Contacts of the helix formed by residues 292 - 305 (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 THR 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A VAL* 3.6 10.8 - - - -
290A LEU* 3.8 16.6 - - + +
291A VAL* 1.3 87.4 - - - +
293A GLU* 1.3 64.9 + - - +
294A VAL* 3.5 7.1 + - - +
295A ARG* 3.3 35.1 + - - +
296A VAL* 2.6 38.9 + - - +
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Residues in contact with GLU 293 (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* 5.2 7.2 - - + +
261A ARG* 5.0 16.6 - - + +
262A GLU* 3.4 46.4 - - + +
265A VAL* 3.4 24.8 - - + +
266A GLU* 3.9 9.7 - - - +
292A THR* 1.3 74.1 - - - +
294A VAL* 1.3 62.0 + - - +
295A ARG 2.8 1.5 + - - -
296A VAL* 3.0 5.6 + - - +
297A TYR* 2.3 38.4 + - - +
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Residues in contact with VAL 294 (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* 6.0 0.2 - - - +
292A THR* 3.5 7.7 + - - +
293A GLU* 1.3 82.3 + - - +
295A ARG* 1.3 70.6 + - + +
297A TYR* 2.8 41.2 - - + +
298A ASN* 2.9 20.1 + - - +
17F A 5.8 3.6 - - - -
18F C 5.9 3.4 - - - +
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Residues in contact with ARG 295 (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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236A PHE* 3.1 42.4 - - - +
238A TRP* 3.6 13.4 + - + -
287A GLY 5.1 0.6 + - - -
288A SER* 3.3 23.0 + - - +
290A LEU* 3.0 24.0 + - - +
292A THR* 3.1 30.6 + - - +
293A GLU 2.8 0.4 - - - -
294A VAL* 1.3 88.2 - - + +
296A VAL* 1.3 63.3 + - - +
298A ASN* 3.3 5.8 + - - +
299A TRP 3.0 15.4 + - - -
17F A 2.7 46.7 + - - +
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Residues in contact with VAL 296 (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* 3.8 15.5 - - + -
246A LEU* 5.1 3.6 - - + -
261A ARG* 3.9 25.6 - - + -
264A LEU* 4.8 9.6 - - + -
265A VAL* 3.8 22.7 - - + +
268A CYS* 5.8 1.6 - - - -
291A VAL* 3.5 21.8 - - + -
292A THR 2.6 27.6 + - - +
293A GLU* 3.4 5.8 - - - +
295A ARG* 1.3 69.0 - - - +
297A TYR* 1.3 68.7 + - - +
299A TRP* 2.7 13.0 + - - +
300A PHE* 3.1 30.3 + - + -
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Residues in contact with TYR 297 (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* 6.4 0.4 - - + -
261A ARG* 4.5 32.5 - - - +
293A GLU 2.3 22.0 + - - +
294A VAL* 2.8 31.8 + - + +
296A VAL* 1.3 66.8 - - - +
298A ASN* 1.3 69.6 + - - +
300A PHE* 2.7 23.1 + - + +
301A ALA* 3.0 9.7 + - + -
304A ARG* 4.1 28.5 - - - -
1E C 4.4 14.1 - - - -
2E T 3.5 52.2 + - + +
3E T 3.8 13.8 - - + +
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Residues in contact with ASN 298 (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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294A VAL* 2.9 21.5 + - - +
295A ARG* 3.8 5.6 - - - +
297A TYR* 1.3 93.9 - - - +
299A TRP* 1.3 61.7 + - - +
300A PHE 3.0 0.4 - - - -
301A ALA* 3.7 9.3 - - - +
302A ASN* 2.9 35.0 + - - +
16F A 5.7 1.6 - - + -
17F A 4.0 35.5 - - + +
18F C 3.9 27.4 - - - +
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Residues in contact with TRP 299 (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* 3.4 43.0 - + + +
243A GLN* 3.1 27.6 - - - +
246A LEU* 3.5 49.1 - - + +
