Contacts of the helix formed by residues 258 - 276 (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 SER 258 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C PHE* 2.5 22.3 + - - +
253C GLU* 3.2 28.9 + - - -
256C VAL 3.7 2.2 + - - -
257C LEU* 1.3 77.8 - - - +
259C ALA* 1.3 61.0 + - - +
260C THR* 3.9 1.9 + - - -
261C LYS* 3.2 31.9 + - - +
262C MET* 3.6 19.9 + - - +
360C GLY* 3.2 13.8 + - - -
361C GLU* 4.4 5.1 + - - -
363C TRP* 4.3 0.4 - - - -
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Residues in contact with ALA 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C LEU 3.6 2.4 + - - -
258C SER* 1.3 70.3 - - - +
260C THR* 1.3 60.0 + - - +
261C LYS 3.2 1.6 - - - -
262C MET* 3.4 1.9 + - - +
263C LEU* 2.9 33.5 + - - +
349C PRO* 4.2 15.1 - - + +
351C ASN 6.0 0.9 - - - +
360C GLY* 2.7 19.5 + - - +
362C THR 4.1 14.6 - - - +
363C TRP* 3.6 36.1 - - + +
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Residues in contact with THR 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C SER* 4.5 2.5 - - - -
259C ALA* 1.3 78.5 - - - +
261C LYS* 1.3 56.9 + - + +
263C LEU* 3.8 5.4 - - - +
264C SER* 2.6 44.0 + - - +
351C ASN* 4.4 14.3 + - - +
353C LYS* 4.4 18.3 + - - +
359C GLN* 4.7 2.1 + - - +
360C GLY* 3.1 27.5 + - - -
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Residues in contact with LYS 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C HIS 4.4 15.2 + - - +
251C PHE* 4.0 14.9 - - + +
252C LEU 5.3 2.4 + - - -
253C GLU* 3.5 32.6 + - + +
258C SER* 3.2 23.3 + - - +
259C ALA 3.2 0.6 - - - -
260C THR* 1.3 77.5 - - + +
262C MET* 1.3 64.9 + - - +
264C SER* 3.1 7.3 + - - -
265C LYS* 3.0 24.8 + - - +
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Residues in contact with MET 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C PHE* 3.1 30.5 - - + -
218C LEU* 3.7 22.0 - - + -
248C LEU* 3.6 24.7 - - + -
251C PHE* 3.6 30.6 - - + -
257C LEU* 4.3 11.9 - - - -
258C SER 3.6 14.4 + - - +
259C ALA* 3.4 4.8 + - - +
261C LYS* 1.3 77.1 - - - +
263C LEU* 1.3 57.4 + - - +
265C LYS* 3.4 0.3 + - - +
266C PHE* 3.0 23.7 + - - +
310C LEU* 4.0 12.1 - - + -
312C LEU* 3.8 19.1 - - + -
363C TRP* 4.0 21.5 - - + -
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Residues in contact with LEU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C ALA 2.9 18.6 + - - +
260C THR* 3.9 4.3 - - - +
262C MET* 1.3 75.0 - - - +
264C SER* 1.3 59.4 + - - +
266C PHE* 3.5 13.7 - - + +
267C ARG* 2.9 35.7 + - + +
287C GLU* 4.2 7.0 - - - +
291C SER 4.4 6.5 - - - +
292C PRO 3.9 18.4 - - - +
293C ALA 5.9 1.1 - - - -
294C VAL* 4.5 10.1 - - + +
310C LEU* 4.1 22.8 - - + +
349C PRO* 4.1 19.3 - - + -
351C ASN* 3.8 35.2 - - - +
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Residues in contact with SER 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C THR* 2.6 33.4 + - - +
261C LYS* 3.1 8.6 + - - -
263C LEU* 1.3 76.8 - - - +
265C LYS* 1.3 57.4 + - - +
267C ARG* 3.5 7.7 + - - +
268C LYS* 2.9 30.1 + - - +
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Residues in contact with LYS 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C GLU* 2.3 39.6 + - - +
189C PHE* 3.9 8.3 - - + -
250C HIS* 4.9 5.3 + - - -
251C PHE* 3.8 15.5 - - + -
261C LYS 3.0 12.3 + - - +
262C MET 3.7 7.0 - - - +
264C SER* 1.3 75.8 - - - +
266C PHE* 1.3 65.2 + - - +
268C LYS* 3.1 25.5 + - + +
269C ILE* 2.9 41.4 + - + +
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Residues in contact with PHE 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C MET* 3.9 19.9 - - + +
189C PHE* 3.5 36.0 - + + -
192C VAL* 5.2 1.1 - - + -
216C PHE* 3.9 23.1 - + + -
262C MET 3.0 17.9 + - - +
263C LEU* 3.5 11.4 - - + +
265C LYS* 1.3 75.5 - - - +
267C ARG* 1.3 56.5 + - - +
269C ILE* 3.4 4.4 + - - +
270C ILE* 3.0 41.0 + - + +
294C VAL* 3.7 15.5 - - + -
308C ILE* 3.6 44.0 - - + -
310C LEU* 3.9 32.8 - - + -
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Residues in contact with ARG 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C LEU* 2.9 21.2 + - - +
