Contacts of the helix formed by residues 502 - 515 (chain B) in PDB entry 2PZI
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 VAL 502 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B ASP* 3.2 9.6 + - - +
500B GLU 3.5 8.3 + - - +
501B SER* 1.3 76.7 + - - +
503B GLU* 1.3 68.1 + - + +
504B LEU 3.3 0.7 - - - -
505B PRO* 3.2 5.7 - - - +
506B LEU* 3.2 39.1 + - + +
528B LEU* 4.1 17.0 - - + +
531B ARG* 4.5 2.0 - - - +
532B VAL* 4.0 22.0 - - + -
535B ARG* 4.0 28.0 - - - +
538B LEU* 4.6 8.7 - - + -
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Residues in contact with GLU 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B PRO 5.2 1.7 - - - +
457B LEU 4.6 0.2 - - - +
458B VAL* 3.5 25.9 - - + +
459B ASP* 2.8 34.9 + - + +
462B ASP* 3.0 30.6 + - + +
468B LEU* 3.6 20.2 - - + +
502B VAL* 1.3 75.9 - - + +
504B LEU* 1.3 58.8 + - - +
506B LEU* 3.3 13.6 + - + +
507B MET* 2.8 30.8 + - - +
510B ARG* 5.8 0.2 + - - -
537B ARG* 3.1 29.4 + - - -
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Residues in contact with LEU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ALA* 3.9 18.8 - - + -
467B VAL* 4.6 4.9 - - + -
468B LEU* 3.7 10.8 - - + +
483B LEU* 4.1 28.4 - - + +
486B ALA* 4.8 2.5 - - + -
487B ARG* 3.7 39.0 - - + -
498B PHE* 4.4 19.7 - - + +
501B SER* 3.1 17.2 + - - +
503B GLU* 1.3 76.0 - - - +
505B PRO* 1.4 71.8 - - + +
507B MET* 3.0 14.6 + - - +
508B GLU* 3.0 32.6 + - + +
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Residues in contact with PRO 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B ARG* 6.2 1.6 - - - -
501B SER* 3.4 22.4 - - - +
502B VAL 3.2 11.7 - - - +
504B LEU* 1.4 99.4 - - + +
506B LEU* 1.3 55.9 + - - +
508B GLU* 3.2 17.4 + - - +
509B VAL* 2.9 34.6 + - - +
524B LYS* 4.2 11.2 - - + +
528B LEU* 4.1 24.5 - - + -
531B ARG* 4.6 2.5 - - - +
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Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B VAL* 3.2 33.1 + - + +
503B GLU* 3.4 18.2 - - - +
505B PRO* 1.3 76.0 - - - +
507B MET* 1.3 61.2 + - - +
509B VAL* 3.3 6.8 + - + +
510B ARG* 2.9 27.2 + - - +
525B LEU* 4.4 6.1 - - + -
528B LEU* 3.8 19.1 - - + -
537B ARG* 3.7 37.2 - - + +
538B LEU* 4.0 17.9 - - + -
541B TYR* 3.7 34.5 - - + -
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Residues in contact with MET 507 (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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458B VAL* 4.0 20.4 - - + -
468B LEU* 3.8 26.5 - - + +
471B THR* 4.7 4.9 - - - +
472B VAL* 6.5 1.1 - - + -
479B THR* 3.8 15.5 - - + -
483B LEU* 3.7 21.3 - - + -
503B GLU 2.8 16.1 + - - +
504B LEU 3.4 7.9 - - - +
506B LEU* 1.3 69.5 - - - +
508B GLU* 1.3 67.7 + - - +
510B ARG* 3.2 57.7 + - - +
511B ALA* 3.0 22.6 + - - +
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Residues in contact with GLU 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU* 3.5 24.0 - - + +
483B LEU* 3.8 26.8 - - + +
484B ARG* 4.0 1.4 + - - +
487B ARG* 2.9 37.9 + - - -
504B LEU* 3.0 23.4 + - - +
505B PRO* 3.4 18.2 - - - +
507B MET* 1.3 76.8 - - - +
509B VAL* 1.3 55.8 + - - +
511B ALA* 3.2 1.4 + - - -
512B LEU* 3.0 35.4 + - - +
524B LYS* 2.9 32.4 - - + -
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Residues in contact with VAL 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B PRO* 2.9 18.7 + - + +
