Contacts of the helix formed by residues 265 - 279 (chain C) in PDB entry 4HRE
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 ASN 265 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C GLN* 2.7 21.2 + - - +
264C GLN* 1.3 77.6 - - - +
266C LYS* 1.3 57.7 + - - +
267C PRO* 3.0 13.7 - - - +
268C LEU* 2.5 49.0 + - + +
269C TYR* 3.1 19.9 + - - +
306C GLU* 3.2 27.3 + - - -
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Residues in contact with LYS 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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134C SER* 3.0 32.8 + - - +
136C THR* 3.9 22.0 - - - +
139C GLU* 5.3 1.4 + - - -
262C CYS* 3.3 42.3 + - + +
265C ASN* 1.3 69.4 - - - +
267C PRO* 1.4 76.4 - - + +
269C TYR* 3.0 5.5 + - - +
270C PHE* 3.0 47.5 + - + -
295C ARG* 4.4 14.9 - - - +
299C ASP* 4.7 1.6 - - - +
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Residues in contact with PRO 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ASN* 3.0 14.1 - - - +
266C LYS* 1.4 90.7 - - + +
268C LEU* 1.3 51.2 + - - +
270C PHE 3.2 1.6 + - - -
271C ALA* 2.8 34.0 + - - +
299C ASP* 4.0 13.7 - - + +
302C LYS* 3.6 49.8 - - + +
303C ILE* 3.6 25.3 - - + +
306C GLU* 4.2 6.1 - - + -
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C ASN* 2.5 40.0 + - + +
267C PRO* 1.3 69.0 - - - +
269C TYR* 1.3 55.0 + - - +
271C ALA* 3.2 7.9 + - + +
272C ASP* 2.8 61.5 + - - +
306C GLU* 3.7 26.7 - - + +
309C ARG* 4.2 13.7 - - - +
310C LYS* 4.0 20.0 - - + +
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Residues in contact with TYR 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C GLU* 3.8 26.3 + - + +
134C SER* 4.4 3.4 - - - -
258C ASN* 2.3 49.6 + - + +
261C GLN* 3.7 40.4 - - + -
262C CYS* 3.6 26.0 - - - +
265C ASN 3.1 15.6 + - - +
266C LYS* 3.0 14.4 + - - +
268C LEU* 1.3 76.5 - - - +
270C PHE* 1.3 88.2 + + - +
272C ASP* 3.4 3.2 + - - +
273C ARG* 3.0 50.9 + - + +
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Residues in contact with PHE 270 (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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130C GLU* 3.9 21.8 - - + -
134C SER* 3.6 23.1 - - - -
135C ARG* 3.8 4.0 - - - -
266C LYS* 3.0 37.4 + - + -
267C PRO 3.8 0.9 - - - +
269C TYR* 1.3 90.5 - + - +
271C ALA* 1.3 57.4 + - - +
273C ARG* 2.9 4.5 + - - +
274C LEU* 2.7 40.1 + - - +
291C ILE* 3.8 29.2 - - + -
294C SER* 5.4 0.7 - - - -
295C ARG* 3.4 45.5 - - + -
299C ASP* 3.7 14.8 - - - -
303C ILE* 3.6 18.2 - - + -
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Residues in contact with ALA 271 (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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267C PRO 2.8 18.5 + - - +
268C LEU* 3.3 17.5 - - + +
270C PHE* 1.3 73.0 - - - +
272C ASP* 1.3 58.5 + - - +
274C LEU* 3.3 1.9 + - - +
275C TYR* 2.9 25.8 + - - +
303C ILE* 3.8 28.6 - - - +
306C GLU* 4.1 1.8 - - + -
307C PHE* 3.5 31.6 - - - +
311C TYR* 4.5 2.5 - - + -
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Residues in contact with ASP 272 (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 GLN* 3.9 16.2 - - - +
268C LEU* 2.8 40.6 + - - +
269C TYR* 3.6 5.2 - - - +
271C ALA* 1.3 72.7 - - - +
273C ARG* 1.3 60.1 + - + +
275C TYR* 3.3 1.4 + - - +
276C ASP* 2.8 40.9 + - - +
310C LYS* 2.7 38.8 + - - +
