Contacts of the helix formed by residues 257 - 271 (chain A) in PDB entry 2H1R
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 ASP 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A VAL* 5.0 6.5 - - + -
136A TYR* 3.5 6.3 - - - +
141A ILE* 4.5 0.9 - - - -
144A LYS* 3.8 13.7 - - - +
255A ASN 4.3 0.2 + - - -
256A LEU* 1.3 75.3 - - - +
258A GLU* 1.3 74.4 + - - +
259A ASN* 2.9 27.7 + - - +
260A ASP* 2.9 36.5 + - - +
261A PHE* 3.2 16.9 + - - -
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Residues in contact with GLU 258 (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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136A TYR* 4.8 0.2 + - - -
141A ILE* 3.9 24.8 - - + +
144A LYS* 3.5 37.9 + - - +
145A LEU* 4.3 26.5 - - + +
176A LYS* 3.8 18.4 + - - +
187A TRP* 3.5 10.8 - - + -
257A ASP* 1.3 75.4 - - - +
259A ASN* 1.3 75.5 + - - +
261A PHE 3.3 0.2 + - - -
262A LEU* 2.9 34.2 + - + +
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Residues in contact with ASN 259 (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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257A ASP* 2.9 15.6 + - - +
258A GLU* 1.3 90.6 + - - +
260A ASP* 1.3 64.9 + - - +
262A LEU* 3.6 17.6 + - - +
263A LYS* 3.3 28.1 + - - +
225B LEU 4.7 2.4 - - - +
227B LYS* 3.1 29.7 + - - +
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Residues in contact with ASP 260 (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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248A MET* 3.6 25.1 - - + +
251A LYS* 5.5 3.3 + - - -
255A ASN 4.7 0.9 - - - +
256A LEU* 3.5 36.1 - - + +
257A ASP* 2.9 37.2 + - - +
259A ASN* 1.3 77.8 - - - +
261A PHE* 1.3 59.6 + - - +
263A LYS* 3.3 8.4 + - - +
264A LEU* 3.1 24.8 + - - +
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Residues in contact with PHE 261 (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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141A ILE* 3.6 29.6 - - + -
187A TRP* 3.5 25.7 - - + -
190A LEU* 3.9 12.1 - - + +
191A LEU* 3.6 16.8 - - + -
194A CYS* 3.7 27.4 - - + -
195A PHE* 3.8 18.2 - + - -
202A LEU* 5.3 0.4 - - + -
253A SER* 3.8 18.2 - - - -
256A LEU* 3.7 26.9 - - + -
257A ASP 3.2 19.0 + - - -
258A GLU 4.0 0.9 - - - +
260A ASP* 1.3 79.4 - - - +
262A LEU* 1.3 58.5 + - - +
264A LEU* 3.6 20.1 - - + +
265A LEU* 2.9 29.8 + - - +
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Residues in contact with LEU 262 (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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145A LEU* 3.9 15.3 - - + -
182A THR* 3.7 23.8 - - + +
187A TRP* 3.5 19.7 - - + -
258A GLU* 2.9 23.5 + - + +
259A ASN* 3.8 17.5 - - - +
260A ASP 3.3 0.2 - - - -
261A PHE* 1.3 77.3 - - - +
263A LYS* 1.3 56.1 + - + +
265A LEU* 3.5 6.6 + - + +
266A LEU* 3.0 30.7 + - - +
225B LEU* 3.6 44.6 - - + +
226B ASN* 4.1 14.8 - - - +
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Residues in contact with LYS 263 (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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246A LEU* 4.0 25.4 - - + -
248A MET* 4.3 11.9 - - + -
259A ASN 3.3 13.6 + - - +
260A ASP* 3.5 9.9 - - - +
262A LEU* 1.3 75.8 - - - +
264A LEU* 1.3 59.6 + - - +
266A LEU* 3.7 9.4 - - + +
267A GLU* 3.0 35.6 + - + +
226B ASN* 5.6 2.9 - - - +
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Residues in contact with LEU 264 (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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190A LEU* 4.2 14.4 - - + -
