Contacts of the helix formed by residues 502 - 516 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A ASP* 3.2 9.7 + - - +
500A GLU 3.4 8.0 + - - +
501A SER* 1.3 73.9 - - - +
503A GLU* 1.3 65.7 + - + +
504A LEU 3.4 0.7 - - - -
505A PRO* 3.3 6.1 - - - +
506A LEU* 3.1 35.0 + - + +
528A LEU* 3.9 17.9 - - + +
531A ARG* 4.4 3.4 - - - +
532A VAL* 3.8 36.1 - - + -
535A ARG* 3.9 23.1 - - - +
538A LEU* 4.4 5.8 - - + -
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Residues in contact with GLU 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A PRO 5.4 1.6 - - - +
457A LEU 5.1 0.2 - - - -
458A VAL* 3.8 21.0 - - + +
459A ASP* 3.0 25.7 + - + +
462A ASP* 3.1 34.4 + - + +
468A LEU* 3.5 20.2 - - + +
502A VAL* 1.3 77.6 - - + +
504A LEU* 1.3 65.0 + - - +
506A LEU* 3.6 13.9 - - - +
507A MET* 2.8 26.3 + - - +
510A ARG* 5.8 1.0 + - - -
537A ARG* 3.0 35.2 + - - -
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Residues in contact with LEU 504 (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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464A ALA* 3.9 12.3 - - + -
467A VAL* 4.7 4.3 - - + -
468A LEU* 3.9 10.1 - - - +
483A LEU* 3.8 34.3 - - + +
486A ALA* 5.1 2.7 - - + -
487A ARG* 3.6 29.8 - - + +
498A PHE* 4.1 33.4 - - + +
501A SER* 3.0 16.6 + - - +
503A GLU* 1.3 79.7 - - - +
505A PRO* 1.4 72.4 - - + +
507A MET* 3.1 10.7 + - - +
508A GLU* 3.1 28.1 + - - +
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Residues in contact with PRO 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ARG* 6.2 1.1 - - - -
498A PHE 5.8 0.4 - - - +
501A SER* 3.1 27.4 - - - +
502A VAL 3.3 7.0 - - - +
504A LEU* 1.4 97.0 - - + +
506A LEU* 1.3 60.1 + - - +
508A GLU* 3.0 18.6 + - - +
509A VAL* 3.0 27.8 + - + +
524A LYS* 4.6 10.1 - - + +
528A LEU* 3.9 27.1 - - + -
531A ARG* 4.8 1.6 - - - +
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Residues in contact with LEU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A VAL* 3.1 35.7 + - + +
503A GLU* 3.2 17.7 + - - +
505A PRO* 1.3 78.9 - - - +
507A MET* 1.3 57.3 + - - +
509A VAL* 3.4 6.8 + - + +
510A ARG* 3.0 26.5 + - - +
525A LEU* 4.4 8.1 - - + -
528A LEU* 4.0 9.6 - - + -
537A ARG* 3.6 35.0 - - + -
538A LEU* 3.8 28.7 - - + +
541A TYR* 3.7 34.7 - - + -
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Residues in contact with MET 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A VAL* 4.1 20.2 - - + -
468A LEU* 3.7 28.0 - - + +
471A THR* 4.6 9.4 - - + -
472A VAL* 6.5 1.6 - - + -
479A THR* 4.0 15.2 - - + +
483A LEU* 3.7 15.9 - - + -
503A GLU* 2.8 13.1 + - - +
504A LEU 3.1 9.2 + - - +
506A LEU* 1.3 76.2 - - - +
508A GLU* 1.3 63.3 + - - +
510A ARG* 3.2 57.3 + - - +
511A ALA* 3.1 22.7 + - - +
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Residues in contact with GLU 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 3.5 23.4 - - + +
483A LEU* 3.7 23.1 - - + +
484A ARG* 4.0 4.0 + - - +
487A ARG* 3.0 32.6 + - - -
504A LEU* 3.1 26.7 + - - +
505A PRO* 3.0 18.7 + - - +
507A MET* 1.3 75.9 - - - +
509A VAL* 1.3 57.3 + - - +
511A ALA 3.1 1.7 + - - -
512A LEU* 2.9 35.8 + - + +
524A LYS* 2.8 38.0 + - + -
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Residues in contact with VAL 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A PRO* 3.0 20.1 + - + +
506A LEU* 3.4 9.9 - - - +
508A GLU* 1.3 71.6 - - - +
510A ARG* 1.3 66.4 + - - +
512A LEU* 3.2 9.2 + - - +
513A LEU* 2.9 45.9 + - + +
521A ALA* 4.0 21.8 - - + +
524A LYS* 4.1 15.5 - - + -
525A LEU* 4.1 25.6 - - + +
