Contacts of the helix formed by residues 571 - 580 (chain B) in PDB entry 1P43
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 571 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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566B LYS* 5.2 0.4 - - + -
567B ASN* 3.1 31.8 + - - +
569B ASN 3.6 0.4 - - - -
570B ASP* 1.3 87.2 - - + +
572B ILE* 1.3 67.3 + - - +
573B ALA 3.5 0.7 - - - -
574B PRO* 3.2 13.5 - - - +
575B ALA* 3.7 12.3 + - - +
596B LEU* 4.1 17.1 - - + +
605B LEU* 3.8 21.5 - - + -
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Residues in contact with ILE 572 (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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505B VAL* 4.8 2.0 - - + -
567B ASN 2.9 16.5 + - - +
568B VAL* 3.7 19.1 - - + +
571B VAL* 1.3 69.4 - - - +
573B ALA* 1.3 58.3 + - - +
575B ALA* 3.4 2.1 + - - +
576B PHE* 2.8 47.2 + - + +
592B PHE* 4.6 0.8 - - + -
593B LEU* 3.8 25.6 - - + -
596B LEU* 3.7 10.8 - - + -
605B LEU* 3.8 29.4 - - + -
609B ALA* 3.8 34.5 - - + +
610B ILE* 4.3 7.9 - - + +
613B VAL* 4.1 13.7 - - + -
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Residues in contact with ALA 573 (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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505B VAL* 3.3 40.1 - - + +
568B VAL 2.7 22.8 + - - +
569B ASN* 3.5 11.2 - - - +
572B ILE* 1.3 73.1 - - - +
574B PRO* 1.3 69.3 - - + +
576B PHE* 3.7 0.5 - - - +
577B VAL* 3.0 31.3 + - + +
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Residues in contact with PRO 574 (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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569B ASN 3.7 11.4 - - - +
570B ASP 3.5 14.6 - - - +
571B VAL* 3.2 21.5 - - - +
573B ALA* 1.3 95.9 - - + +
575B ALA* 1.3 60.2 + - - +
577B VAL* 3.7 4.7 + - + +
578B LYS* 3.2 25.0 + - - +
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Residues in contact with ALA 575 (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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571B VAL 3.7 14.1 - - - +
572B ILE 3.4 1.3 + - - +
573B ALA 3.4 0.4 - - - -
574B PRO* 1.3 79.5 - - + +
576B PHE* 1.3 61.6 + - - +
578B LYS* 3.6 8.0 + - - +
579B ALA* 3.0 23.4 + - - +
592B PHE* 3.3 25.5 - - + -
596B LEU* 4.3 15.3 - - + -
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Residues in contact with PHE 576 (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* 3.9 32.4 - - + +
505B VAL* 3.9 19.3 - - + -
523B LEU* 4.2 12.1 - - + -
572B ILE* 2.8 26.0 + - + +
573B ALA 3.7 3.1 - - - +
575B ALA* 1.3 71.8 - - - +
577B VAL* 1.3 65.8 + - - +
579B ALA* 3.2 12.5 + - - +
580B ASN* 3.4 8.0 + - - -
581B ILE* 3.9 25.4 + - + +
583B VAL* 5.2 1.3 - - + -
589B VAL* 3.9 30.7 - - + -
592B PHE* 3.5 26.0 - + + -
593B LEU* 4.0 8.5 - - + -
613B VAL* 3.7 25.4 - - + -
617B ALA* 4.9 0.7 - - + -
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Residues in contact with VAL 577 (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* 3.6 25.7 - - + +
503B SER* 4.0 26.0 - - - +
504B LYS* 4.2 8.1 - - - +
505B VAL* 4.3 12.3 - - + +
573B ALA* 3.0 19.2 + - + +
574B PRO* 4.1 3.8 - - + +
576B PHE* 1.3 76.1 - - - +
578B LYS* 1.3 63.4 + - - +
580B ASN* 3.2 15.4 + - - +
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Residues in contact with LYS 578 (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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574B PRO 3.2 17.3 + - - +
575B ALA* 3.9 7.9 - - - +
577B VAL* 1.3 80.5 - - - +
579B ALA* 1.3 61.9 + - - +
580B ASN* 3.3 4.9 + - - +
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Residues in contact with ALA 579 (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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575B ALA 3.0 18.3 + - - +
576B PHE 3.5 7.0 - - - +
577B VAL 3.2 0.6 - - - -
578B LYS* 1.3 75.5 - - - +
580B ASN* 1.3 72.6 + - - +
581B ILE* 3.6 24.7 - - + +
592B PHE* 4.0 13.0 - - + -
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Residues in contact with ASN 580 (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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501B ALA* 4.2 24.2 - - - +
502B VAL* 5.0 5.6 + - - +
576B PHE 3.4 2.4 + - - -
577B VAL* 3.2 12.7 + - - +
578B LYS 3.2 7.3 - - - +
579B ALA* 1.3 81.7 - - - +
581B ILE* 1.3 65.0 + - - +
582B ASP 4.0 0.5 + - - -
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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