Contacts of the strand formed by residues 279 - 283 (chain A) 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 VAL 279 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A THR* 4.3 10.5 - - + +
209A LEU* 4.3 13.2 - - + +
212A ALA* 3.5 29.6 - - + -
214A ARG 3.9 1.0 - - - +
215A PRO* 3.4 2.4 - - + +
216A LEU 3.0 25.5 + - - +
277A ALA* 4.3 0.5 - - - +
278A ASP* 1.3 94.4 + - - +
280A VAL* 1.3 66.6 - - - +
281A LEU 4.2 0.2 - - - -
300A ARG* 6.0 0.2 - - - -
301A TYR* 3.3 36.1 - - + +
303A LEU* 3.8 29.2 - - + -
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Residues in contact with VAL 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A LEU* 3.4 9.0 - - + +
218A TYR* 3.8 28.7 - - + -
274A LEU* 4.0 23.1 - - + -
277A ALA* 4.3 11.7 - - + -
279A VAL* 1.3 80.7 - - - +
281A LEU* 1.3 64.0 - - - +
282A PHE* 3.7 7.6 + - + +
296A PHE* 4.2 15.5 - - + -
299A THR* 3.9 22.0 - - + +
301A TYR 3.2 6.9 + - - +
302A PHE* 3.8 8.0 - - + -
303A LEU* 2.9 28.6 + - - +
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Residues in contact with LEU 281 (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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205A LEU* 3.9 12.6 - - + -
209A LEU* 4.3 23.6 - - + +
216A LEU 2.9 14.1 + - - +
217A ILE* 3.6 21.4 - - + -
218A TYR 2.8 32.6 + - - +
233A LEU* 5.6 0.9 - - + -
279A VAL 4.2 0.4 - - - -
280A VAL* 1.3 70.1 - - - +
282A PHE* 1.3 56.7 + - - +
283A VAL* 3.5 17.9 + - + +
303A LEU* 3.4 27.1 - - + +
305A ILE* 3.8 21.5 - - + -
330A LEU* 4.3 9.6 - - + -
333A ILE* 4.2 22.0 - - + -
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Residues in contact with PHE 282 (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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218A TYR* 3.4 19.1 - + + -
280A VAL* 3.7 2.7 + - + +
281A LEU* 1.3 69.8 - - - +
283A VAL* 1.3 57.9 + - - +
285A ASN* 3.1 60.6 - - + -
287A TYR* 4.0 13.2 - - + -
296A PHE* 3.8 19.5 - + - -
302A PHE* 3.4 38.6 - + + -
303A LEU 2.7 13.7 + - - +
304A GLN* 3.2 23.0 - - - +
305A ILE 3.0 22.9 + - - -
315A ARG* 4.2 23.3 - - + -
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 4.4 8.7 - - + -
218A TYR 3.1 7.6 + - - +
219A TYR* 3.2 11.0 - - + +
220A GLY 2.9 20.1 + - - +
223A ALA* 4.4 3.3 - - + +
281A LEU* 3.5 34.1 - - + +
282A PHE* 1.3 76.2 - - - +
284A GLY* 1.3 68.8 + - - +
285A ASN* 3.2 3.4 + - - +
305A ILE* 3.5 28.7 - - + -
326A ALA* 3.8 25.6 - - + -
330A LEU* 4.2 18.2 - - + -
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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