528A LEU* 5.9 1.6 - - + -
541A TYR* 3.8 20.9 - - + -
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Residues in contact with ARG 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A ARG* 3.9 18.1 - - - +
455A VAL* 3.4 45.5 - - + +
456A PRO 3.6 12.9 + - - -
458A VAL* 4.6 5.3 - - - +
503A GLU* 5.8 1.0 + - - -
506A LEU 3.0 12.4 + - - +
507A MET* 3.2 49.0 - - - +
508A GLU 3.4 0.2 - - - -
509A VAL* 1.3 74.4 - - - +
511A ALA* 1.3 59.5 + - - +
513A LEU* 3.5 4.3 + - - +
514A ASP* 3.0 31.9 + - - +
541A TYR* 3.0 38.9 + - + +
473B LEU* 3.8 20.2 - - - +
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Residues in contact with ALA 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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476A PRO* 3.8 25.0 - - + +
479A THR* 4.3 10.1 - - + -
480A LEU* 3.8 16.8 - - + -
507A MET* 3.1 11.6 + - - +
508A GLU 3.5 6.7 - - - +
510A ARG* 1.3 80.5 - - - +
512A LEU* 1.3 65.2 + - - +
514A ASP* 3.1 18.9 + - - +
515A LEU* 3.1 19.3 + - - +
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Residues in contact with LEU 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LEU* 3.8 15.5 - - + -
508A GLU 2.9 27.2 + - - +
509A VAL 3.7 2.7 - - - +
511A ALA* 1.3 75.7 - - - +
513A LEU* 1.3 60.6 + - - +
515A LEU* 3.2 7.8 + - - +
516A GLY 3.1 4.0 + - - -
517A ASP* 2.9 49.2 + - + +
520A LYS* 4.1 15.9 - - + -
521A ALA* 4.0 20.0 - - + +
524A LYS* 4.1 22.2 - - + +
634B ARG* 3.4 29.2 - - - +
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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
----------------------------------------------------------
447A ASN* 5.3 1.9 + - - -
450A VAL* 3.7 10.1 - - + +
509A VAL* 2.9 33.0 + - + +
510A ARG* 3.7 4.5 - - - +
512A LEU* 1.3 76.5 - - - +
514A ASP* 1.3 60.2 + - - +
516A GLY* 3.1 10.4 + - - +
517A ASP 4.9 0.9 - - - +
518A VAL* 4.2 7.6 - - + -
521A ALA* 3.8 18.8 - - + -
541A TYR* 3.6 31.6 - - + +
544A VAL* 3.8 20.9 - - + -
545A ALA* 3.8 19.3 - - + +
548A LEU* 3.5 38.9 - - + +
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Residues in contact with ASP 514 (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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419A ARG* 2.9 43.4 + - - -
447A ASN* 4.1 9.4 + - - -
450A VAL* 3.9 15.2 - - - +
451A THR* 3.8 25.5 - - + +
476A PRO* 3.9 23.9 - - + +
510A ARG* 3.0 21.9 + - - +
511A ALA* 3.1 11.6 + - - +
513A LEU* 1.3 73.5 - - - +
515A LEU* 1.3 59.0 + - - +
516A GLY 3.4 0.2 - - - -
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Residues in contact with LEU 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ASN* 5.7 1.6 - - - -
476A PRO* 3.5 25.8 - - + -
477A VAL* 3.7 29.4 - - + -
480A LEU* 3.7 27.1 - - + -
511A ALA 3.1 14.0 + - - +
512A LEU* 3.6 7.0 - - - +
513A LEU 3.1 1.0 - - - -
514A ASP* 1.3 76.4 - - - +
516A GLY* 1.3 60.1 + - - +
517A ASP* 3.6 14.0 + - - +
755A GOL 4.4 4.5 - - - +
634B ARG* 4.0 13.7 - - - +
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Residues in contact with GLY 516 (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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447A ASN* 5.5 4.2 - - - +
512A LEU 3.1 2.7 + - - -
513A LEU 3.1 12.6 + - - -
514A ASP 3.4 0.6 - - - -
515A LEU* 1.3 78.0 - - - +
517A ASP* 1.3 52.8 + - - +
518A VAL* 2.8 28.9 + - - +
548A LEU* 4.8 10.4 - - - +
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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
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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