311C TYR* 2.9 14.9 + - - +
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Residues in contact with ARG 273 (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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126C ASP* 4.1 31.4 + - - +
130C GLU* 2.7 38.5 + - - +
254C ASN* 5.5 0.6 + - - -
258C ASN* 3.5 20.7 + - - +
269C TYR* 3.0 49.4 + - + +
270C PHE* 2.9 8.1 + - - +
272C ASP* 1.3 77.0 - - + +
274C LEU* 1.3 59.3 + - - +
276C ASP* 3.5 11.5 + - - +
277C SER* 3.1 26.9 + - - -
287C VAL* 4.2 16.3 - - + +
290C ARG* 3.2 12.5 - - - +
291C ILE* 3.6 16.4 - - + -
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Residues in contact with LEU 274 (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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270C PHE 2.7 17.3 + - - +
271C ALA* 3.5 5.2 - - - +
273C ARG* 1.3 71.1 - - - +
275C TYR* 1.3 64.3 + - - +
277C SER* 2.4 24.7 + - - -
278C MET* 3.2 13.0 - - + +
288C LEU* 3.7 33.9 - - + +
291C ILE* 3.6 40.6 - - + -
292C MET* 4.4 6.5 - - - -
300C MET* 5.2 0.7 - - - -
303C ILE* 3.7 30.7 - - + -
307C PHE* 4.7 1.6 - - + -
315C LEU* 3.7 31.0 - - + -
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Residues in contact with TYR 275 (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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271C ALA 2.9 7.6 + - - +
272C ASP 3.6 4.9 - - - +
274C LEU* 1.3 75.0 - - - +
276C ASP* 1.3 66.8 + - - +
278C MET* 3.0 15.0 + - - +
279C LYS* 3.1 48.8 + - + +
307C PHE* 3.7 19.8 - + + -
311C TYR* 3.4 67.6 - + + -
318C TYR* 3.3 34.2 + + - -
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Residues in contact with ASP 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ASP* 2.8 30.8 + - - +
273C ARG* 3.7 11.9 - - - +
274C LEU 3.3 0.2 - - - -
275C TYR* 1.3 78.9 - - - +
277C SER* 1.3 61.3 + - - +
279C LYS* 3.6 34.4 + - - +
284C ARG* 3.4 15.9 + - - +
311C TYR* 4.6 3.3 + - - -
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Residues in contact with SER 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ARG 3.1 12.3 + - - -
274C LEU* 2.4 30.8 + - - -
276C ASP* 1.3 77.8 - - - +
278C MET* 1.3 64.8 + - - +
283C THR* 3.4 2.1 - - - -
284C ARG* 2.7 61.9 + - - -
287C VAL* 4.3 7.2 - - - -
288C LEU* 4.0 19.7 - - - +
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Residues in contact with MET 278 (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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274C LEU 3.2 20.9 - - - +
275C TYR 3.0 4.1 + - - +
277C SER* 1.3 84.6 - - - +
279C LYS* 1.3 61.5 + - - +
280C GLY 3.6 4.0 + - - +
282C GLY 3.7 5.2 - - - +
283C THR* 4.4 4.9 - - - -
284C ARG* 3.9 2.2 - - - -
288C LEU* 3.9 34.3 - - + -
307C PHE* 5.0 1.6 - - + -
315C LEU* 3.5 31.2 - - + -
318C TYR* 3.8 44.0 - - + +
319C ILE* 4.3 7.6 - - + -
322C ASP* 2.8 41.0 - - + +
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Residues in contact with LYS 279 (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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275C TYR* 3.1 49.2 + - + +
276C ASP* 3.6 33.8 + - - +
278C MET* 1.3 74.6 - - - +
280C GLY* 1.3 70.2 + - - +
284C ARG* 3.6 3.1 - - - +
318C TYR* 5.4 6.1 - - + -
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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