Contacts of the strand formed by residues 281 - 285 (chain C) in PDB entry 2W93
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 LEU 281 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C LEU* 3.8 18.4 - - + +
208C VAL* 3.8 40.2 - - + +
211C ALA* 3.8 17.5 - - + -
213C ASN 4.0 0.2 + - - -
214C PRO* 3.3 12.6 - - + +
215C VAL 2.9 25.8 + - - -
279C ALA* 3.4 6.7 - - - +
280C ASP* 1.3 82.1 + - - +
282C ILE* 1.3 65.8 + - - +
283C LEU* 4.2 13.7 - - + -
303C THR* 4.3 0.6 - - - +
305C ASN* 3.3 27.8 - - + +
307C VAL* 3.9 25.6 - - + -
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Residues in contact with ILE 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C VAL* 3.5 22.2 - - + -
217C LEU* 4.5 16.4 - - + -
276C VAL* 4.2 11.0 - - + +
279C ALA* 3.8 6.1 - - + +
281C LEU* 1.3 77.2 - - - +
283C LEU* 1.3 65.3 - - - +
284C SER* 3.4 19.0 + - - +
301C TYR* 3.4 52.0 - - + -
303C THR* 4.2 4.9 - - - +
305C ASN 2.9 9.3 + - - +
306C ILE* 3.7 19.9 - - + -
307C VAL* 2.8 33.6 + - - +
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C ILE* 4.2 14.6 - - + -
208C VAL* 4.6 8.1 - - + -
215C VAL 2.8 15.2 + - - +
216C ILE* 3.4 15.4 - - + -
217C LEU 2.9 24.5 + - - -
234C LEU* 4.3 23.1 - - + -
240C PHE* 4.2 30.3 - - + -
281C LEU* 4.2 16.6 - - + -
282C ILE* 1.3 70.3 - - - +
284C SER* 1.3 61.8 - - - +
285C VAL* 3.6 7.0 + - + +
307C VAL* 3.8 28.9 - - + -
309C PHE* 4.1 16.4 - - + -
333C LEU* 5.9 0.4 - - + -
337C ILE* 5.4 1.3 - - + -
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Residues in contact with SER 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C LEU* 3.6 15.7 + - - +
219C ASP* 5.5 0.7 - - - +
282C ILE* 4.3 15.0 - - - -
283C LEU* 1.3 71.7 - - - +
285C VAL* 1.3 60.0 + - - +
286C GLY 3.6 1.2 + - - -
287C ALA* 3.5 27.4 + - - +
301C TYR* 5.9 1.6 - - - -
306C ILE* 4.6 4.9 - - - -
307C VAL 2.8 17.8 + - - -
308C GLU* 3.6 12.0 - - - +
309C PHE* 2.7 31.3 + - - -
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Residues in contact with VAL 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ILE* 4.5 13.5 - - + -
217C LEU 2.8 14.0 + - - +
218C ALA* 4.4 3.6 - - - -
219C ASP 2.9 27.5 + - - -
222C CYS* 3.6 19.6 - - + +
227C VAL* 3.8 15.3 - - + -
231C THR* 3.7 26.2 - - + +
234C LEU* 4.6 10.3 - - + -
283C LEU 3.9 10.5 - - - +
284C SER* 1.3 73.9 + - - +
286C GLY* 1.3 58.9 + - - +
287C ALA 3.6 0.7 - - - -
309C PHE* 4.1 19.1 - - + -
326C MET* 4.6 6.1 - - - -
330C LEU* 4.6 7.9 - - + -
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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