247A TYR* 3.6 39.7 - + - -
250A TYR* 4.6 8.5 - + + -
295A ARG 3.0 11.5 + - - +
296A VAL* 2.7 14.0 + - - +
298A ASN* 1.3 77.5 - - - +
300A PHE* 1.3 83.8 + + + +
302A ASN* 4.0 4.0 - - - +
303A ARG* 3.3 33.5 - - + +
16F A 5.0 2.9 - - - -
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Residues in contact with PHE 300 (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* 3.5 31.0 - - + -
249A ALA 4.6 9.0 - - - -
250A TYR* 3.8 23.6 - + - -
253A GLN 3.6 11.2 - - - -
254A LYS 3.6 10.8 - - - -
256A PRO* 3.0 43.7 - - + -
261A ARG* 5.9 0.9 - - + -
264A LEU* 4.2 13.0 - - + -
296A VAL* 3.2 26.9 - - + -
297A TYR* 2.7 11.1 + + + +
299A TRP* 1.3 86.2 - + - +
301A ALA* 1.3 71.7 + - - +
303A ARG* 2.5 26.1 + - - +
304A ARG* 3.0 20.8 + - - +
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Residues in contact with ALA 301 (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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297A TYR* 3.0 14.9 + - + +
298A ASN* 4.2 9.4 - - - +
300A PHE* 1.3 83.9 - - - +
302A ASN* 1.3 66.9 + - - +
304A ARG* 3.4 25.1 - - + +
305A LYS* 2.6 38.2 + - - +
3E T 3.9 11.0 - - + +
18F C 5.6 0.7 - - - +
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Residues in contact with ASN 302 (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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298A ASN* 2.9 24.6 + - - +
299A TRP* 4.0 4.7 - - - +
300A PHE 2.7 3.7 + - - -
301A ALA* 1.3 74.9 - - - +
303A ARG* 1.3 87.0 + - - +
305A LYS* 2.6 42.6 + - + +
306A GLU* 3.8 13.6 - - + +
16F A 4.3 14.6 - - + +
17F A 3.3 36.4 + - - +
18F C 3.9 3.3 + - - -
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Residues in contact with ARG 303 (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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243A GLN* 4.5 5.3 - - - +
247A TYR* 3.0 45.4 + - - -
250A TYR* 3.0 32.3 + - + -
299A TRP* 3.3 42.7 + - + +
300A PHE* 2.5 19.3 + - - +
302A ASN* 1.3 102.5 + - - +
304A ARG* 1.3 64.3 + - - +
305A LYS 3.8 0.4 - - - +
306A GLU* 2.8 37.9 + - - +
307A GLU* 4.8 3.5 - - - +
15F T 5.0 8.7 + - - -
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Residues in contact with ARG 304 (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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250A TYR* 3.8 14.6 - - + +
254A LYS* 2.7 29.7 + - - -
255A ASN* 3.0 31.0 + - - +
256A PRO* 3.7 11.3 + - - +
297A TYR* 4.1 17.6 - - - -
300A PHE* 3.3 26.3 - - - +
301A ALA* 3.2 19.1 - - - +
303A ARG* 1.3 80.0 - - + +
305A LYS* 1.3 55.5 - - - +
306A GLU 2.2 20.7 + - - -
307A GLU* 3.3 21.6 + - - +
2E T 5.0 1.0 - - - -
3E T 2.2 55.8 + - - +
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Residues in contact with LYS 305 (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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301A ALA* 2.6 22.1 + - - +
302A ASN* 2.6 34.5 + - + +
304A ARG* 1.3 80.1 - - - +
306A GLU* 1.3 61.7 + - + +
307A GLU 3.4 1.5 + - - -
308A ALA* 4.8 8.6 + - - +
3E T 6.2 1.3 - - + -
4E G 4.4 26.6 + - + +
5E G 2.7 42.2 + - + +
6E T 3.5 16.8 - - + +
17F A 3.7 7.0 - - - +
18F C 3.5 9.3 - - - +
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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