523A GLY 3.2 16.0 + - - +
554A ARG* 4.0 8.7 - - + +
555A ALA 3.2 25.4 - - - +
556A PHE* 3.6 31.2 - - + +
557A SER* 3.3 5.3 - - - +
558A ILE 2.9 22.9 + - - -
559A GLN* 3.9 28.9 - - + +
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Residues in contact with GLY 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515A CYS* 3.8 3.2 - - - -
519A ILE* 1.3 80.4 - - - +
521A ARG* 1.3 64.6 + - - +
522A THR 3.2 0.2 - - - -
523A GLY 3.8 0.2 - - - -
524A THR* 2.9 27.2 + - - -
558A ILE* 4.3 1.2 - - - +
559A GLN* 3.4 21.9 + - - -
563A GLN* 3.3 25.4 - - - +
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Residues in contact with ARG 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A THR* 2.9 48.2 + - - +
402A THR* 3.6 4.8 - - - +
406A GLU* 2.9 39.3 + - - -
411A LYS* 4.4 6.5 - - - +
468A TRP* 3.3 65.4 + - + +
469A PRO 3.6 8.5 + - - -
470A ASP 4.6 5.1 + - - -
515A CYS* 3.7 6.1 - - + -
520A GLY* 1.3 72.0 - - - +
522A THR* 1.3 62.0 + - - +
524A THR* 3.6 7.0 - - - -
525A PHE* 2.9 27.4 + - - +
563A GLN* 4.0 5.5 - - - +
591A CL 3.8 19.9 - - + +
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Residues in contact with THR 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A MET* 4.7 5.4 - - + -
374A GLY* 4.1 12.3 - - - -
401A THR* 4.5 0.6 + - - -
513A VAL* 3.8 29.8 - - + +
514A HIS* 3.3 10.0 + - - -
515A CYS* 3.2 29.0 + - - -
518A GLY* 3.5 28.6 - - - +
520A GLY 3.2 0.4 - - - -
521A ARG* 1.3 80.1 - - - +
523A GLY* 1.3 57.7 + - - +
525A PHE* 3.5 1.2 + - - +
526A CYS* 3.0 36.2 + - - -
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Residues in contact with GLY 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ILE* 3.2 21.5 + - - +
520A GLY 3.7 0.2 - - - -
522A THR* 1.3 80.7 - - - +
524A THR* 1.3 56.9 + - - +
527A SER* 2.9 35.0 + - - -
550A MET* 3.7 18.5 - - - +
557A SER* 4.3 6.1 - - - -
558A ILE* 3.4 10.8 - - - -
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Residues in contact with THR 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A TRP* 3.9 16.1 - - + -
480A LEU* 4.8 2.5 - - + -
520A GLY 2.9 18.1 + - - -
521A ARG 3.6 4.0 - - - -
523A GLY* 1.3 74.7 - - - +
525A PHE* 1.3 66.1 + - - +
527A SER* 3.4 0.9 + - - -
528A LEU* 2.9 27.0 + - + +
558A ILE* 3.4 15.2 - - - +
563A GLN* 3.8 18.9 + - + +
566A PHE* 3.6 37.0 - - + -
567A CYS* 4.2 12.1 - - - -
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Residues in contact with PHE 525 (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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372A TYR* 4.9 10.8 - + - -
399A VAL* 4.2 12.8 - - + -
401A THR* 4.9 7.2 - - + -
468A TRP* 5.6 1.1 - - + -
480A LEU* 4.2 27.5 - - + +
483A PHE* 3.9 27.8 - + - -
484A LEU* 3.6 37.3 - - + +
487A VAL* 4.3 18.2 - - + -
511A ILE* 5.5 2.0 - - + -
513A VAL* 3.9 37.2 - - + -
521A ARG 2.9 17.0 + - - +
522A THR 3.8 3.1 - - - +
524A THR* 1.3 79.0 - - - +
526A CYS* 1.3 68.0 + - - +
528A LEU* 3.7 4.7 - - - +
529A ASP* 3.0 23.0 + - - +
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Residues in contact with CYS 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A MET* 4.0 11.7 - - + -
372A TYR* 3.7 43.3 - - + -
513A VAL* 4.2 10.1 - - - -
522A THR* 3.0 23.9 + - - +
525A PHE* 1.3 86.6 - - - +
527A SER* 1.3 58.5 + - - +
529A ASP* 3.3 6.7 + - - +
530A ILE* 3.0 33.4 + - - +
550A MET* 3.5 22.7 - - + -
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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
----------------------------------------------------------
523A GLY 2.9 23.4 + - - -
524A THR 3.9 2.7 - - - -
526A CYS* 1.3 78.0 - - - +
528A LEU* 1.3 62.1 + - - +
530A ILE* 3.3 2.1 + - - +
531A CYS* 3.0 31.9 + - - -
543A VAL* 6.1 0.9 - - - -
546A THR* 3.9 12.4 - - - +
547A VAL* 3.8 19.4 - - - +
550A MET* 3.2 21.4 - - - +
558A ILE* 4.2 1.9 - - - +
567A CYS* 4.3 17.9 - - - -
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Residues in contact with LEU 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ALA* 5.0 0.4 - - + -
480A LEU* 4.0 28.9 - - + -
481A ILE* 4.0 19.7 - - + -
484A LEU* 5.2 4.0 - - + -
524A THR* 2.9 17.1 + - + +
525A PHE* 3.7 3.8 - - - +
527A SER* 1.3 75.4 - - - +
529A ASP* 1.3 58.4 + - - +
531A CYS* 3.3 2.9 + - + +
532A LEU* 2.8 48.5 + - + +
566A PHE* 4.5 5.4 - - + -
567A CYS* 4.1 14.0 - - + +
570A ALA* 3.7 28.3 - - + -
571A ILE* 3.5 29.8 - - + -
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Residues in contact with ASP 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A TYR* 2.6 35.1 + - + +
484A LEU* 3.4 26.7 - - + +
488A ARG* 2.7 52.8 + - - +
511A ILE* 5.6 2.6 - - - +
525A PHE* 3.0 15.7 + - + +
