Contacts of the helix formed by residues 252 - 270 (chain C) in PDB entry 4U1D
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 252 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C LYS* 3.8 42.0 - - + +
199C PHE* 3.8 29.4 - - + -
200C LYS* 4.0 31.9 - - + +
247C SER* 3.0 12.2 + - - +
250C LEU* 3.6 24.9 - - + +
251C GLU* 1.3 75.6 - - - +
253C TRP* 1.3 59.1 + - - +
254C HIS 3.3 2.9 - - - -
255C GLU* 3.1 6.8 + - + +
256C ALA* 2.8 26.3 + - - +
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Residues in contact with TRP 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C VAL* 3.8 39.5 - - + -
251C GLU* 3.2 49.5 + - + +
252C LEU* 1.3 68.8 - - - +
254C HIS* 1.3 65.1 + - + +
256C ALA* 3.5 5.5 - - + +
257C TYR* 2.8 32.3 + - - +
288C LYS* 4.7 4.9 - - + -
289C VAL* 4.0 40.1 - - + +
292C VAL* 3.6 44.7 - - + +
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Residues in contact with HIS 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B HIS* 3.0 53.4 + + + +
258B ARG* 6.1 0.9 - - - -
200C LYS* 5.1 5.8 - - - +
252C LEU 3.3 0.4 - - - -
253C TRP* 1.3 81.7 - - + +
255C GLU* 1.3 58.3 + - - +
257C TYR* 3.4 8.0 + - - +
258C ARG* 3.1 49.6 + - - +
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Residues in contact with GLU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C PHE* 3.9 16.2 - - + -
200C LYS* 4.0 22.9 - - + +
203C ALA* 3.5 14.2 - - - +
207C ARG* 2.6 38.4 + - - -
247C SER* 3.7 14.1 - - - +
252C LEU* 3.1 20.4 + - + +
254C HIS* 1.3 78.4 - - - +
256C ALA* 1.3 66.2 + - - +
258C ARG* 2.9 28.3 + - - +
259C SER* 3.0 30.7 + - - +
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Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C VAL* 4.4 4.4 - - + +
247C SER* 3.5 22.5 - - - -
248C VAL* 4.2 10.1 - - + -
252C LEU 2.8 14.4 + - - +
253C TRP* 3.5 13.2 - - + +
255C GLU* 1.3 73.6 - - - +
257C TYR* 1.3 63.3 - - - +
259C SER* 3.1 14.3 + - - -
260C ILE* 3.1 19.8 + - - +
289C VAL* 4.0 24.2 - - + -
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Residues in contact with TYR 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C TRP 2.8 17.6 + - - +
254C HIS* 3.5 9.6 - - - +
256C ALA* 1.3 78.0 - - - +
258C ARG* 1.3 66.2 + - + +
260C ILE* 3.4 22.9 + - + +
261C GLU* 3.8 5.4 + - - +
289C VAL* 5.0 14.3 - - + +
290C PHE* 5.0 5.4 - + - -
293C SER* 5.2 4.7 - - - -
295C ASP* 4.9 3.8 - - - -
347C PRO 4.1 3.5 + - - -
348C HIS* 3.2 47.8 - + + -
350C ARG* 5.7 4.9 + - - +
351C MET* 2.9 45.7 + - + +
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Residues in contact with ARG 258 (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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254B HIS* 5.5 6.3 + - - -
200C LYS* 4.2 13.3 - - - +
204C GLU* 6.2 0.4 - - - -
207C ARG* 3.3 21.3 + - - +
254C HIS* 3.1 30.5 + - - +
255C GLU* 2.9 44.0 + - - +
257C TYR* 1.3 80.2 - - + +
259C SER* 1.3 61.4 + - - +
261C GLU* 3.2 20.8 + - - +
262C ASP* 3.3 13.7 + - - +
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Residues in contact with SER 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240C ARG 5.1 0.2 - - - -
243C GLN* 2.8 36.3 + - - +
244C VAL* 3.5 21.1 - - - -
247C SER* 4.0 3.1 + - - -
255C GLU* 3.0 22.4 + - - -
256C ALA* 3.1 6.7 + - - -
258C ARG* 1.3 74.7 - - - +
260C ILE* 1.3 59.5 + - - +
261C GLU 3.2 0.2 - - - -
262C ASP* 3.2 11.7 + - - +
263C VAL* 2.8 32.7 + - - +
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Residues in contact with ILE 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C VAL* 4.5 8.1 - - + -
256C ALA 3.1 15.8 + - - +
257C TYR* 3.6 13.7 - - + +
258C ARG 3.2 0.2 - - - -
259C SER* 1.3 77.4 - - - +
261C GLU* 1.3 55.7 + - - +
263C VAL* 3.4 2.5 + - - +
264C PHE* 3.0 27.0 + - - +
282C TYR* 3.5 19.0 + - - +
286C LEU* 3.5 34.5 - - + -
289C VAL* 4.0 24.0 - - + -
290C PHE* 4.3 12.1 - - + -
351C MET* 3.7 24.5 - - + -
354C LEU* 4.7 9.2 - - + +
355C LEU* 4.9 2.0 - - + -
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Residues in contact with GLU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C TYR 3.8 3.6 + - - +
258C ARG* 3.2 14.9 + - - +
