Contacts of the helix formed by residues 475 - 488 (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 GLN 475 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ARG* 2.8 21.6 + - + +
420A SER* 4.2 9.9 - - - +
451A THR* 5.4 4.2 + - - +
475A GLN* 5.0 10.6 + - - +
757A GOL 3.1 26.4 - - - +
473B LEU 3.6 9.7 + - - -
474B SER* 1.3 70.3 - - - +
476B PRO* 1.4 77.2 - - + +
477B VAL 3.5 0.7 - - - -
478B GLN* 3.3 2.1 + - - +
479B THR* 2.9 29.9 + - - -
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Residues in contact with PRO 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A GOL 3.8 5.6 - - - +
474B SER 4.7 0.2 - - - +
475B GLN* 1.4 100.4 - - + +
477B VAL* 1.3 61.7 + - - +
479B THR* 3.6 4.0 + - - +
480B LEU* 3.1 27.5 + - - +
511B ALA* 3.7 16.7 - - + +
514B ASP* 4.0 26.0 - - + +
515B LEU* 3.7 31.2 - - + -
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Residues in contact with VAL 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ARG* 3.7 38.6 - - + +
635A HIS* 4.0 14.8 - - + +
757A GOL 3.2 38.6 + - - +
476B PRO* 1.3 75.4 - - - +
478B GLN* 1.3 56.7 + - - +
480B LEU* 3.4 5.7 + - - +
481B ASP* 2.9 29.3 + - - +
515B LEU* 3.8 26.9 - - + -
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Residues in contact with GLN 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A SER* 3.8 14.7 + - - +
419A ARG 3.8 10.8 - - - +
420A SER* 4.0 8.1 - - - -
421A THR* 3.5 25.9 - - - +
601A GLY 4.3 8.1 + - - -
603A ILE* 5.7 2.0 - - - +
754A GOL 2.9 46.4 + - - +
757A GOL 3.3 20.5 + - - +
474B SER* 4.1 4.9 - - - -
475B GLN 3.3 5.8 + - - +
476B PRO 3.3 0.2 - - - -
477B VAL* 1.3 75.6 - - - +
479B THR* 1.3 55.4 + - - +
481B ASP* 3.2 13.8 + - - +
482B SER* 2.8 42.8 + - - -
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Residues in contact with THR 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B THR* 4.0 13.7 + - - +
474B SER* 3.0 23.6 + - - -
475B GLN 2.9 21.0 + - - -
476B PRO* 3.6 8.0 - - - +
478B GLN* 1.3 74.1 - - - +
480B LEU* 1.3 57.8 + - + +
482B SER* 3.2 6.5 + - - -
483B LEU* 2.9 53.8 + - + +
507B MET* 3.8 20.0 - - + -
511B ALA* 4.4 12.1 - - + -
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ARG* 4.0 17.9 - - + +
476B PRO 3.1 15.8 + - - +
477B VAL* 3.7 7.0 - - - +
479B THR* 1.3 78.7 - - - +
481B ASP* 1.3 59.3 + - - +
483B LEU* 3.8 3.2 - - - +
484B ARG* 2.8 34.5 + - - +
508B GLU* 3.5 47.6 - - + +
511B ALA* 3.8 8.7 - - + -
512B LEU* 3.7 28.3 - - + -
515B LEU* 3.9 19.5 - - + -
524B LYS* 6.0 0.4 - - - -
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Residues in contact with ASP 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ILE* 3.8 8.6 - - + +
632A THR* 4.1 7.3 + - - +
633A SER* 2.8 31.8 + - - +
634A ARG* 3.0 29.0 + - - +
635A HIS* 3.5 17.3 + - - -
477B VAL* 2.9 25.8 + - - +
478B GLN* 3.2 15.4 + - - +
480B LEU* 1.3 70.7 - - - +
482B SER* 1.3 57.9 + - - +
484B ARG* 4.0 3.9 - - - +
485B ALA* 3.0 29.1 + - - +
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Residues in contact with SER 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754A GOL 3.5 25.8 + - - -
471B THR* 4.2 20.7 - - - +
474B SER* 5.0 1.3 + - - -
478B GLN* 2.8 25.6 + - - +
479B THR* 3.5 4.7 - - - -
481B ASP* 1.3 72.3 - - - +
483B LEU* 1.3 60.4 + - - +
485B ALA* 3.4 6.9 + - - +
486B ALA* 3.0 26.5 + - - +
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Residues in contact with LEU 483 (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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467B VAL* 4.6 10.5 - - + +
468B LEU* 3.8 20.4 - - + -
471B THR* 4.1 16.2 - - + -
479B THR* 2.9 26.6 + - + +
480B LEU 4.0 1.8 - - - +
482B SER* 1.3 75.7 - - - +
484B ARG* 1.3 61.4 + - - +
485B ALA 3.2 0.2 - - - -
486B ALA* 3.4 6.1 + - + +
487B ARG* 3.0 33.1 + - - +
504B LEU* 4.1 18.5 - - + +
507B MET* 3.7 37.2 - - + -
508B GLU* 3.8 29.4 - - + +
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Residues in contact with ARG 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A PRO 4.4 8.7 + - - -
632A THR* 3.4 44.7 + - + +
633A SER 5.5 1.2 - - - -
634A ARG* 5.8 3.2 - - - +
480B LEU 2.8 19.4 + - - +
481B ASP 4.0 2.9 - - - +
483B LEU* 1.3 72.9 - - - +
485B ALA* 1.3 61.3 + - - +
487B ARG* 3.6 22.8 - - - +
488B HIS* 2.7 30.3 + - - -
489B GLY* 3.5 13.9 + - - +
490B ALA* 3.3 34.7 + - - +
508B GLU* 4.0 1.0 + - - +
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Residues in contact with ALA 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A PRO* 6.4 0.7 - - + -
632A THR* 4.4 14.0 + - - +
481B ASP 3.0 20.4 + - - +
482B SER* 3.4 7.9 - - - +
483B LEU 3.2 0.2 - - - -
484B ARG* 1.3 78.5 - - - +
486B ALA* 1.3 61.8 + - - +
488B HIS* 3.0 28.4 + - - +
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Residues in contact with ALA 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B VAL* 5.0 9.9 - - + -
482B SER 3.0 16.9 + - - +
483B LEU* 3.6 13.2 - - + +
484B ARG 3.3 0.2 - - - -
485B ALA* 1.3 75.9 - - - +
487B ARG* 1.3 63.1 + - - +
488B HIS* 3.7 12.3 + - - -
498B PHE* 3.7 34.7 - - + -
504B LEU* 4.8 7.4 - - + -
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Residues in contact with ARG 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU 3.0 15.7 + - - +
484B ARG* 3.6 29.6 - - - +
486B ALA* 1.3 73.9 - - - +
488B HIS* 1.3 76.7 + - - +
489B GLY 2.7 26.2 + - - +
490B ALA* 3.7 16.8 + - - +
498B PHE* 4.9 12.8 - - + +
504B LEU* 3.7 26.0 - - + -
505B PRO* 6.2 1.1 - - - -
508B GLU* 2.9 36.0 + - - -
524B LYS* 4.4 9.7 - - - +
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Residues in contact with HIS 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A THR* 3.6 13.8 - - - +
484B ARG 2.7 18.9 + - - -
485B ALA* 3.0 21.6 + - - +
486B ALA* 3.8 11.6 + - - -
487B ARG* 1.3 78.5 + - - +
489B GLY* 1.3 56.7 + - - +
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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