506B LEU* 3.4 10.8 - - + +
508B GLU* 1.3 74.4 - - - +
510B ARG* 1.3 64.6 + - - +
512B LEU* 3.2 10.2 + - - +
513B LEU* 3.0 34.7 + - + +
521B ALA* 3.8 11.8 - - + +
524B LYS* 3.7 29.2 - - + -
525B LEU* 4.1 21.8 - - + +
528B LEU* 6.0 1.6 - - + -
541B TYR* 3.7 32.8 - - + -
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Residues in contact with ARG 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LEU* 3.6 31.5 - - - +
419B ARG* 4.2 16.9 - - - +
455B VAL* 3.5 27.4 - - + +
456B PRO 3.4 24.2 + - - -
457B LEU* 5.5 0.2 - - - +
458B VAL* 4.4 6.9 - - - +
503B GLU* 5.8 0.4 + - - -
506B LEU 2.9 9.0 + - - +
507B MET* 3.2 49.0 + - - +
509B VAL* 1.3 75.8 - - - +
511B ALA* 1.3 63.0 + - - +
513B LEU* 3.5 3.7 + - - +
514B ASP* 3.2 26.2 + - - +
541B TYR* 2.9 42.6 + - + +
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Residues in contact with ALA 511 (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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476B PRO* 3.7 30.0 - - + +
479B THR* 4.4 11.4 - - + -
480B LEU* 3.8 12.3 - - + -
507B MET* 3.0 16.4 + - - +
508B GLU 3.6 4.5 - - - +
510B ARG* 1.3 77.7 - - - +
512B LEU* 1.3 63.4 + - - +
514B ASP* 3.4 9.5 + - - +
515B LEU* 3.2 28.9 + - - +
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ARG* 3.3 30.7 - - - +
480B LEU* 3.7 16.6 - - + -
508B GLU 3.0 21.6 + - - +
509B VAL 3.2 4.7 + - - +
511B ALA* 1.3 78.4 - - - +
513B LEU* 1.3 58.8 + - - +
515B LEU* 3.3 4.1 + - - -
516B GLY 3.2 3.3 + - - -
517B ASP* 2.9 42.7 + - + +
520B LYS* 4.1 14.6 - - + +
521B ALA* 3.8 31.4 - - + +
524B LYS* 4.0 24.0 - - + +
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Residues in contact with LEU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ASN* 5.3 1.0 + - - -
450B VAL* 3.7 11.2 - - + +
509B VAL* 3.0 39.4 + - + +
510B ARG* 3.9 4.0 - - - +
512B LEU* 1.3 74.3 - - - +
514B ASP* 1.3 59.6 + - - +
515B LEU 3.1 0.2 - - - -
516B GLY* 3.0 18.4 + - - +
517B ASP 4.8 0.7 - - - +
518B VAL* 4.1 6.5 - - + -
521B ALA* 3.8 17.0 - - + -
525B LEU* 5.7 0.2 - - + -
541B TYR* 3.8 27.6 - - + +
544B VAL* 3.9 22.2 - - + -
545B ALA* 3.6 32.1 - - + +
548B LEU* 3.7 24.2 - - + +
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Residues in contact with ASP 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ARG* 2.9 43.9 + - - -
447B ASN* 5.5 3.3 + - - +
450B VAL* 3.8 13.1 - - - +
451B THR* 3.7 28.8 - - + +
476B PRO* 4.0 22.9 - - + +
510B ARG* 3.2 18.7 + - - +
511B ALA* 3.5 11.3 - - - +
513B LEU* 1.3 76.1 - - - +
515B LEU* 1.3 60.6 + - - +
516B GLY 3.6 0.3 + - - -
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Residues in contact with LEU 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ARG* 4.2 12.3 - - - +
757A GOL 4.4 4.7 - - - +
447B ASN* 5.4 1.1 - - - -
476B PRO* 3.7 24.5 - - + -
477B VAL* 3.8 31.0 - - + -
480B LEU* 3.9 20.4 - - + -
511B ALA 3.2 16.2 + - - +
512B LEU* 3.7 7.6 - - - +
513B LEU 3.1 1.0 - - - -
514B ASP* 1.3 76.4 - - - +
516B GLY* 1.3 59.1 + - - +
517B ASP* 3.2 17.3 + - - +
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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
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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