Contacts of the helix formed by residues 265 - 279 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A GLN* 2.9 15.0 + - - +
264A GLN* 1.3 78.4 - - + +
266A LYS* 1.3 58.4 + - - +
267A PRO* 3.2 13.4 - - - +
268A LEU* 3.0 43.0 + - + +
269A TYR* 2.9 22.9 + - - +
306A GLU* 3.3 28.7 + - - +
309A ARG* 5.1 2.8 - - - +
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Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A CYS 5.2 0.6 + - - -
134A SER* 3.3 32.6 + - - +
135A ARG 5.0 0.8 - - - -
136A THR* 4.0 21.4 - - - +
222A VAL* 5.7 6.9 - - - +
262A CYS* 3.5 35.7 + - - +
265A ASN* 1.3 70.6 - - - +
267A PRO* 1.4 76.6 - - + +
269A TYR* 3.1 20.9 + - - +
270A PHE* 3.2 24.4 + - + -
295A ARG* 4.1 17.5 - - - +
299A ASP* 4.4 2.2 - - - +
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Residues in contact with PRO 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASN* 3.2 11.0 - - - +
266A LYS* 1.4 95.4 - - + +
268A LEU* 1.3 60.9 + - - +
270A PHE* 3.0 15.4 + - - +
271A ALA 3.0 9.9 + - - -
299A ASP* 4.1 11.4 - - + +
302A LYS* 3.8 34.8 - - + +
303A ILE* 3.7 39.9 - - + +
306A GLU* 4.0 4.9 - - + +
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASN* 3.0 38.3 + - + +
267A PRO* 1.3 75.5 - - - +
269A TYR* 1.3 65.7 + - - +
271A ALA* 3.2 3.4 + - + +
272A ASP* 3.0 44.4 + - - +
306A GLU* 3.8 36.0 - - + +
309A ARG* 4.4 12.8 - - - +
310A LYS* 4.1 24.9 - - + +
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Residues in contact with TYR 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ILE 4.8 0.2 + - - -
130A GLU* 3.7 21.6 - - + -
133A CYS* 5.4 0.2 - - - +
134A SER* 4.5 3.8 - - - -
258A ASN* 2.3 53.3 + - + +
261A GLN* 3.6 43.1 - - + -
262A CYS* 3.5 23.6 - - - +
265A ASN 2.9 14.6 + - - +
266A LYS* 3.1 14.8 + - - +
268A LEU* 1.3 77.3 - - - +
270A PHE* 1.3 88.7 + + - +
272A ASP* 3.4 3.8 + - + +
273A ARG* 3.0 50.0 + - + +
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 4.5 10.3 - - + -
134A SER* 3.6 28.7 - - - -
135A ARG* 4.0 7.6 - - - -
266A LYS* 3.2 35.6 + - + -
267A PRO 3.0 6.6 + - - +
269A TYR* 1.3 95.5 - + - +
271A ALA* 1.3 51.9 + - - +
273A ARG* 2.9 4.8 + - - +
274A LEU* 2.6 39.8 + - - +
291A ILE* 3.6 31.9 - - + -
294A SER* 5.3 0.9 - - - -
295A ARG* 3.6 39.0 - - + -
299A ASP* 4.0 10.3 - - - -
303A ILE* 3.7 20.6 - - + -
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Residues in contact with ALA 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PRO 3.0 12.6 + - - +
268A LEU* 3.5 15.3 - - + +
270A PHE* 1.3 75.5 - - - +
272A ASP* 1.3 54.7 + - - +
274A LEU* 3.2 3.8 + - - +
275A TYR* 2.7 36.4 + - - +
303A ILE* 3.5 26.1 - - - +
306A GLU* 4.5 2.2 - - + +
307A PHE* 3.7 29.2 - - + +
311A TYR* 4.4 3.4 - - + -
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Residues in contact with ASP 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A GLN* 4.1 16.1 - - - +
268A LEU* 3.0 23.3 + - - +
269A TYR 3.6 7.9 - - - +
271A ALA* 1.3 74.7 - - - +
273A ARG* 1.3 53.3 + - + +
