Contacts of the helix formed by residues 520 - 539 (chain B) 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 GLY 520 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B CYS* 4.0 4.2 - - - -
519B ILE* 1.3 82.2 - - - +
521B ARG* 1.3 64.3 + - - +
522B THR 3.2 0.4 - - - -
524B THR* 2.8 29.0 + - - -
558B ILE* 4.3 1.0 - - - +
559B GLN* 4.5 8.2 + - - -
563B GLN* 3.4 31.2 - - - +
701B EDO 4.9 2.2 + - - -
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Residues in contact with ARG 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B THR* 2.9 43.7 + - - +
402B THR* 3.6 12.7 - - - +
406B GLU* 2.8 39.9 + - - -
411B LYS* 5.7 3.7 - - - +
468B TRP* 3.5 70.1 + - + +
515B CYS* 3.8 9.4 - - + -
520B GLY* 1.3 73.5 - - - +
522B THR* 1.3 56.9 + - - +
524B THR* 3.3 1.4 + - - -
525B PHE* 2.9 30.7 + - - +
563B GLN* 4.5 4.8 - - - +
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Residues in contact with THR 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B MET* 4.8 4.9 - - + -
374B GLY* 4.0 13.7 - - - -
401B THR* 5.0 0.7 - - - -
513B VAL* 3.7 33.0 - - + +
514B HIS* 3.2 9.5 + - - -
515B CYS* 3.1 30.7 + - - +
518B GLY* 3.6 28.3 - - - +
520B GLY 3.2 0.4 - - - -
521B ARG* 1.3 78.8 - - - +
523B GLY* 1.3 57.6 + - - +
525B PHE* 3.4 1.2 + - - +
526B CYS* 3.0 34.7 + - - -
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Residues in contact with GLY 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B MET* 5.2 0.4 - - - -
519B ILE* 3.4 18.2 + - - +
520B GLY 3.2 3.4 + - - -
522B THR* 1.3 80.3 - - - +
524B THR* 1.3 57.7 + - - +
527B SER* 2.8 34.7 + - - -
550B MET* 3.6 18.6 - - - +
557B SER* 4.4 6.5 - - - -
558B ILE* 3.5 10.3 - - - -
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Residues in contact with THR 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B TRP* 3.8 16.2 - - + -
520B GLY 2.8 18.4 + - - -
521B ARG* 3.6 5.3 - - - -
523B GLY* 1.3 72.6 - - - +
525B PHE* 1.3 65.9 + - - +
527B SER* 3.9 0.3 - - - -
528B LEU* 2.9 35.5 + - + +
558B ILE* 3.4 15.4 - - - +
563B GLN* 4.1 15.7 + - + +
566B PHE* 3.6 36.1 - - + -
567B CYS* 4.0 14.1 - - - -
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Residues in contact with PHE 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B TYR* 5.1 5.6 - + - -
399B VAL* 4.0 14.8 - - + -
401B THR* 4.8 5.2 - - + -
468B TRP* 4.3 7.8 - - + -
480B LEU* 4.4 17.7 - - + -
483B PHE* 3.8 28.0 - + - -
484B LEU* 4.2 26.9 - - + +
487B VAL* 4.1 23.1 - - + -
488B ARG* 6.3 0.2 - - + -
511B ILE* 5.4 2.2 - - + -
513B VAL* 3.9 36.8 - - + -
521B ARG 2.9 21.2 + - - +
522B THR 3.7 3.6 - - - +
524B THR* 1.3 73.3 - - - +
526B CYS* 1.3 66.6 + - - +
528B LEU* 3.8 7.2 - - - +
529B ASP* 3.0 28.3 + - + +
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Residues in contact with CYS 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B MET* 4.0 15.5 - - + -
372B TYR* 3.7 41.5 - - + -
513B VAL* 3.9 20.6 - - - -
522B THR* 3.0 22.3 + - - +
523B GLY 4.0 0.4 - - - +
525B PHE* 1.3 77.7 - - - +
527B SER* 1.3 64.7 + - - +
529B ASP* 3.3 6.1 + - - +
530B ILE* 3.0 27.5 + - - +
550B MET* 3.7 17.9 - - + -
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Residues in contact with SER 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B GLY 2.8 24.0 + - - -
524B THR 3.9 3.1 - - - -
526B CYS* 1.3 78.1 - - - +
528B LEU* 1.3 61.6 + - - +
530B ILE* 3.4 1.6 + - - +
531B CYS* 3.0 32.4 + - - -
543B VAL* 6.1 0.7 - - - -
546B THR* 3.9 11.6 - - - +
547B VAL* 3.7 24.9 - - - +
550B MET* 3.2 21.5 - - - +
558B ILE* 4.2 1.8 - - - +
567B CYS* 4.4 12.8 - - - -
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Residues in contact with LEU 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 3.9 29.2 - - + -
481B ILE* 4.4 13.7 - - + -
484B LEU* 4.1 10.8 - - + -
524B THR* 2.9 32.4 + - + +
525B PHE* 3.8 4.9 - - - +
527B SER* 1.3 76.6 - - - +
529B ASP* 1.3 56.0 + - - +
531B CYS* 3.3 3.5 + - - +
532B LEU* 2.9 38.6 + - + +
566B PHE* 4.3 7.0 - - + -
567B CYS* 3.8 31.9 - - + +
570B ALA* 4.1 12.8 - - + -
571B ILE* 3.8 18.6 - - + +
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Residues in contact with ASP 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B TYR* 2.5 35.6 + - + +
484B LEU* 3.3 34.3 - - + +
488B ARG* 3.7 13.5 - - - +
511B ILE* 5.6 2.6 - - - +
