Contacts of the helix formed by residues 257 - 276 (chain A) in PDB entry 2H8R
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 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A GLN* 4.0 4.0 - - - +
255A ASN 3.8 4.6 + - - -
256A PRO* 1.3 75.5 - - - +
258A LYS* 1.3 62.7 + - - +
259A GLU* 3.0 4.0 - - - +
260A GLU* 2.2 42.2 + - - +
261A ARG* 4.0 0.7 - - - +
2E T 3.2 18.9 + - - -
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Residues in contact with LYS 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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257A SER* 1.3 73.6 + - - +
259A GLU* 1.3 70.3 + - - +
261A ARG* 3.5 34.0 - - - +
262A GLU* 3.0 46.6 + - - +
293A GLU* 5.2 7.2 - - + +
1E C 6.0 1.1 - - - -
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Residues in contact with GLU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A SER 2.7 4.7 + - - +
258A LYS* 1.3 78.4 - - - +
260A GLU* 1.3 69.8 + - - +
262A GLU* 2.9 25.8 - - - +
263A ALA* 3.2 5.9 + - - +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ARG* 4.6 14.8 + - - -
253A GLN* 2.9 42.0 + - + +
256A PRO* 3.4 17.5 - - + -
257A SER 2.2 37.8 + - - +
259A GLU* 1.3 73.7 - - - +
261A ARG* 1.3 73.3 - - - +
263A ALA* 3.0 18.5 + - - +
264A LEU* 3.8 7.4 + - + +
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Residues in contact with ARG 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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256A PRO* 2.6 43.7 + - + +
257A SER 3.3 1.5 + - - +
258A LYS* 3.5 37.8 - - - +
260A GLU* 1.3 88.6 - - - +
262A GLU* 1.3 51.3 + - - +
263A ALA 2.4 13.5 + - - -
264A LEU* 2.5 26.7 + - - +
265A VAL* 4.4 2.5 - - - -
293A GLU* 5.0 15.2 - - + +
294A VAL* 6.0 0.2 - - - +
296A VAL* 3.9 24.5 - - + -
297A TYR* 4.5 44.0 - - - +
300A PHE* 5.9 0.9 - - + -
1E C 4.9 5.5 - - - -
2E T 2.9 40.0 + - - -
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Residues in contact with GLU 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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258A LYS* 3.0 35.5 + - - +
259A GLU* 2.9 21.4 - - - +
261A ARG* 1.3 72.4 - - - +
263A ALA* 1.3 60.3 + - - +
264A LEU 3.2 0.2 - - - -
265A VAL* 3.4 15.7 + - - +
266A GLU* 3.0 30.8 - - - +
293A GLU* 3.4 35.7 - - + +
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Residues in contact with ALA 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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259A GLU 3.2 6.9 + - - +
260A GLU* 3.0 17.8 + - - +
261A ARG 2.4 10.1 + - - -
262A GLU* 1.3 70.3 - - - +
264A LEU* 1.3 58.1 + - + +
266A GLU* 2.9 24.7 + - - +
267A GLU* 3.1 16.2 + - - +
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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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245A ILE* 3.8 35.4 - - + +
246A LEU* 4.3 14.1 - - + -
249A ALA* 4.2 22.7 - - + -
256A PRO* 6.0 0.9 - - + -
260A GLU* 4.7 6.5 - - + +
261A ARG* 2.5 25.0 + - - +
263A ALA* 1.3 71.1 - - + +
265A VAL* 1.3 66.9 + - - +
266A GLU 2.9 1.6 - - - -
267A GLU* 2.8 29.6 + - + +
268A CYS* 2.9 20.9 + - - +
296A VAL* 4.8 10.5 - - + -
300A PHE* 4.2 21.1 - - + -
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Residues in contact with VAL 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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261A ARG 3.7 0.6 + - - -
262A GLU* 3.5 16.4 - - - +
263A ALA 3.2 0.2 - - - -
264A LEU* 1.3 79.2 - - - +
266A GLU* 1.3 70.4 + - - +
269A ASN* 2.8 33.7 + - - +
291A VAL* 3.6 32.7 - - - +
292A THR* 3.6 8.7 - - - -
293A GLU* 3.4 47.1 - - + +
296A VAL* 3.8 9.1 - - + +
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Residues in contact with GLU 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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262A GLU* 3.0 26.1 - - - +
263A ALA* 2.9 7.8 + - - +
264A LEU 2.9 0.6 - - - -
265A VAL* 1.3 92.1 - - - +
267A GLU* 1.3 63.6 + - - +
269A ASN* 3.9 5.5 - - - +
270A ARG* 3.3 32.2 + - - +
293A GLU* 3.9 8.7 - - - +
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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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245A ILE* 3.5 30.7 - - + +
248A GLN* 5.7 0.5 - - - +
263A ALA* 3.1 10.7 + - - +
264A LEU* 2.8 27.0 + - + +
266A GLU* 1.3 74.5 - - - +
268A CYS* 1.4 68.2 + - - +
