Contacts of the helix formed by residues 475 - 488 (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 GLN 475 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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473A LEU 3.7 4.1 + - - +
474A SER* 1.3 72.0 - - - +
476A PRO* 1.3 67.3 - - + +
477A VAL 3.5 0.4 - - - -
478A GLN 3.2 2.4 + - - -
479A THR* 2.8 34.7 + - - -
755A GOL 3.1 30.3 - - - +
419B ARG* 2.9 17.7 + - + +
420B SER* 3.5 12.7 + - - -
451B THR* 4.5 19.3 + - - +
475B GLN* 5.0 11.6 + - - +
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Residues in contact with PRO 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A SER 4.6 0.4 - - - +
475A GLN* 1.3 94.2 - - + +
477A VAL* 1.3 62.7 + - - +
479A THR* 3.3 5.2 - - - +
480A LEU* 3.0 25.5 + - - +
511A ALA* 3.8 17.0 - - + +
514A ASP* 3.9 28.0 - - + +
515A LEU* 3.5 32.8 - - + -
755A GOL 3.7 6.5 - - - +
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Residues in contact with VAL 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A PRO* 1.3 72.0 - - - +
478A GLN* 1.3 53.7 + - - -
480A LEU* 3.2 7.8 + - - +
481A ASP* 2.9 29.0 + - - +
515A LEU* 3.7 30.5 - - + -
755A GOL 2.8 39.4 - - - +
634B ARG* 3.8 38.8 - - + +
635B HIS* 3.9 15.5 - - + +
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Residues in contact with GLN 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A SER* 3.9 8.1 - - - +
475A GLN 3.2 7.7 + - - +
477A VAL* 1.3 74.0 - - - +
479A THR* 1.3 58.0 + - - +
481A ASP* 3.4 13.3 + - - +
482A SER* 2.9 36.5 + - - +
755A GOL 2.8 21.6 - - - +
418B SER* 3.5 32.1 - - - +
419B ARG 3.7 16.2 - - - +
420B SER* 3.9 16.2 - - - +
421B THR* 4.0 13.5 - - - +
601B GLY 4.9 10.5 + - - +
603B ILE* 6.2 1.1 - - - +
754B GOL 4.7 8.1 + - - -
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Residues in contact with THR 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A THR* 4.2 21.1 + - + +
474A SER* 2.9 21.7 + - - -
475A GLN 2.8 19.8 + - - -
476A PRO* 3.3 12.9 - - - +
478A GLN* 1.3 74.1 - - - +
480A LEU* 1.3 66.9 + - + +
482A SER* 3.2 2.6 + - - -
483A LEU* 2.9 32.8 + - + +
507A MET* 4.0 28.9 - - + +
511A ALA* 4.3 13.0 - - + -
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A PRO 3.0 14.1 + - - +
477A VAL* 3.2 7.8 + - - +
479A THR* 1.3 75.1 - - + +
481A ASP* 1.3 60.7 + - - +
483A LEU* 3.9 3.3 - - - +
484A ARG* 2.9 33.6 + - - +
508A GLU* 3.5 48.1 - - + +
511A ALA* 3.8 7.4 - - + -
512A LEU* 3.8 22.2 - - + -
515A LEU* 3.7 23.8 - - + -
634B ARG* 3.7 28.7 - - + +
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Residues in contact with ASP 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A VAL* 2.9 20.5 + - - +
478A GLN* 3.7 14.7 + - - +
480A LEU* 1.3 77.0 - - - +
482A SER* 1.3 57.5 + - - +
484A ARG* 4.1 3.6 - - - +
485A ALA* 3.0 31.0 + - - +
603B ILE* 4.1 6.7 - - + +
632B THR* 4.3 7.1 + - - +
633B SER* 3.0 26.9 + - - -
634B ARG* 3.0 36.6 + - - +
635B HIS* 3.5 17.5 + - - -
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Residues in contact with SER 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A THR* 4.2 14.8 + - - -
474A SER* 5.2 2.1 + - - -
478A GLN* 2.9 34.4 + - - +
479A THR 3.7 3.4 - - - -
481A ASP* 1.3 76.7 - - - +
483A LEU* 1.3 60.1 + - - +
485A ALA* 3.5 4.9 + - - +
486A ALA* 2.9 30.9 + - - +
417B PRO* 5.9 2.9 - - - +
754B GOL 5.0 4.2 + - - -
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Residues in contact with LEU 483 (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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467A VAL* 4.6 13.5 - - + +
468A LEU* 3.7 21.1 - - + -
471A THR* 4.6 12.3 - - + +
479A THR* 2.9 26.3 + - + +
480A LEU 4.0 1.8 - - - +
482A SER* 1.3 79.5 - - - +
484A ARG* 1.3 59.6 + - - +
486A ALA* 3.4 4.7 + - + +
487A ARG* 2.8 30.7 + - - +
504A LEU* 3.8 30.5 - - + +
507A MET* 3.7 37.7 - - + -
508A GLU* 3.7 24.0 - - + +
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Residues in contact with ARG 484 (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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480A LEU 2.9 19.0 + - - +
481A ASP 4.1 2.0 - - - +
483A LEU* 1.3 74.0 - - - +
485A ALA* 1.3 60.0 + - - +
487A ARG* 3.2 37.3 + - - +
488A HIS* 3.0 61.1 + - + -
508A GLU* 4.0 1.1 + - - +
524A LYS* 4.6 10.1 - - - +
631B PRO 5.4 0.2 - - - -
632B THR* 3.3 36.1 - - - +
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Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ASP 3.0 19.3 + - - +
482A SER* 3.8 5.6 - - - +
484A ARG* 1.3 74.7 - - - +
486A ALA* 1.3 65.6 + - - +
488A HIS* 3.0 15.9 + - - +
489A GLY 3.5 15.6 - - - +
632B THR* 4.5 17.2 - - - +
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Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A VAL* 5.1 13.5 - - + -
482A SER 2.9 19.5 + - - +
483A LEU* 3.6 11.0 - - + +
485A ALA* 1.3 75.5 - - - +
487A ARG* 1.3 60.0 + - - +
489A GLY* 3.6 14.9 + - - -
498A PHE* 3.5 30.8 - - + -
504A LEU* 5.1 4.5 - - + -
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Residues in contact with ARG 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A LEU 2.8 12.2 + - - +
484A ARG* 3.3 54.2 - - - +
485A ALA 3.1 0.2 - - - -
486A ALA* 1.3 77.7 - - - +
488A HIS* 1.3 66.1 + - + +
489A GLY 3.2 4.8 + - - -
498A PHE* 4.7 14.1 - - + +
504A LEU* 3.6 25.1 - - + -
505A PRO* 6.2 1.6 - - - -
508A GLU* 3.0 32.0 + - - -
524A LYS* 4.1 8.9 - - - +
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Residues in contact with HIS 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ARG* 3.0 58.4 + - + +
485A ALA* 3.0 6.3 + - - +
487A ARG* 1.3 86.5 + - + +
489A GLY* 1.3 60.4 + - - +
632B THR* 4.0 21.4 - - + +
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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
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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