Contacts of the helix formed by residues 517 - 533 (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 ASP 517 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634A ARG* 2.6 39.8 + - - -
512B LEU* 2.9 26.8 + - + +
515B LEU* 3.8 12.5 - - - +
516B GLY* 1.3 74.9 - - - +
518B VAL* 1.3 62.4 + - - +
519B ALA 3.3 3.1 + - - -
520B LYS* 3.5 17.7 + - + +
521B ALA* 3.2 22.0 + - - +
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Residues in contact with VAL 518 (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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513B LEU* 4.1 4.7 - - + -
516B GLY 2.8 14.8 + - - +
517B ASP* 1.3 70.1 - - - +
519B ALA* 1.3 68.1 + - + +
521B ALA* 3.3 5.4 + - - +
522B THR* 3.0 28.1 + - + -
545B ALA* 3.4 42.2 - - + +
548B LEU* 4.0 21.1 - - + -
549B THR* 3.6 24.7 - - + -
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Residues in contact with ALA 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ASP 3.3 0.8 - - - -
518B VAL* 1.3 82.2 - - + +
520B LYS* 1.3 64.5 + - + +
522B THR* 3.2 17.4 + - - -
523B ARG* 3.3 35.0 + - - +
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Residues in contact with LYS 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ARG* 4.1 27.7 - - - +
512B LEU* 4.1 17.5 - - + +
517B ASP* 3.5 19.3 + - + +
518B VAL 3.4 0.2 - - - -
519B ALA* 1.3 79.8 - - + +
521B ALA* 1.3 60.5 + - - +
523B ARG* 3.5 26.9 + - - +
524B LYS* 3.2 22.5 + - - +
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Residues in contact with ALA 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B VAL* 3.8 11.5 - - + +
512B LEU* 3.8 23.3 - - + -
513B LEU* 3.8 29.8 - - + -
517B ASP 3.2 16.5 + - - +
518B VAL 3.7 4.9 - - - +
519B ALA 3.2 1.0 - - - -
520B LYS* 1.3 77.1 - - - +
522B THR* 1.3 59.8 + - + +
524B LYS* 3.3 4.9 + - - +
525B LEU* 2.9 28.8 + - - +
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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
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518B VAL* 3.0 24.2 + - + +
519B ALA* 3.2 11.8 + - - -
521B ALA* 1.3 76.1 - - - +
523B ARG* 1.3 58.6 + - - +
525B LEU* 3.8 10.3 - - + +
526B ASP* 2.9 38.9 + - - -
542B ARG* 6.0 2.7 - - + -
545B ALA* 3.6 30.1 - - + -
549B THR* 5.8 1.8 - - + -
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Residues in contact with ARG 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ALA* 3.3 43.6 + - - +
520B LYS* 3.9 27.4 + - - +
521B ALA 3.4 0.2 - - - -
522B THR* 1.3 75.4 - - - +
524B LYS* 1.3 58.8 + - - +
526B ASP* 3.9 6.6 - - - +
527B ASP* 3.0 41.0 + - - +
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Residues in contact with LYS 524 (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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480B LEU* 6.0 0.4 - - - -
487B ARG* 4.4 12.7 - - - +
490B ALA 4.8 7.9 + - - -
505B PRO* 4.2 10.4 - - + +
508B GLU* 2.9 47.1 + - + -
509B VAL* 3.7 15.4 - - + +
512B LEU* 4.0 17.8 - - + +
520B LYS 3.2 12.4 + - - +
521B ALA* 3.5 9.6 - - - +
522B THR 3.3 0.2 - - - -
523B ARG* 1.3 74.5 - - - +
525B LEU* 1.3 64.2 + - - +
527B ASP* 3.6 6.0 + - - +
528B LEU* 3.1 23.6 + - - +
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Residues in contact with LEU 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B LEU* 4.4 9.0 - - + -
509B VAL* 4.1 15.0 - - + +