270A ARG* 3.1 29.7 + - - +
271A ALA* 3.0 16.5 + - - +
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Residues in contact with CYS 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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238A TRP* 4.3 5.2 - - - -
242A SER* 3.2 52.9 - - - +
245A ILE* 3.9 15.2 - - - +
246A LEU* 4.0 14.6 - - - -
264A LEU* 2.9 22.3 + - - +
267A GLU* 1.4 69.2 - - - +
269A ASN* 1.3 55.3 + - - +
270A ARG 2.5 1.0 + - - -
271A ALA* 2.1 34.8 + - - +
272A GLU* 2.8 12.1 + - - -
291A VAL* 3.7 13.5 - - + -
296A VAL* 5.8 1.1 - - - -
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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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265A VAL* 2.8 28.4 + - - +
266A GLU* 3.9 8.6 - - - +
268A CYS* 1.3 77.6 - - - +
270A ARG* 1.3 59.6 + - - +
272A GLU* 4.1 6.2 - - - +
273A CYS* 3.4 23.4 + - - -
283A ALA* 3.4 13.4 - - + +
286A LEU* 3.8 10.3 - - - +
290A LEU* 3.6 18.9 - - - +
291A VAL* 3.2 45.7 - - - +
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Residues in contact with ARG 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLU* 3.3 21.6 + - + +
267A GLU* 3.1 31.4 + - - +
268A CYS 2.5 2.6 + - - -
269A ASN* 1.3 76.3 - - - +
271A ALA* 1.4 59.8 + - - +
273A CYS* 2.7 28.6 + - - +
274A LEU* 3.0 13.4 + - - +
280A PRO* 4.2 31.0 - - + +
283A ALA* 5.6 0.2 - - - -
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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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241A ALA* 4.5 18.6 - - + -
242A SER 5.1 0.4 - - - +
245A ILE* 5.2 9.0 - - + -
267A GLU 3.0 8.6 + - - +
268A CYS* 2.1 26.9 + - - +
270A ARG* 1.4 69.4 - - + +
272A GLU* 1.3 53.6 + - - +
274A LEU* 2.7 43.8 + - + +
275A GLN* 3.1 5.5 + - - +
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Residues in contact with GLU 272 (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 ASN* 4.4 4.3 + - - -
239A GLY* 3.7 11.8 - - - -
241A ALA* 3.3 21.5 - - - +
242A SER* 2.7 31.5 + - - +
268A CYS* 2.8 13.0 + - + +
269A ASN* 4.1 1.8 - - - +
271A ALA* 1.3 70.0 - - - +
273A CYS* 1.4 60.2 + - - +
275A GLN* 3.4 20.5 + - - +
276A ARG* 2.6 62.2 + - - +
286A LEU* 3.4 27.8 - - + -
289A ASN* 5.5 4.6 - - - +
291A VAL* 5.0 4.5 - - + -
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Residues in contact with CYS 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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183A PHE* 5.2 1.1 - - - -
269A ASN 3.4 4.3 - - - +
270A ARG 2.7 20.6 + - - +
272A GLU* 1.4 72.3 - - - +
274A LEU* 1.3 65.2 + - - +
275A GLN 3.1 1.1 - - - -
276A ARG* 3.5 0.6 + - - -
277A GLY 3.3 2.9 + - - -
278A VAL* 2.9 58.5 + - + +
279A SER 3.9 6.3 - - - -
280A PRO* 4.3 11.7 - - + -
283A ALA* 3.2 42.6 - - - -
286A LEU* 4.6 7.4 - - - -
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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 ARG* 3.0 11.0 + - + +
271A ALA* 2.7 24.4 + - + +
273A CYS* 1.3 73.8 - - - +
275A GLN* 1.3 55.3 + - - +
277A GLY* 2.5 30.5 + - - -
278A VAL 4.9 4.9 - - - +
280A PRO* 5.5 5.6 - - + +
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Residues in contact with GLN 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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130A GLN 3.6 9.1 + - - -
131A GLN* 2.5 62.6 + - + +
133A ASN* 4.3 6.3 - - - +
240A PRO* 4.0 16.5 - - - +
241A ALA* 3.6 26.2 + - + +
271A ALA 3.1 6.3 + - - +
272A GLU* 3.5 21.9 + - - +
273A CYS 3.1 0.6 - - - -
274A LEU* 1.3 81.4 - - - +
276A ARG* 1.3 67.2 + - + +
277A GLY 3.4 1.0 + - - -
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Residues in contact with ARG 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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131A GLN* 3.4 38.0 + - + +
132A HIS* 3.0 61.2 + - + +
133A ASN* 4.4 5.5 - - - +
179A ILE* 6.2 0.8 - - - +
183A PHE* 4.2 16.9 - - + -
272A GLU* 2.6 47.4 + - - +
273A CYS* 4.2 6.1 - - - +
274A LEU 3.0 0.6 - - - -
275A GLN* 1.3 80.2 - - - +
277A GLY* 1.3 64.7 + - - +
278A VAL* 3.6 8.7 - - + +
286A LEU* 3.4 35.2 + - - +
289A ASN* 5.0 6.7 - - - +
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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
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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