526A CYS* 3.5 6.3 - - - +
528A LEU* 1.3 77.4 - - - +
530A ILE* 1.3 57.2 + - - +
533A ALA* 2.9 28.3 + - - +
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Residues in contact with ILE 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A HIS* 3.5 49.4 - - + +
364A ASP 3.8 8.7 - - - +
365A GLY* 4.0 0.2 - - - -
366A TYR* 3.9 30.1 - - + +
372A TYR* 3.7 13.9 - - + +
526A CYS 3.0 22.7 + - - +
527A SER 3.3 3.6 + - - +
529A ASP* 1.3 76.4 - - - +
531A CYS* 1.3 63.2 + - - +
533A ALA* 3.3 3.7 + - - +
534A GLN* 3.1 25.0 + - - +
546A THR* 3.9 20.2 - - + +
550A MET* 3.5 19.5 - - + -
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Residues in contact with CYS 531 (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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527A SER* 3.0 22.4 + - - +
528A LEU* 3.9 4.0 - - - +
530A ILE* 1.3 78.2 - - - +
532A LEU* 1.3 58.9 + - - +
534A GLN* 3.2 5.6 + - - +
535A LEU* 2.9 30.0 + - - +
541A LEU* 3.9 29.2 - - + +
542A ASN 4.5 2.5 - - - -
543A VAL* 4.3 23.1 - - - -
546A THR* 3.8 24.5 - - - -
567A CYS* 6.2 2.0 - - - -
571A ILE* 4.2 13.2 - - + -
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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
----------------------------------------------------------
481A ILE* 4.1 30.5 - - + -
484A LEU* 3.8 22.0 - - + -
488A ARG* 3.9 10.8 - - - +
528A LEU* 2.8 29.8 + - + +
531A CYS* 1.3 72.6 - - - +
533A ALA* 1.3 58.6 + - - +
535A LEU* 3.7 6.9 - - + +
536A GLU* 2.9 40.8 + - + +
571A ILE* 3.2 27.1 - - + -
574A PHE* 3.7 39.2 - - + -
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Residues in contact with ALA 533 (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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366A TYR* 3.8 26.7 - - + -
488A ARG* 3.6 6.9 - - - +
529A ASP* 2.9 19.4 + - - +
530A ILE* 3.5 5.6 - - - +
531A CYS 3.2 0.2 - - - -
532A LEU* 1.3 77.2 - - - +
534A GLN* 1.3 62.8 + - - +
536A GLU* 3.2 13.1 + - - +
537A GLU* 3.0 24.4 + - - +
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Residues in contact with GLN 534 (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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280A VAL 4.2 3.6 - - - +
281A PRO* 3.7 24.8 - - + +
282A GLY 4.1 1.1 + - - +
285A ALA* 3.4 20.6 - - - +
366A TYR* 3.6 39.7 - - + +
530A ILE* 3.1 17.2 + - - +
531A CYS* 3.2 4.0 + - - +
533A ALA* 1.3 73.8 - - - +
535A LEU* 1.3 61.6 + - - +
538A LEU* 2.8 30.8 + - + -
539A GLY 3.5 1.2 + - - -
540A THR* 3.0 36.3 + - - +
541A LEU* 3.7 9.4 - - - +
542A ASN* 4.7 3.0 + - - +
546A THR* 5.5 2.4 + - - -
549A ARG* 5.7 0.2 + - - -
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Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ILE* 3.9 34.3 - - + -
531A CYS 2.9 17.3 + - - +
532A LEU* 3.7 12.8 - - + +
534A GLN* 1.3 76.0 - - - +
536A GLU* 1.3 59.9 + - + +
539A GLY* 3.0 45.5 + - - +
540A THR 3.1 9.1 + - - +
541A LEU* 4.0 12.8 - - + -
571A ILE* 4.4 9.0 - - + -
574A PHE* 3.7 36.3 - - + -
580A MET* 5.0 11.9 - - + +
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Residues in contact with GLU 536 (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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488A ARG* 2.8 35.5 + - - -
532A LEU* 2.9 30.2 + - - +
533A ALA* 3.5 8.7 - - - +
535A LEU* 1.3 80.5 - - + +
537A GLU* 1.3 62.6 + - - +
539A GLY 4.6 0.9 + - - -
574A PHE* 5.7 10.2 - - + -
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Residues in contact with GLU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A TYR* 2.8 36.4 + - + -
367A LYS* 2.8 26.2 + - - +
533A ALA 3.0 16.6 + - - +
534A GLN 3.3 2.4 + - - +
536A GLU* 1.3 77.5 - - - +
538A LEU* 1.3 77.6 + - + +
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Residues in contact with LEU 538 (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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281A PRO* 3.5 26.9 - - + -
366A TYR* 3.3 22.4 - - - +
367A LYS* 5.1 1.8 - - - +
534A GLN* 2.8 12.3 + - + +
537A GLU* 1.3 100.2 - - + +
539A GLY* 1.3 63.8 + - - +
540A THR* 3.4 18.9 + - + +
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Residues in contact with GLY 539 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A THR* 3.6 19.3 - - - +
288A ILE* 4.3 1.7 + - - +
535A LEU* 3.0 34.6 + - - +
536A GLU 4.5 0.4 + - - -
537A GLU 3.8 0.6 - - - -
538A LEU* 1.3 78.3 - - - +
540A THR* 1.3 62.9 + - - +
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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
------------------------------------------------------------
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