259C SER 3.2 0.2 - - - -
260C ILE* 1.3 78.2 - - - +
262C ASP* 1.3 66.4 + - - +
264C PHE* 3.4 3.1 + - - +
265C HIS* 3.2 47.9 + - + +
350C ARG* 3.2 35.9 + - - -
354C LEU* 3.6 26.2 - - + +
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Residues in contact with ASP 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C ARG* 2.8 52.1 + - - +
240C ARG* 4.7 17.7 - - + -
243C GLN* 3.2 15.5 + - - +
258C ARG 3.3 7.2 + - - +
259C SER* 3.2 10.7 + - - +
261C GLU* 1.3 82.7 - - - +
263C VAL* 1.3 62.6 + - - +
265C HIS* 3.6 5.1 + - - +
266C LEU* 3.3 28.4 + - + +
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Residues in contact with VAL 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C LEU* 3.8 5.1 - - + +
240C ARG* 3.3 42.2 - - + +
241C PHE* 3.8 15.9 - - + +
244C VAL* 3.9 10.5 - - + -
259C SER 2.8 21.0 + - - +
260C ILE 3.8 3.6 - - - +
262C ASP* 1.3 70.3 - - - +
264C PHE* 1.3 67.9 + - - +
266C LEU* 3.0 6.4 + - - +
267C MET* 2.9 38.3 + - + +
282C TYR* 3.8 28.3 - - + +
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Residues in contact with PHE 264 (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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260C ILE 3.0 17.9 + - - +
261C GLU 3.8 2.9 - - - +
263C VAL* 1.3 80.2 - - - +
265C HIS* 1.3 89.1 + + - +
267C MET* 3.0 13.0 + - + +
268C LYS* 3.0 48.7 + - + +
282C TYR* 5.6 1.3 - - - +
353C ARG* 3.8 15.9 - - + -
354C LEU* 3.4 49.1 - - + +
356C ASN* 3.5 24.7 - - - -
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Residues in contact with HIS 265 (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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261C GLU* 3.2 41.3 + - + +
262C ASP* 3.9 8.1 - - - +
263C VAL 3.3 0.2 - - - -
264C PHE* 1.3 105.0 - + - +
266C LEU* 1.3 64.9 + - + +
268C LYS* 3.6 22.9 + - - +
269C ILE* 3.3 26.9 + - - +
354C LEU* 5.3 1.8 - - + -
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Residues in contact with LEU 266 (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 LEU* 3.5 29.4 - - + -
233C LEU* 4.9 11.1 - - + +
236C TYR* 3.4 47.6 - - + +
237C LEU* 3.5 24.2 - - + +
240C ARG* 3.6 12.3 - - + +
262C ASP* 3.3 17.0 - - + +
263C VAL* 3.0 4.0 + - - +
265C HIS* 1.3 80.2 - - + +
267C MET* 1.3 60.8 + - - +
268C LYS 3.1 0.2 - - - -
269C ILE* 3.5 4.8 + - + +
270C SER* 2.9 30.9 + - - -
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Residues in contact with MET 267 (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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237C LEU* 3.8 20.2 - - + -
241C PHE* 4.1 11.7 - - + -
263C VAL* 2.9 31.8 + - - +
264C PHE* 3.0 14.3 + - + +
266C LEU* 1.3 77.0 - - - +
268C LYS* 1.3 63.9 + - - +
270C SER* 3.4 20.3 - - - +
274C PRO* 5.2 6.7 - - + -
279C LEU* 4.4 21.5 - - + -
282C TYR* 4.7 7.6 - - - -
283C TYR* 4.5 11.4 - - + +
356C ASN* 5.6 8.1 - - - +
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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
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264C PHE* 3.0 41.8 + - + +
265C HIS* 3.6 31.0 + - - +
266C LEU 3.1 0.2 - - - -
267C MET* 1.3 80.9 - - - +
269C ILE* 1.3 72.8 + - + +
270C SER 3.4 4.9 + - - +
271C LYS* 5.4 3.6 - - - +
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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
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227C LEU* 3.9 13.9 - - + +
228C SER* 5.9 0.4 - - - -
233C LEU* 3.6 24.7 - - + +
265C HIS 3.3 17.9 - - - +
266C LEU* 3.5 5.5 + - - +
268C LYS* 1.3 88.2 - - + +
270C SER* 1.3 65.7 + - - +
271C LYS* 3.3 22.1 + - - +
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Residues in contact with SER 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C ALA* 5.7 0.9 + - - +
233C LEU* 3.8 20.7 - - - +
234C GLN* 5.1 3.5 + - - -
237C LEU* 4.3 14.7 - - - +
266C LEU 2.9 20.1 + - - -
267C MET* 3.4 19.9 - - - +
268C LYS 3.2 4.8 - - - +
269C ILE* 1.3 77.3 - - - +
271C LYS* 1.3 61.8 + - - +
272C ARG* 2.8 28.0 + - - +
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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