521B ALA* 2.9 18.7 + - + +
522B THR* 3.8 11.4 - - + +
523B ARG 3.4 0.2 - - - -
524B LYS* 1.3 73.4 - - - +
526B ASP* 1.3 60.5 + - - +
528B LEU* 3.1 5.3 + - + +
529B ALA* 2.8 30.5 + - - +
534B TRP* 4.3 10.5 - - + -
538B LEU* 3.6 46.0 - - + +
541B TYR* 3.8 15.5 - - + +
542B ARG* 3.6 37.9 - - + +
545B ALA* 5.1 4.7 - - + -
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Residues in contact with ASP 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B THR* 2.9 30.2 + - - +
523B ARG* 3.9 7.2 - - - +
525B LEU* 1.3 72.7 - - - +
527B ASP* 1.3 66.9 + - - +
529B ALA* 3.4 6.7 + - - +
530B GLU* 3.1 27.2 + - + +
534B TRP* 3.5 21.5 - - - -
542B ARG* 5.5 2.4 + - - -
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Residues in contact with ASP 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B ARG* 3.0 26.9 + - - +
524B LYS* 3.9 5.9 - - - +
526B ASP* 1.3 77.6 - - - +
528B LEU* 1.3 62.1 - - - +
530B GLU* 3.3 31.2 - - - +
531B ARG* 3.6 6.9 + - - +
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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
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502B VAL* 4.1 15.3 - - + +
505B PRO* 4.1 23.8 - - + -
506B LEU* 3.8 31.2 - - + +
509B VAL* 6.0 1.1 - - + -
524B LYS 3.1 19.2 + - - +
525B LEU* 3.5 6.3 - - + +
527B ASP* 1.3 73.1 - - - +
529B ALA* 1.3 65.6 + - - +
531B ARG* 2.9 47.7 + - - +
532B VAL* 3.1 25.0 + - + +
538B LEU* 3.8 22.4 - - + -
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Residues in contact with ALA 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B LEU 2.8 19.9 + - - +
526B ASP 3.5 4.9 - - - +
528B LEU* 1.3 73.1 - - - +
530B GLU* 1.3 58.0 + - - +
533B GLY* 2.7 39.3 + - - -
534B TRP* 3.3 48.3 - - + +
538B LEU* 3.5 3.2 - - + +
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Residues in contact with GLU 530 (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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526B ASP* 3.1 20.0 + - + +
527B ASP* 3.3 23.5 - - - +
528B LEU 3.1 0.2 - - - -
529B ALA* 1.3 77.7 - - - +
531B ARG* 1.3 61.6 + - - +
533B GLY 4.7 0.3 + - - -
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Residues in contact with ARG 531 (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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499B SER 3.9 14.7 + - - -
500B GLU* 3.1 35.9 + - - +
501B SER 2.8 26.1 + - - -
502B VAL* 4.5 1.6 - - - +
505B PRO* 4.6 3.0 - - - +
527B ASP 3.6 6.2 + - - +
528B LEU* 2.9 31.4 + - - +
530B GLU* 1.3 81.9 - - - +
532B VAL* 1.3 73.0 + - + +
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Residues in contact with VAL 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B VAL* 4.0 18.2 - - + -
528B LEU* 3.1 30.9 + - + +
531B ARG* 1.3 109.1 - - + +
533B GLY* 1.3 70.8 + - - +
535B ARG* 3.5 45.6 + - - +
538B LEU* 4.4 5.6 - - + -
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Residues in contact with GLY 533 (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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529B ALA* 2.7 26.7 + - - -
530B GLU 4.6 0.8 + - - -
531B ARG 3.8 0.4 - - - -
532B VAL* 1.3 85.8 - - - +
534B TRP* 1.3 63.6 + - - -
535B ARG* 3.0 8.7 + - - -
538B LEU* 3.7 11.6 - - - +
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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