264C SER* 3.5 8.3 - - - +
266C PHE* 1.3 77.0 - - - +
268C LYS* 1.3 56.6 + - - +
270C ILE* 3.2 3.3 + - - +
271C LYS* 2.9 57.4 + - + +
284C VAL* 4.0 8.4 - - - +
285C GLU 2.8 29.3 + - - -
286C LYS* 3.7 1.4 - - - +
287C GLU* 3.1 48.6 + - - +
293C ALA 4.3 4.8 + - - -
294C VAL* 3.9 46.7 - - + +
295C THR 4.8 1.0 - - - +
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Residues in contact with LYS 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C SER 2.9 17.7 + - - +
265C LYS* 3.1 26.7 + - + +
267C ARG* 1.3 76.9 - - - +
269C ILE* 1.3 64.5 + - + +
271C LYS* 3.3 10.5 + - - +
272C GLU* 2.4 61.5 + - + +
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Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ARG* 3.8 39.7 + - + +
182C MET* 4.1 20.9 - - + -
187C SER* 3.8 28.7 - - - -
188C GLU* 5.1 1.1 - - - +
189C PHE* 3.8 22.9 - - + -
265C LYS* 2.9 30.7 + - + +
266C PHE 3.6 6.5 - - - +
268C LYS* 1.3 77.1 - - + +
270C ILE* 1.3 64.4 + - - +
272C GLU* 3.1 10.5 + - - +
273C GLU* 3.0 21.5 + - - +
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Residues in contact with ILE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C LEU* 4.3 17.6 - - + +
182C MET* 3.7 18.6 - - + -
216C PHE* 5.2 1.1 - - + -
266C PHE* 3.0 37.1 + - + +
267C ARG 3.2 4.7 + - - +
269C ILE* 1.3 77.0 - - - +
271C LYS* 1.3 56.7 + - - +
273C GLU* 3.3 5.9 + - - +
274C VAL* 2.9 32.3 + - + +
284C VAL* 4.8 0.9 - - + -
294C VAL* 4.0 21.8 - - + -
296C LEU* 4.1 19.3 - - + -
308C ILE* 3.6 36.6 - - + -
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Residues in contact with LYS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ARG* 2.9 50.0 + - + +
268C LYS* 3.5 11.6 - - - +
270C ILE* 1.3 74.4 - - - +
272C GLU* 1.3 59.7 + - + +
274C VAL* 3.1 7.0 + - - +
275C LYS* 2.9 44.4 + - - +
284C VAL* 4.2 31.6 - - + -
285C GLU 5.7 0.2 - - - -
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Residues in contact with GLU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C ARG* 4.0 19.3 + - - +
185C ARG* 4.9 6.6 + - - -
268C LYS* 2.4 55.0 + - + +
269C ILE* 3.1 8.5 + - - +
271C LYS* 1.3 77.8 - - + +
273C GLU* 1.3 61.5 + - - +
275C LYS* 3.7 23.8 - - - +
276C GLU* 3.4 22.7 - - - +
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Residues in contact with GLU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C ARG* 3.4 35.5 + - + +
178C LEU* 4.0 19.0 - - + +
181C ARG* 3.1 56.9 + - + +
269C ILE 3.0 11.4 + - - +
270C ILE* 4.0 4.5 - - - +
271C LYS 3.2 0.2 - - - -
272C GLU* 1.3 76.3 - - - +
274C VAL* 1.3 61.5 + - - +
275C LYS 3.3 0.4 - - - -
276C GLU* 3.5 13.6 + - - +
277C ILE* 3.3 17.2 - - - +
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Residues in contact with VAL 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C VAL* 5.5 1.8 - - + -
178C LEU* 4.3 12.3 - - + -
270C ILE* 2.9 23.8 + - + +
271C LYS 3.1 3.8 + - - +
273C GLU* 1.3 73.6 - - - +
275C LYS* 1.3 67.3 - - + +
276C GLU 3.1 1.6 - - - -
277C ILE* 3.1 23.1 + - + +
282C VAL* 3.5 39.7 - - + +
283C SER* 4.2 3.4 - - - -
284C VAL* 4.1 27.8 - - + +
296C LEU* 4.1 16.2 - - + -
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Residues in contact with LYS 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LYS* 2.9 33.6 + - - +
272C GLU* 3.7 19.9 - - - +
274C VAL* 1.3 79.2 - - - +
276C GLU* 1.3 65.2 + - - +
277C ILE 3.3 7.4 + - - +
278C LYS* 5.0 8.0 - - - +
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Residues in contact with GLU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C ARG* 2.4 38.1 + - - +
272C GLU 3.4 18.1 + - - +
273C GLU* 3.5 13.5 + - - +
274C VAL 3.1 1.6 - - - -
275C LYS* 1.3 84.2 - - + +
277C ILE* 1.3 53.7 + - - +
278C LYS* 4.3 18.7 + - - +
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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
------------------------------------------------------------
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