Contacts of the strand formed by residues 304 - 314 (chain C) in PDB entry 4LEY
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 304 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167C ALA* 3.8 26.9 - - + +
170C THR* 5.6 1.3 - - - -
171C VAL* 4.0 13.5 - - + -
209C PRO 4.1 9.2 - - - +
210C ASN* 3.5 7.2 - - - +
212C PHE* 3.6 31.9 - - + -
296C LEU 3.6 1.0 - - - +
297C LEU* 3.7 3.3 - - - +
298C ILE* 2.9 44.5 + - + +
300C ASN* 3.9 24.2 - - + +
302C GLU* 3.4 19.1 - - + +
303C GLU* 1.3 76.1 - - - +
305C SER* 1.3 66.8 + - - +
306C VAL* 4.4 3.4 - - + -
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Residues in contact with SER 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210C ASN 2.8 18.8 + - - -
211C GLU* 3.4 18.0 - - - +
212C PHE 2.9 24.3 + - - +
285C GLU* 6.1 0.2 - - - -
295C THR* 4.3 13.9 - - - -
296C LEU 3.3 7.2 - - - -
297C LEU* 4.7 9.6 - - - -
304C ILE* 1.3 76.4 - - - +
306C VAL* 1.3 63.7 + - - +
307C ASP* 4.2 1.8 - - - -
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Residues in contact with VAL 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C VAL* 4.0 24.2 - - + -
174C VAL* 6.5 0.2 - - + -
175C VAL* 4.4 13.9 - - + -
212C PHE* 3.4 13.0 - - + +
214C VAL* 4.6 7.0 - - + -
294C VAL 3.6 0.5 - - - +
295C THR* 3.3 2.3 - - - +
296C LEU* 2.8 50.0 + - + +
298C ILE* 4.2 23.1 - - + -
304C ILE* 4.4 2.7 - - + -
305C SER* 1.3 79.8 - - - +
307C ASP* 1.3 65.7 + - - +
308C ILE* 3.5 27.6 + - + -
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Residues in contact with ASP 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C PHE 2.9 9.5 + - - -
213C ASP* 3.2 23.8 - - - +
214C VAL* 2.9 32.7 + - - +
291C SER* 5.4 1.3 + - - -
293C ALA* 3.7 16.8 - - + -
294C VAL 4.1 1.8 - - - -
295C THR* 2.5 38.6 + - - +
305C SER* 4.2 1.5 - - - -
306C VAL* 1.3 71.3 - - - +
308C ILE* 1.3 60.5 + - - +
309C ILE* 3.6 8.9 + - + +
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Residues in contact with ILE 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C VAL* 4.5 8.5 - - + -
178C LEU* 4.5 8.3 - - + -
214C VAL* 3.6 9.0 - - + -
216C PHE* 4.0 35.4 - - + -
266C PHE* 3.6 29.4 - - + -
270C ILE* 3.6 21.1 - - + -
293C ALA* 3.3 1.8 - - - -
294C VAL 2.9 42.0 + - - +
296C LEU* 4.3 17.9 - - + -
306C VAL* 3.9 19.7 - - + -
307C ASP* 1.3 71.0 - - - +
309C ILE* 1.3 62.5 + - - +
310C LEU 3.7 1.7 + - - -
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Residues in contact with ILE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C THR* 4.9 2.2 - - - +
213C ASP* 4.5 16.6 - - + -
214C VAL 2.9 18.8 + - - +
215C MET* 3.5 21.6 - - + -
216C PHE 2.9 27.0 + - - -
266C PHE* 4.7 1.6 - - - -
292C PRO* 4.0 20.9 - - + +
293C ALA* 3.6 18.6 - - + -
307C ASP* 3.9 14.8 - - + +
308C ILE* 1.3 71.5 - - - +
310C LEU* 1.3 64.1 + - - +
311C ALA* 3.4 1.6 + - + -
348C VAL* 3.9 26.7 - - + -
368C SER* 6.2 0.4 - - - +
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C PHE* 4.0 15.0 - - + -
192C VAL* 5.6 1.3 - - + -
216C PHE 3.8 7.4 - - - +
218C LEU* 5.3 4.0 - - + -
262C MET* 4.0 38.1 - - + +
263C LEU* 4.1 31.9 - - + +
266C PHE* 3.9 37.9 - - + -
292C PRO 3.6 6.8 + - - +
308C ILE 3.7 3.2 + - - -
309C ILE* 1.3 71.0 - - - +
311C ALA* 1.3 69.8 + - - +
312C LEU* 5.5 0.2 - - + -
347C LEU 4.1 0.3 - - - +
348C VAL* 3.7 6.9 - - - +
349C PRO* 3.3 32.2 - - + +
363C TRP* 4.9 4.9 - - + -
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Residues in contact with ALA 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C MET* 3.5 31.9 - - + -
216C PHE 3.0 14.0 + - - +
217C LYS* 3.4 7.6 - - - -
218C LEU* 2.9 28.6 + - - +
309C ILE 3.4 3.5 + - - +
310C LEU* 1.3 76.9 - - - +
312C LEU* 1.3 65.7 + - - +
346C TYR* 4.1 8.5 - - + -
347C LEU 3.7 3.8 - - - +
348C VAL* 4.2 10.1 - - + -
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Residues in contact with LEU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C LEU* 3.5 2.9 - - + +
220C VAL* 3.6 29.6 - - + -
223C ILE* 5.8 3.4 - - + -
237C VAL* 4.5 13.2 - - + -
257C LEU* 3.8 22.9 - - + -
262C MET* 3.8 26.2 - - + -
310C LEU* 5.4 1.6 - - + -
311C ALA* 1.3 77.7 - - - +
313C GLU* 1.3 61.0 + - - +
314C SER* 5.6 0.2 - - - -
345C PHE 3.7 0.2 - - - +
346C TYR* 3.1 10.7 - - - +
347C LEU* 2.9 46.8 + - + +
363C TRP* 3.6 38.8 - - + -
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Residues in contact with GLU 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217C LYS* 2.9 34.1 + - + -
218C LEU 2.9 10.0 + - - +
219C GLU* 3.6 34.8 - - + +
220C VAL* 3.0 29.6 + - - +
223C ILE* 5.5 0.6 - - - +
312C LEU* 1.3 74.6 - - - +
314C SER* 1.3 63.3 + - - +
315C LYS* 3.7 16.0 - - + -
344C PRO* 3.7 22.9 - - + +
345C PHE 3.7 2.0 - - - -
346C TYR* 2.9 32.1 + - + -
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Residues in contact with SER 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C GLU* 5.8 0.2 - - - -
220C VAL 4.6 5.3 + - - -
223C ILE* 3.6 24.7 - - - +
312C LEU 5.6 0.4 - - - -
313C GLU* 1.3 76.2 - - - +
315C LYS* 1.3 65.2 + - - +
316C GLY* 3.4 5.5 + - - -
344C PRO* 3.2 3.6 - - - +
345C PHE* 2.9 71.7 + - - -
347C LEU* 5.8 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