Contacts of the helix formed by residues 578 - 592 (chain B) in PDB entry 2R1Z
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 SER 578 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576B GLY 3.9 1.2 + - - -
577B LEU* 1.3 76.0 - - - +
579B SER* 1.3 58.7 + - - +
580B GLU* 3.8 5.2 + - - +
581B GLN* 3.0 36.4 + - - +
582B GLN* 2.8 30.8 + - - +
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Residues in contact with SER 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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578B SER* 1.3 74.0 - - - +
580B GLU* 1.3 57.7 + - - +
582B GLN* 3.3 12.7 + - - +
583B LYS* 3.0 40.1 + - - +
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Residues in contact with GLU 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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578B SER* 3.4 5.2 + - - +
579B SER* 1.3 80.0 - - - +
581B GLN* 1.3 57.6 + - + +
583B LYS* 3.4 35.1 + - + +
584B MET* 3.0 42.1 + - + +
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Residues in contact with GLN 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B GLY 4.4 0.2 + - - -
577B LEU* 3.4 18.0 - - + +
578B SER* 3.0 39.4 + - - +
580B GLU* 1.3 76.5 - - + +
582B GLN* 1.3 58.7 + - - +
584B MET* 3.3 0.9 + - - -
585B LEU* 2.9 26.5 + - - +
610B PRO* 3.4 32.8 - - - +
633B PHE* 3.5 51.0 - - + -
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Residues in contact with GLN 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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577B LEU* 3.3 38.5 + - + +
578B SER 2.8 18.6 + - - +
579B SER* 3.5 11.2 - - - +
581B GLN* 1.3 71.6 - - - +
583B LYS* 1.3 61.2 - - + +
585B LEU* 3.3 3.1 + - - +
586B SER* 2.9 34.1 + - - +
596B LYS* 4.7 9.0 + - + +
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Residues in contact with LYS 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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579B SER* 3.0 24.9 + - - +
580B GLU* 3.4 35.0 + - + +
582B GLN* 1.3 75.6 - - + +
584B MET* 1.3 58.6 + - + +
586B SER* 3.5 8.5 - - - -
587B GLU* 3.0 28.8 + - - +
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Residues in contact with MET 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 GLU* 3.0 26.9 + - + +
581B GLN* 3.6 5.8 - - - +
582B GLN 3.3 0.4 - - - -
583B LYS* 1.3 75.2 - - + +
585B LEU* 1.3 58.5 + - - +
587B GLU* 3.3 5.6 + - - +
588B LEU* 2.8 28.6 + - - +
633B PHE* 3.4 34.3 - - + -
636B VAL* 3.9 4.3 - - + -
637B LYS* 3.7 32.5 - - + -
640B LEU* 3.7 27.0 - - + +
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Residues in contact with LEU 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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572B LEU* 4.1 22.0 - - + -
573B ILE* 3.7 7.9 - - - +
574B GLY* 3.5 28.7 - - - +
577B LEU* 3.7 19.5 - - + -
581B GLN 2.9 17.1 + - - +
582B GLN* 3.8 4.5 - - - +
584B MET* 1.3 71.2 - - - +
586B SER* 1.3 68.1 + - - +
588B LEU* 3.3 4.4 + - + +
589B ALA* 2.9 24.1 + - - +
596B LYS* 4.1 21.1 - - + -
608B VAL* 3.8 15.0 - - + -
635B TRP* 4.9 0.7 - - + -
636B VAL* 3.7 31.1 - - + +
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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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582B GLN 2.9 17.8 + - - -
583B LYS* 3.5 9.8 - - - -
585B LEU* 1.3 73.9 - - - +
587B GLU* 1.3 61.4 + - - +
589B ALA* 3.1 20.8 + - - +
590B VAL* 3.2 12.1 + - - +
596B LYS* 3.1 34.7 + - - +
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Residues in contact with GLU 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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583B LYS 3.0 14.5 + - - +
584B MET* 3.7 6.7 - - - +
586B SER* 1.3 76.1 - - - +
588B LEU* 1.3 64.8 + - - +
590B VAL* 3.3 23.0 + - - +
591B ILE* 3.2 32.3 + - + +
640B LEU* 4.1 16.6 - - + -
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Residues in contact with LEU 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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572B LEU* 4.6 6.1 - - + -
584B MET 2.8 19.8 + - - +
585B LEU* 3.3 6.9 + - + +
587B GLU* 1.3 72.2 - - - +
589B ALA* 1.3 64.6 + - - +
591B ILE* 3.1 9.0 + - + +
592B LEU* 2.9 46.4 + - + +
635B TRP* 3.7 34.8 - - + -
636B VAL* 3.9 21.3 - - + -
639B CYS* 3.4 38.6 - - + +
640B LEU* 4.2 12.7 - - + +
644B VAL 4.9 0.4 - - - +
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Residues in contact with ALA 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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572B LEU* 3.7 19.0 - - + +
585B LEU 2.9 13.0 + - - +
586B SER* 3.1 13.9 - - - +
588B LEU* 1.3 76.6 - - - +
590B VAL* 1.3 58.1 + - + +
592B LEU 3.6 0.2 + - - -
593B LYS 3.2 2.3 + - - -
594B ALA* 2.7 44.2 + - - +
596B LYS* 3.8 26.7 - - + +
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Residues in contact with VAL 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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586B SER 3.2 12.3 + - - +
587B GLU* 3.4 26.2 - - - +
589B ALA* 1.3 77.2 - - + +
591B ILE* 1.3 65.6 + - + +
593B LYS* 3.1 17.4 + - - +
594B ALA 5.1 0.4 - - - -
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Residues in contact with ILE 591 (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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587B GLU* 3.2 24.0 + - + +
588B LEU* 3.1 11.5 + - + +
590B VAL* 1.3 79.7 - - + +
592B LEU* 1.3 66.8 + - + +
593B LYS* 3.3 13.5 + - - +
639B CYS 5.9 1.6 - - - +
640B LEU* 3.6 33.9 - - + +
643B LYS* 4.8 23.1 - - + +
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Residues in contact with LEU 592 (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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570B LEU* 4.5 16.8 - - + +
572B LEU* 5.0 5.8 - - + -
588B LEU* 2.9 45.2 + - + +
591B ILE* 1.3 81.6 - - + +
593B LYS* 1.3 72.0 + - - +
594B ALA* 4.3 12.1 - - + +
635B TRP* 4.2 15.0 - - + -
639B CYS* 5.2 0.2 - - - -
644B VAL* 4.2 2.7 - - - -
645B CYS* 3.7 51.6 - - + +
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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