Contacts of the strand formed by residues 389 - 392 (chain A) 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 ILE 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 4.0 17.3 - - + -
387A ASP 3.9 1.8 - - - +
388A ALA* 1.3 73.2 - - - +
390A TYR* 1.3 70.3 + - - +
391A SER 4.1 0.2 - - - -
412A ARG* 3.3 15.7 - - + +
414A ILE* 5.4 2.0 - - + -
432A ALA* 3.7 22.2 - - + +
436A TYR* 3.3 47.6 - - + -
439A ARG* 3.6 35.0 - - + +
440A GLN 2.9 10.6 + - - +
441A VAL* 3.3 10.9 - - + +
442A PHE* 2.9 28.1 + - - +
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Residues in contact with TYR 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A VAL* 3.8 18.2 - - + +
381A ASN* 5.0 2.6 + - - -
384A ALA* 3.2 28.4 - - - +
388A ALA* 3.8 24.6 - - + +
389A ILE* 1.3 75.2 - - - +
391A SER* 1.3 58.7 + - - +
392A ILE* 3.9 12.8 - - + -
405A LEU* 3.7 21.0 - - + +
406A LYS 5.6 1.0 + - - -
407A LEU* 3.5 30.8 - - + +
411A ASN* 3.8 4.4 + - - -
412A ARG 2.9 18.4 + - - -
413A HIS* 3.1 14.1 - - + +
414A ILE* 2.9 28.8 + - - +
442A PHE* 3.4 33.2 - + + -
444A LEU* 4.0 7.6 - - + -
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Residues in contact with SER 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ILE* 4.1 1.2 - - - +
390A TYR* 1.3 73.2 - - - +
392A ILE* 1.3 61.4 + - - +
414A ILE* 3.7 11.9 + - - +
424A VAL* 3.4 6.2 + - - +
425A GLY* 2.7 21.8 + - - -
428A GLY* 3.2 19.5 - - - -
429A ALA* 3.4 22.7 - - - -
432A ALA* 5.4 1.8 - - - -
441A VAL* 5.4 0.4 - - - +
442A PHE 2.9 12.8 + - - -
443A ASN* 3.3 4.9 - - - +
444A LEU* 2.9 24.9 + - - +
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Residues in contact with ILE 392 (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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245A TYR* 4.1 10.8 - - + +
390A TYR* 4.1 15.3 - - + +
391A SER* 1.3 78.5 + - - +
393A ASP* 1.3 71.1 + - - +
397A ILE* 3.8 28.5 - - + +
398A ASN* 3.7 12.6 - - - +
401A ALA* 3.9 20.6 - - + -
405A LEU* 4.2 6.7 - - + -
413A HIS* 4.1 26.9 - - + +
414A ILE 2.9 13.9 + - - +
415A THR* 2.8 29.3 + - - -
424A VAL* 3.4 10.7 - - - +
425A GLY* 4.3 3.4 + - - -
444A LEU* 3.5 10.5 - - + -
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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