Contacts of the helix formed by residues 581 - 589 (chain B) in PDB entry 2EZT
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 581 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B LYS* 4.0 2.2 - - - +
272B GLU* 3.5 11.4 - - - +
352B ASN* 4.3 0.4 - - - -
557B LEU* 3.6 28.9 - - + +
558B ASP* 3.8 29.2 - - + +
561B MET* 5.6 0.7 - - + -
579B LEU 4.6 1.1 - - - +
580B GLN* 1.3 93.3 - - + +
582B LEU* 1.3 66.6 + - - +
583B SER* 3.6 14.4 - - - +
584B THR* 3.1 33.4 + - - +
585B TYR* 3.8 4.2 - - - -
1616B PYR 4.4 1.6 - - - +
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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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272B GLU* 2.9 60.5 + - + +
273B ALA* 3.8 12.6 - - + +
276B GLN* 4.1 16.4 - - + -
345B TRP* 4.7 1.8 - - + -
348B ALA* 4.1 14.4 - - + +
349B ASN* 4.4 9.0 - - - +
352B ASN* 3.8 30.3 - - + +
580B GLN 3.8 0.2 + - - -
581B PRO* 1.3 71.6 - - - +
583B SER* 1.3 53.6 + - - +
585B TYR* 2.8 24.6 + - + -
586B LEU* 2.9 33.5 + - + -
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Residues in contact with SER 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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558B ASP* 3.0 34.5 + - - -
581B PRO* 3.6 9.2 - - - +
582B LEU* 1.3 76.8 - - - +
584B THR* 1.3 58.7 + - - +
586B LEU* 4.1 13.0 - - - +
587B LYS* 2.9 50.5 + - - +
593B ASP* 3.8 21.1 + - - -
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Residues in contact with THR 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 GLN* 4.2 25.1 + - + +
581B PRO* 3.1 29.9 + - - +
583B SER* 1.3 80.7 + - - +
585B TYR* 1.3 68.3 + - + +
587B LYS* 3.7 15.2 + - - +
588B GLN* 3.0 28.4 + - + +
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Residues in contact with TYR 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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348B ALA* 3.6 23.3 - - + +
351B ALA* 3.6 20.2 - - + -
352B ASN* 3.5 40.8 - - + -
355B ASN* 3.0 35.3 + - + +
580B GLN* 3.2 29.5 - - + +
581B PRO 3.8 7.2 - - - -
582B LEU* 2.8 12.4 + - + +
584B THR* 1.3 77.1 - - + +
586B LEU* 1.3 63.6 + - - +
588B GLN* 3.3 26.6 + - - +
589B PHE* 3.1 29.9 + - + -
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Residues in contact with LEU 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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214B ARG* 5.8 1.1 - - - -
276B GLN* 4.1 19.7 - - + +
345B TRP* 4.0 20.0 - - + -
348B ALA* 3.8 20.4 - - + +
582B LEU* 2.9 32.2 + - + +
583B SER* 3.7 11.0 - - - +
585B TYR* 1.3 76.3 - - - +
587B LYS* 1.3 53.5 + - - +
589B PHE* 3.1 5.0 + - - +
590B GLY 3.0 10.6 + - - -
591B LEU* 2.8 60.4 + - + +
592B ASP 4.4 7.6 - - - +
593B ASP* 3.7 22.9 - - - +
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Residues in contact with LYS 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 SER* 2.9 38.7 + - - +
584B THR* 4.0 16.9 + - - +
586B LEU* 1.3 75.9 - - + +
588B GLN* 1.3 64.0 + - - +
590B GLY* 3.2 12.2 + - - -
591B LEU 3.6 15.5 - - - +
592B ASP* 5.5 1.8 - - - -
593B ASP* 5.3 3.8 - - - +
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Residues in contact with GLN 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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351B ALA* 5.1 1.0 - - - +
584B THR* 3.0 20.3 + - + +
585B TYR* 3.4 37.1 - - - +
587B LYS* 1.3 76.9 - - - +
589B PHE* 1.3 86.0 + - + +
590B GLY 3.4 0.4 + - - -
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Residues in contact with PHE 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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344B PRO* 3.2 45.1 - - + +
347B GLN* 3.6 45.3 - - + -
348B ALA* 3.6 15.3 - - + -
351B ALA* 4.2 9.9 - - + -
585B TYR* 3.1 23.1 + - + +
586B LEU 3.1 6.7 + - - +
588B GLN* 1.3 109.4 - - + +
590B GLY* 1.3 57.5 + - - +
591B LEU* 3.7 0.4 - - + -
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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