Contacts of the helix formed by residues 575 - 590 (chain B) in PDB entry 2C3O
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 PRO 575 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568B PHE 4.8 0.7 - - - +
573B VAL 4.9 0.2 - - - +
574B LEU* 1.3 94.2 - - + +
576B PHE* 1.3 69.4 + - - +
577B GLU* 4.8 3.4 - - + +
578B LYS* 4.2 26.2 - - + +
579B ALA* 3.4 13.0 + - - +
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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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568B PHE 5.4 2.6 - - - +
569B LYS* 3.4 53.2 - - + +
575B PRO* 1.3 77.3 - - - +
577B GLU* 1.3 76.6 + - + +
579B ALA* 3.7 2.1 - - - +
580B VAL* 3.4 32.1 + - + +
610B VAL* 4.3 17.9 - - + -
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Residues in contact with GLU 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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575B PRO* 3.6 3.2 - - + +
576B PHE* 1.3 90.4 - - + +
578B LYS* 1.3 71.0 + - - +
579B ALA 2.6 0.9 + - - -
580B VAL* 2.8 13.7 + - - +
581B ASP* 3.2 9.0 + - + -
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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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444B ASN* 3.2 32.6 + - - +
445B THR* 4.3 12.3 - - - +
574B LEU* 4.9 6.7 - - + -
575B PRO* 4.2 28.6 + - + +
576B PHE 3.9 0.2 - - - -
577B GLU* 1.3 75.8 - - - +
579B ALA* 1.3 64.6 + - - +
581B ASP* 3.1 9.6 + - - +
582B LEU* 2.9 45.2 + - + +
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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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440B ILE* 5.1 0.7 - - - +
568B PHE* 3.9 35.8 - - + +
574B LEU* 3.9 25.5 - - + +
575B PRO 3.4 19.3 + - - +
576B PHE 3.7 3.3 + - - +
577B GLU 2.6 4.6 + - - -
578B LYS* 1.3 73.6 - - - +
580B VAL* 1.3 65.5 + - + +
582B LEU* 2.8 17.3 + - - +
583B LEU* 2.9 13.7 + - - +
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Residues in contact with VAL 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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565B THR* 6.2 1.6 - - + -
568B PHE* 5.2 6.5 - - + +
569B LYS* 6.0 5.4 - - + -
576B PHE* 3.4 34.3 - - + +
577B GLU* 2.8 11.0 + - - +
579B ALA* 1.3 73.1 - - + +
581B ASP* 1.3 55.6 + - - +
583B LEU* 3.2 9.0 + - - +
584B LYS* 2.8 42.6 + - + +
606B VAL* 4.3 23.8 - - + -
607B ASP* 5.5 1.8 - - - +
610B VAL* 5.1 11.2 - - + -
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Residues in contact with ASP 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B GLU* 3.2 6.1 + - + +
578B LYS* 3.1 19.1 + - - +
580B VAL* 1.3 81.9 - - - +
582B LEU* 1.3 66.4 + - + +
584B LYS* 3.5 7.0 + - - +
585B LYS* 3.0 46.9 + - - +
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Residues in contact with LEU 582 (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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440B ILE* 3.6 25.1 - - + +
444B ASN* 3.3 45.5 - - + +
574B LEU* 4.5 10.8 - - + -
578B LYS* 2.9 47.3 + - + +
579B ALA 2.8 7.0 + - - +
581B ASP* 1.3 85.1 - - + +
583B LEU* 1.3 67.0 + - - +
585B LYS* 3.0 13.2 + - + +
586B SER* 2.9 22.3 + - - -
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Residues in contact with LEU 583 (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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440B ILE* 4.7 3.0 - - - +
561B MET* 3.4 25.4 - - + -
564B GLN* 4.1 5.2 - - + -
565B THR* 4.1 25.1 - - + +
568B PHE* 3.4 38.8 - - + -
579B ALA 2.9 11.2 + - - +
580B VAL* 3.6 12.6 - - + +
582B LEU* 1.3 74.6 - - - +
584B LYS* 1.3 63.5 + - - +
586B SER* 2.5 28.5 + - - +
587B ILE* 3.0 28.3 + - + -
606B VAL* 4.0 11.0 - - + -
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Residues in contact with LYS 584 (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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580B VAL* 2.8 28.6 + - + +
581B ASP* 3.6 8.7 - - - +
583B LEU* 1.3 75.9 - - - +
585B LYS* 1.3 60.2 + - + +
587B ILE* 3.1 23.4 + - + +
588B HIS* 2.7 35.2 + - + -
603B THR* 3.4 41.5 - - + +
606B VAL* 3.9 16.8 - - + -
607B ASP* 3.2 28.5 + - - -
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Residues in contact with LYS 585 (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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581B ASP* 3.0 36.7 + - - +
582B LEU* 3.0 13.3 + - + +
584B LYS* 1.3 79.4 - - + +
586B SER* 1.3 61.7 + - - +
588B HIS* 3.0 14.0 + - + +
589B LYS* 3.0 19.3 + - - +
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Residues in contact with SER 586 (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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436B GLN* 4.5 4.7 - - - -
440B ILE* 3.5 30.2 - - - +
582B LEU 2.9 6.6 + - - -
583B LEU* 2.5 31.9 + - - +
585B LYS* 1.3 76.7 - - - +
587B ILE* 1.3 62.0 + - - +
589B LYS* 3.2 20.2 - - - +
590B ALA* 3.0 27.2 + - - +
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Residues in contact with ILE 587 (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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561B MET* 4.7 8.5 - - - -
583B LEU* 3.0 37.6 + - + +
584B LYS* 3.1 28.0 + - + +
586B SER* 1.3 78.5 - - - +
588B HIS* 1.3 55.9 + - + +
590B ALA 2.8 15.6 - - - +
591B TYR* 3.4 20.9 - - + +
592B GLY 4.4 0.3 + - - -
599B VAL* 4.0 23.8 - - + +
602B ASN* 3.8 31.9 - - + +
603B THR* 4.2 2.9 - - - +
606B VAL* 3.6 19.5 - - + -
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Residues in contact with HIS 588 (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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584B LYS* 2.7 35.7 + - + -
585B LYS* 3.0 11.4 + - + +
587B ILE* 1.3 74.6 - - + +
589B LYS* 1.3 70.8 + - - +
590B ALA 2.8 7.1 - - - +
592B GLY* 3.8 16.2 - - - +
596B GLU* 4.1 18.8 + - - -
599B VAL* 3.9 26.9 - - + +
603B THR* 4.5 10.1 - - + -
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Residues in contact with LYS 589 (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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436B GLN* 2.6 39.8 + - - +
439B LYS* 4.3 11.5 - - - +
440B ILE* 4.7 5.9 - - - +
585B LYS 3.0 7.2 + - - +
586B SER* 3.2 27.2 - - - +
588B HIS* 1.3 81.6 - - - +
590B ALA* 1.3 68.0 + - - +
591B TYR 4.0 4.7 - - - +
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Residues in contact with ALA 590 (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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436B GLN* 6.2 3.1 - - + -
586B SER 3.0 10.6 + - - +
587B ILE 2.8 15.6 - - - +
588B HIS 2.8 2.6 - - - +
589B LYS* 1.3 90.9 - - + +
591B TYR* 1.3 86.7 + - + +
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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