Contacts of the helix formed by residues 517 - 533 (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 ASP 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512A LEU* 2.9 28.0 + - + +
515A LEU* 3.8 14.1 - - - +
516A GLY* 1.3 74.5 - - - +
518A VAL* 1.3 58.5 + - - +
519A ALA 3.4 2.9 - - - +
520A LYS* 3.7 23.2 + - + +
521A ALA* 3.1 27.4 + - - +
634B ARG* 2.5 37.4 + - - -
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Residues in contact with VAL 518 (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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513A LEU* 4.2 4.3 - - + -
516A GLY 2.8 16.7 + - - +
517A ASP* 1.3 70.9 - - - +
519A ALA* 1.3 58.5 + - + +
521A ALA* 3.2 6.3 + - - +
522A THR* 2.7 42.0 + - + +
545A ALA* 3.6 39.9 - - + +
548A LEU* 4.3 21.8 - - + +
549A THR* 4.1 15.7 - - - +
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Residues in contact with ALA 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ASP* 3.4 0.8 - - - +
518A VAL* 1.3 79.7 - - + +
520A LYS* 1.3 65.4 + - - +
522A THR* 3.2 8.2 + - - -
523A ARG* 3.1 40.7 + - - +
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Residues in contact with LYS 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A LEU* 4.1 20.1 - - + +
517A ASP* 3.7 37.6 + - + +
518A VAL 3.5 0.2 - - - -
519A ALA* 1.3 77.2 - - - +
521A ALA* 1.3 61.4 + - - +
523A ARG* 3.4 28.5 + - - +
524A LYS* 3.0 24.3 + - - +
634B ARG* 4.3 7.0 - - - +
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Residues in contact with ALA 521 (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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509A VAL* 4.0 11.9 - - + +
512A LEU* 4.0 18.7 - - + +
513A LEU* 3.8 31.4 - - + -
517A ASP 3.1 19.4 + - - +
518A VAL 3.2 5.1 + - - +
520A LYS* 1.3 75.4 - - - +
522A THR* 1.3 60.5 + - + +
524A LYS* 3.3 5.2 + - - +
525A LEU* 2.9 31.5 + - - +
545A ALA* 5.6 0.4 - - + -
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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
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518A VAL* 2.7 29.0 + - + +
519A ALA* 3.2 10.9 + - - -
521A ALA* 1.3 70.8 - - - +
523A ARG* 1.3 66.4 + - - +
525A LEU* 3.3 12.7 + - + +
526A ASP* 2.8 37.9 + - - +
542A ARG* 5.8 3.8 - - + -
545A ALA* 3.7 29.6 - - + -
546A GLU* 6.5 0.2 - - + -
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Residues in contact with ARG 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ALA* 3.1 22.8 + - - +
520A LYS* 3.5 46.9 + - - +
522A THR* 1.3 75.8 - - - +
524A LYS* 1.3 63.8 + - - +
526A ASP* 3.2 4.7 + - - +
527A ASP* 2.9 34.2 + - - +
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Residues in contact with LYS 524 (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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484A ARG* 4.6 9.3 - - - +
487A ARG* 4.1 17.5 - - - +
505A PRO* 4.6 10.6 - - + +
508A GLU* 2.8 47.0 + - + -
509A VAL* 4.1 13.9 - - + -
512A LEU* 4.1 16.5 - - + +
520A LYS 3.0 13.2 + - - +
521A ALA* 3.5 5.6 - - - +
523A ARG* 1.3 79.8 - - - +
525A LEU* 1.3 55.9 + - - +
527A ASP* 3.5 9.4 + - - +
528A LEU* 3.1 27.5 + - - +
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Residues in contact with LEU 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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506A LEU* 4.4 6.5 - - + -
509A VAL* 4.1 27.7 - - + +
521A ALA 2.9 17.5 + - - +
522A THR* 3.5 19.1 - - + +
524A LYS* 1.3 70.2 - - - +
526A ASP* 1.3 60.2 + - - +
528A LEU* 3.1 7.1 + - + +
529A ALA* 2.7 36.8 + - - +
534A TRP* 4.0 9.9 - - + -
538A LEU* 3.9 39.7 - - + +
541A TYR* 4.0 8.3 - - + +
542A ARG* 3.7 38.4 - - + +
545A ALA* 5.4 0.4 - - + -
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Residues in contact with ASP 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A THR* 2.8 30.4 + - - +
523A ARG* 3.7 5.3 - - - +
525A LEU* 1.3 71.2 - - - +
527A ASP* 1.3 67.2 - - - +
529A ALA* 3.5 7.3 + - - +
530A GLU* 3.1 22.8 + - - +
534A TRP* 3.4 25.5 - - - -
542A ARG* 5.2 2.9 + - - -
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Residues in contact with ASP 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A ARG* 2.9 30.2 + - - +
524A LYS* 3.6 7.7 - - - +
526A ASP* 1.3 77.4 - - - +
528A LEU* 1.3 63.3 + - - +
530A GLU* 3.0 26.5 + - - +
531A ARG* 3.3 10.6 + - - +
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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
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502A VAL* 3.9 33.4 - - + +
505A PRO* 3.9 24.9 - - + -
506A LEU* 4.0 18.4 - - + +
509A VAL* 5.9 1.1 - - + -
524A LYS 3.1 15.1 + - - +
525A LEU* 3.1 8.3 + - + +
527A ASP* 1.3 79.1 - - - +
529A ALA* 1.3 55.9 + - - +
531A ARG* 3.0 39.8 + - - +
532A VAL* 2.9 43.4 + - + +
538A LEU* 4.0 8.7 - - + -
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Residues in contact with ALA 529 (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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525A LEU 2.7 18.7 + - - +
526A ASP 3.8 4.5 - - - +
527A ASP 3.3 0.2 - - - -
528A LEU* 1.3 71.8 - - - +
530A GLU* 1.3 57.8 + - - +
531A ARG 3.3 0.2 - - - -
533A GLY* 2.9 35.8 + - - +
534A TRP* 3.3 43.9 + - + +
538A LEU* 3.5 10.8 - - + +
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Residues in contact with GLU 530 (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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526A ASP 3.1 11.2 + - - +
527A ASP* 3.0 18.9 + - - +
529A ALA* 1.3 78.2 - - - +
531A ARG* 1.3 62.2 + - - +
533A GLY 4.6 0.2 - - - -
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Residues in contact with ARG 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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499A SER 3.8 12.3 + - - -
500A GLU* 3.1 41.0 + - - +
501A SER 3.1 26.1 + - - -
502A VAL* 4.4 1.2 - - - +
505A PRO* 4.8 1.6 - - - +
527A ASP 3.3 8.0 + - - +
528A LEU* 3.0 32.2 + - - +
530A GLU* 1.3 81.2 - - - +
532A VAL* 1.3 73.8 + - + +
533A GLY 3.7 0.2 - - - -
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Residues in contact with VAL 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A VAL* 3.8 26.5 - - + -
528A LEU* 2.9 35.7 + - + +
531A ARG* 1.3 98.8 - - + +
533A GLY* 1.3 69.1 + - - +
535A ARG* 3.6 47.0 + - - +
538A LEU* 4.4 5.8 - - + -
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Residues in contact with GLY 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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529A ALA* 2.9 25.2 + - - -
531A ARG 3.7 1.0 - - - -
532A VAL* 1.3 82.6 - - - +
534A TRP* 1.3 62.3 + - - -
535A ARG 3.0 8.1 + - - -
538A LEU* 3.3 18.5 - - - +
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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