525B PHE* 3.0 19.4 + - + +
526B CYS* 3.5 6.5 - - - +
528B LEU* 1.3 76.7 - - - +
530B ILE* 1.3 62.4 + - - +
532B LEU* 3.3 2.9 + - - +
533B ALA* 2.9 25.8 + - - +
702B EDO 3.5 13.6 - - - -
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Residues in contact with ILE 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B HIS* 3.5 45.3 - - + +
364B ASP 3.8 7.9 - - - +
365B GLY* 4.0 0.4 - - - -
366B TYR* 3.9 18.7 - - + +
372B TYR* 3.6 7.0 - - + +
526B CYS 3.0 21.2 + - - +
527B SER 3.7 3.1 - - - +
529B ASP* 1.3 75.4 - - - +
531B CYS* 1.3 64.6 + - - +
533B ALA* 3.3 4.2 + - - +
534B GLN* 3.0 24.2 + - - +
546B THR* 3.6 22.9 - - + +
550B MET* 3.6 19.1 - - + -
702B EDO 3.5 20.4 - - - +
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Residues in contact with CYS 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B SER* 3.0 22.8 + - - +
528B LEU* 3.7 4.3 - - - +
530B ILE* 1.3 78.7 - - - +
532B LEU* 1.3 58.3 + - - +
534B GLN* 3.3 3.9 + - - +
535B LEU* 3.0 27.3 + - - +
541B LEU* 3.7 18.4 - - + +
542B ASN 4.3 3.1 - - - -
543B VAL* 4.1 33.2 - - - -
546B THR* 3.8 21.5 - - - -
567B CYS* 6.3 1.1 - - - -
571B ILE* 3.9 21.1 - - + -
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Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B ILE* 3.8 38.8 - - + -
484B LEU* 4.5 14.6 - - + -
528B LEU* 2.9 27.4 + - + +
529B ASP* 4.0 4.0 - - - +
531B CYS* 1.3 75.3 - - + +
533B ALA* 1.3 59.2 + - - +
535B LEU* 3.4 17.3 + - + +
536B GLU* 2.9 32.1 + - - +
541B LEU* 5.4 0.2 - - + -
571B ILE* 4.8 19.7 - - + -
574B PHE* 3.9 32.8 - - + -
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Residues in contact with ALA 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B TYR* 3.7 26.4 - - + +
529B ASP* 2.9 18.8 + - - +
530B ILE 3.5 4.7 - - - +
532B LEU* 1.3 74.3 - - - +
534B GLN* 1.3 64.2 + - - +
536B GLU* 3.3 11.8 + - - +
537B GLU* 3.1 22.9 + - - +
702B EDO 4.0 12.1 - - - -
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Residues in contact with GLN 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B VAL 4.8 2.1 - - - +
281B PRO* 4.1 22.5 - - - +
282B GLY 4.8 0.2 - - - +
285B ALA* 3.6 18.0 - - - +
366B TYR* 3.6 40.5 - - + +
530B ILE* 3.0 13.9 + - + +
531B CYS* 3.3 7.4 + - - +
533B ALA* 1.3 76.1 - - - +
535B LEU* 1.3 57.1 + - - +
537B GLU 3.3 0.2 + - - -
538B LEU* 2.8 34.8 + - + -
539B GLY 3.5 0.3 + - - -
540B THR* 3.0 32.9 + - - +
541B LEU* 3.7 10.0 - - - +
542B ASN* 4.5 7.6 + - - +
546B THR* 5.3 3.5 + - - -
549B ARG* 5.9 0.2 + - - -
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Residues in contact with LEU 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 4.0 37.9 - - + +
531B CYS 3.0 16.9 + - - +
532B LEU* 3.5 26.5 - - + +
533B ALA 3.2 0.2 - - - -
534B GLN* 1.3 76.7 - - - +
536B GLU* 1.3 60.4 + - - +
539B GLY* 2.8 51.3 + - - +
540B THR* 3.1 10.6 + - - +
541B LEU* 4.1 11.2 - - + -
571B ILE* 5.4 0.2 - - + -
574B PHE* 4.6 3.4 - - + -
580B MET* 4.2 24.7 - - + -
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Residues in contact with GLU 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LEU 2.9 16.2 + - - +
533B ALA* 3.4 14.6 - - - +
534B GLN 3.3 0.2 - - - -
535B LEU* 1.3 78.7 - - - +
537B GLU* 1.3 63.0 + - - +
539B GLY 4.5 0.5 + - - -
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Residues in contact with GLU 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B TYR* 2.6 39.9 + - + +
367B LYS* 2.9 27.0 + - - +
533B ALA 3.1 13.0 + - - +
536B GLU* 1.3 80.4 - - - +
538B LEU* 1.3 71.8 + - + +
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Residues in contact with LEU 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PRO* 2.9 41.5 - - + -
366B TYR* 3.3 16.2 - - - +
367B LYS* 4.9 3.1 - - - +
534B GLN* 2.8 19.5 + - + +
537B GLU* 1.3 96.8 - - + +
539B GLY* 1.3 63.1 + - - +
540B THR* 3.4 19.4 + - + +
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Residues in contact with GLY 539 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B THR* 3.5 21.1 - - - +
288B ILE 4.4 0.5 + - - -
535B LEU* 2.8 40.6 + - - +
536B GLU 4.5 0.6 + - - -
537B GLU 3.7 0.6 - - - -
538B LEU* 1.3 72.1 - - - +
540B THR* 1.3 61.3 + - - +
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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