Contacts of the strand formed by residues 320 - 323 (chain B) in PDB entry 2EZ9
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 320 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ALA* 4.0 20.2 - - + +
204B ARG* 3.7 37.5 - - + +
205B LEU* 3.7 33.0 - - + +
208B THR* 4.1 11.4 - - - +
302B PHE 3.7 2.2 + - - -
303B LEU* 3.4 14.7 - - + +
304B GLN 2.9 24.3 + - - +
318B THR* 3.4 4.7 - - - +
319B ASP* 1.3 86.7 - - + +
321B ALA* 1.3 64.4 + - - +
322B VAL* 4.1 13.7 - - + -
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Residues in contact with ALA 321 (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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188A SER* 3.9 27.3 + - - +
190A GLN* 4.5 16.6 + - - +
304B GLN* 3.5 20.2 - - - +
312B LEU* 4.1 12.9 - - + +
318B THR* 3.7 16.5 - - + +
320B ILE* 1.3 76.7 - - - +
322B VAL* 1.3 62.3 + - - +
323B LEU 3.8 2.3 + - - -
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Residues in contact with VAL 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B ASP* 4.7 13.0 - - + +
201B ALA* 3.9 31.9 - - + +
202B VAL* 4.0 21.8 - - + +
205B LEU* 3.9 23.1 - - + -
304B GLN 2.8 14.6 + - - +
305B ILE* 3.5 9.0 - - + -
306B ASP 3.2 25.6 + - - +
312B LEU* 4.2 3.4 - - - +
320B ILE* 4.2 2.9 - - + -
321B ALA* 1.3 74.3 - - - +
323B LEU* 1.3 62.4 + - - +
324B ALA* 3.4 23.4 + - + -
329B THR* 4.6 3.6 - - + -
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Residues in contact with LEU 323 (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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190A GLN* 4.0 18.7 - - + +
191A THR 3.3 26.2 - - - +
193A LEU* 3.4 39.8 - - + +
198B ASP* 5.3 6.1 + - - +
306B ASP 3.3 11.7 - - - +
307B ILE* 3.3 29.6 - - - +
308B ASP 3.8 1.6 - - - +
309B PRO* 3.7 30.7 - - + -
312B LEU* 4.1 14.8 - - + +
321B ALA 3.8 3.8 + - - -
322B VAL* 1.3 69.9 - - - +
324B ALA* 1.3 63.7 + - - +
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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
------------------------------------------------------------
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