194A CYS* 4.4 4.5 - - - -
202A LEU* 4.0 20.2 - - + -
206A PHE* 4.8 2.0 - - + -
242A VAL* 4.3 2.9 - - + -
243A LEU* 3.7 20.9 - - + -
246A LEU* 3.8 21.2 - - + +
248A MET* 4.2 9.9 - - - -
256A LEU* 5.7 0.7 - - + -
260A ASP 3.1 10.6 + - - +
261A PHE* 3.6 32.3 - - + +
263A LYS* 1.3 76.4 - - - +
265A LEU* 1.3 66.8 + - - +
267A GLU* 3.5 1.4 + - - +
268A PHE* 2.9 58.1 + - + -
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Residues in contact with LEU 265 (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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182A THR* 4.3 11.4 - - + -
183A ASN* 4.7 4.5 - - + +
186A GLU* 4.0 16.4 - - + +
187A TRP* 4.1 36.8 - - + +
190A LEU* 3.9 13.4 - - + +
261A PHE 2.9 17.6 + - - +
262A LEU* 3.8 8.1 - - + +
264A LEU* 1.3 76.8 - - - +
266A LEU* 1.3 58.9 + - - +
268A PHE* 3.5 2.5 + - - -
269A ASN* 2.8 52.7 + - - +
275A PHE* 3.8 27.8 - - + -
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A LEU 3.0 18.2 + - - +
263A LYS* 3.7 9.6 - - + +
264A LEU 3.3 0.2 - - - -
265A LEU* 1.3 78.1 - - - +
267A GLU* 1.3 68.8 + - - +
269A ASN* 3.8 5.5 - - + +
270A LYS* 3.0 35.9 + - + +
222B TRP* 3.8 28.9 - - + +
226B ASN* 4.1 20.9 - - + +
228B GLN* 3.8 31.4 - - - +
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Residues in contact with GLU 267 (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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242A VAL* 3.7 22.6 - - + +
245A HIS* 3.9 25.8 + - - +
246A LEU* 3.9 20.5 - - + +
263A LYS* 3.0 17.6 + - - +
264A LEU 4.1 0.2 - - - +
266A LEU* 1.3 85.3 - - + +
268A PHE* 1.3 66.6 + - - +
270A LYS* 3.5 23.3 + - - +
271A LYS* 3.4 23.9 + - - +
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Residues in contact with PHE 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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190A LEU* 4.3 1.1 - - + -
206A PHE* 3.7 35.9 - + - -
239A CYS* 3.7 35.2 - - - -
242A VAL* 3.9 20.6 - - + +
243A LEU* 4.4 6.7 - - + -
264A LEU* 2.9 57.4 + - + +
265A LEU 3.9 0.9 - - - +
267A GLU* 1.3 70.9 - - - +
269A ASN* 1.3 63.9 + - - +
271A LYS* 3.0 14.6 + - - +
273A ILE* 3.1 46.8 + - + +
275A PHE* 3.4 26.9 - + + -
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Residues in contact with ASN 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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183A ASN* 6.2 0.2 - - - +
186A GLU* 3.0 27.5 + - - +
222A TRP* 5.6 0.3 + - - -
265A LEU* 2.8 43.1 + - - +
266A LEU* 3.9 5.2 - - - +
268A PHE* 1.3 72.7 - - - +
270A LYS* 1.3 55.7 + - - +
272A GLY* 2.8 23.0 + - - -
273A ILE 2.9 20.8 + - - +
274A HIS* 3.5 23.6 + - + -
275A PHE* 4.6 0.8 - - - -
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Residues in contact with LYS 270 (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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266A LEU* 3.0 23.3 + - + +
267A GLU* 3.6 28.3 - - - +
269A ASN* 1.3 75.9 - - - +
271A LYS* 1.3 59.9 + - + +
272A GLY 3.5 0.7 + - - -
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Residues in contact with LYS 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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219A TYR* 3.3 13.9 - - - -
238A TYR* 2.6 83.3 + - + +
241A ASP* 3.5 20.6 + - - +
242A VAL* 3.4 26.4 - - + +
267A GLU 3.4 5.8 + - - +
268A PHE 3.0 12.4 + - - +
270A LYS* 1.3 78.4 - - + +
272A GLY* 1.3 58.4 + - - +
273A ILE* 4.2 5.8 - - + -
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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