275A TYR* 3.1 1.6 + - - +
276A ASP* 2.7 45.9 + - - +
310A LYS* 3.4 30.5 + - - +
311A TYR* 3.4 23.1 + - - +
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Residues in contact with ARG 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ASP* 3.9 23.8 + - - +
130A GLU* 2.2 54.0 + - - +
254A ASN* 6.1 1.2 - - - +
258A ASN* 4.1 8.6 + - - -
269A TYR* 3.0 48.5 + - + +
270A PHE* 2.9 8.6 + - - +
272A ASP* 1.3 76.6 - - - +
274A LEU* 1.3 62.7 + - - +
276A ASP* 3.4 9.4 + - - +
277A SER* 3.1 22.5 + - - -
287A VAL* 3.6 26.6 - - - +
290A ARG* 3.6 8.7 - - - +
291A ILE* 3.5 15.3 - - + -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A PHE 2.6 18.4 + - - +
271A ALA* 3.4 6.1 - - - +
273A ARG* 1.3 72.2 - - - +
275A TYR* 1.3 60.9 + - - +
277A SER* 2.5 23.4 + - - -
278A MET* 3.3 14.9 - - + +
287A VAL* 5.7 0.2 - - - -
288A LEU* 3.6 27.6 - - + +
291A ILE* 3.5 37.5 - - + -
292A MET* 4.0 9.9 - - - -
300A MET* 5.3 0.4 - - - -
303A ILE* 3.5 33.0 - - + -
307A PHE* 4.5 2.7 - - + -
315A LEU* 3.9 31.6 - - + -
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Residues in contact with TYR 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ALA 2.7 20.9 + - - +
272A ASP 3.4 4.3 - - - +
274A LEU* 1.3 73.2 - - - +
276A ASP* 1.3 61.4 + - - +
277A SER 3.2 0.2 + - - -
278A MET* 3.4 3.3 + - - +
279A LYS* 3.0 61.6 + - + +
307A PHE* 3.8 16.8 - + + -
311A TYR* 3.4 54.4 - + + -
318A TYR* 3.4 37.0 + + - -
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Residues in contact with ASP 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ASP* 2.7 29.0 + - - +
273A ARG* 3.8 8.7 + - - +
275A TYR* 1.3 77.9 - - - +
277A SER* 1.3 61.2 + - - +
278A MET 3.6 0.2 + - - -
279A LYS* 3.2 40.2 + - + +
284A ARG* 3.1 16.8 + - - -
311A TYR* 5.4 0.7 + - - -
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Residues in contact with SER 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ARG 3.1 12.2 + - - -
274A LEU* 2.5 26.0 + - - -
275A TYR 3.1 0.2 - - - -
276A ASP* 1.3 79.0 - - - +
278A MET* 1.3 63.7 + - - +
283A THR* 3.2 1.4 - - - -
284A ARG* 2.8 64.1 + - - +
287A VAL* 4.3 6.5 - - - -
288A LEU* 4.0 20.1 - - - +
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Residues in contact with MET 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU 3.3 19.5 - - - +
275A TYR* 3.4 2.8 + - - +
277A SER* 1.3 80.2 - - - +
279A LYS* 1.3 63.6 + - - +
280A GLY 3.2 9.6 + - - +
282A GLY 3.7 3.5 - - - +
283A THR* 4.3 9.0 - - + +
288A LEU* 4.0 25.4 - - + -
307A PHE* 5.0 2.2 - - + -
315A LEU* 3.5 33.0 - - + -
318A TYR* 3.6 43.9 - - + +
319A ILE* 3.9 8.3 - - + +
322A ASP* 2.8 45.5 - - + +
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A TYR* 3.0 44.5 + - + +
276A ASP* 3.2 40.0 + - - +
277A SER 3.5 2.0 - - - -
278A MET* 1.3 76.5 - - - +
280A GLY* 1.3 68.0 + - - +
284A ARG* 5.0 0.7 - - - +
318A TYR* 6.0 1.8 - - - -
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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