Contacts of the helix formed by residues 295 - 311 (chain A) in PDB entry 2C1H
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294A ILE* 1.3 73.3 - - - +
296A GLU* 1.3 62.9 + - - +
297A ASP* 3.1 26.4 + - - +
298A ARG* 3.3 50.2 + - + +
299A VAL* 3.0 26.7 + - - +
204B SER* 5.2 1.6 + - - -
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Residues in contact with GLU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A VAL* 4.1 11.2 - - + +
286A LYS* 3.0 39.2 + - + +
289A ALA* 3.7 24.1 - - + +
294A ILE 3.8 4.2 + - - -
295A ASP* 1.3 72.8 + - - +
297A ASP* 1.3 75.1 + - - +
299A VAL* 3.9 0.3 - - - -
300A MET* 2.9 47.2 + - + +
319A TYR* 3.8 16.6 + - + -
322A GLU* 5.5 1.7 - - - +
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Residues in contact with ASP 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ASP* 3.1 12.3 + - - +
296A GLU* 1.3 86.0 + - - +
298A ARG* 1.3 64.6 + - + +
300A MET* 3.9 1.0 - - - +
301A MET* 3.2 30.9 + - - +
319A TYR* 3.8 14.3 + - - -
326A LYS* 2.8 35.9 + - - +
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Residues in contact with ARG 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ASP* 3.3 42.7 + - - +
297A ASP* 1.3 79.3 - - - +
299A VAL* 1.3 56.9 + - - +
301A MET* 3.9 2.8 - - - +
302A GLU* 2.9 31.4 + - - +
203B SER 5.5 0.4 + - - -
204B SER* 3.6 41.0 + - - +
221B ASP* 6.4 0.2 - - - +
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 6.3 0.2 - - + -
285A VAL* 3.8 30.5 - - + -
294A ILE* 4.2 18.6 - - + -
295A ASP 3.0 20.5 + - - +
296A GLU 4.1 1.3 - - - +
298A ARG* 1.3 73.0 - - - +
300A MET* 1.3 55.0 + - - +
302A GLU* 3.9 0.3 - - - +
303A SER* 2.6 38.6 + - - +
204B SER* 3.4 31.2 - - - +
205B PHE* 3.7 31.3 - - + -
284B MET* 4.3 8.1 - - + -
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Residues in contact with MET 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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277A HIS* 4.2 17.9 + - - -
282A TYR* 3.8 25.1 - - + +
285A VAL* 3.8 32.5 - - + -
286A LYS* 3.9 18.8 - - + -
296A GLU* 2.9 24.7 + - + +
297A ASP 3.9 0.9 - - - +
299A VAL* 1.3 76.4 - - - +
301A MET* 1.3 57.4 + - - +
303A SER* 2.9 17.0 + - - -
304A LEU* 3.2 24.5 + - - +
319A TYR* 3.5 58.8 - - + -
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Residues in contact with MET 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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31A LEU* 3.7 26.2 - - + +
297A ASP 3.2 18.1 + - - +
298A ARG* 4.1 3.1 - - - +
300A MET* 1.3 74.9 - - - +
302A GLU* 1.3 61.9 + - - +
304A LEU* 3.3 10.8 + - - +
305A LEU* 3.0 29.6 + - - +
319A TYR* 4.4 6.1 - - + -
323A ALA* 4.0 28.5 - - - +
326A LYS* 4.0 26.5 - - + -
327A LEU* 4.0 26.7 - - + -
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Residues in contact with GLU 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 ARG 2.9 17.7 + - - +
299A VAL 3.9 3.1 - - - +
301A MET* 1.3 75.0 - - - +
303A SER* 1.3 58.0 + - - +
305A LEU* 3.2 10.6 + - - +
306A CYS* 2.9 32.1 + - - -
202B ALA 4.5 0.6 - - - +
203B SER* 2.6 28.8 + - - -
204B SER* 2.7 40.4 + - - -
205B PHE* 3.5 13.8 - - + -
229B PRO* 4.1 16.3 - - + +
258B TYR* 2.8 27.1 + - - +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A LEU* 3.4 35.6 - - - +
277A HIS* 4.3 10.5 - - - -
285A VAL* 5.5 1.4 - - - +
299A VAL* 2.6 26.5 + - - +
300A MET* 2.9 16.8 + - - -
302A GLU* 1.3 77.1 - - - +
304A LEU* 1.3 58.4 + - - -
306A CYS* 3.4 10.2 - - - +
307A MET* 3.4 26.4 + - - +
205B PHE* 4.5 10.0 - - - -
257B ALA* 5.1 0.4 - - - -
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Residues in contact with LEU 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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31A LEU* 3.7 16.9 - - + +
36A LEU* 4.3 4.9 - - + -
277A HIS* 4.7 6.1 - - + -
300A MET 3.2 27.2 + - - +
301A MET* 3.6 15.5 - - - +
302A GLU 3.3 0.2 - - - -
303A SER* 1.3 75.0 - - - +
305A LEU* 1.3 64.0 + - - +
307A MET* 3.4 8.2 + - - -
308A LYS* 3.3 18.9 + - - +
315A ILE* 3.5 46.8 - - + +
317A THR* 3.9 21.3 - - + +
319A TYR* 4.4 8.1 - - + -
323A ALA* 3.8 29.2 - - + -
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Residues in contact with LEU 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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27A GLN* 4.9 7.4 - - - +
29A ASN* 3.8 20.2 - - + +
30A THR* 4.4 6.3 - - - -
31A LEU* 4.4 16.5 - - + +
301A MET 3.0 13.7 + - - +
302A GLU* 3.5 11.7 - - - +
304A LEU* 1.3 73.2 - - - +
306A CYS* 1.3 61.3 + - - +
307A MET 3.1 0.2 - - - -
308A LYS* 3.1 6.1 + - + +
309A ARG* 2.8 27.8 + - - +
228B ASN* 5.0 3.8 - - - +
229B PRO* 4.7 12.3 - - + +
230B ALA* 3.6 38.4 - - + +
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Residues in contact with CYS 306 (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 LEU* 4.7 0.2 - - + -
259A LEU* 3.2 17.1 - - + +
302A GLU* 2.9 25.2 + - - -
303A SER* 3.4 12.3 - - - +
305A LEU* 1.3 77.2 - - - +
307A MET* 1.3 55.8 + - - +
309A ARG* 3.4 25.9 + - - +
310A ALA 3.0 22.3 + - - -
205B PHE* 6.0 0.4 - - - -
229B PRO* 4.7 1.3 - - - -
257B ALA* 3.3 35.2 - - + +
258B TYR* 3.5 24.2 - - - -
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Residues in contact with MET 307 (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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255A GLY* 3.9 10.8 - - - -
256A LEU* 3.8 29.4 - - + +
259A LEU* 3.9 12.3 - - + -
275A ILE* 3.7 24.9 - - + -
277A HIS* 3.5 34.5 - - + +
303A SER 3.4 14.0 + - - +
304A LEU* 3.6 13.9 - - - +
305A LEU 3.1 0.6 - - - -
306A CYS* 1.3 73.8 - - - +
308A LYS* 1.3 63.3 + - - +
310A ALA* 3.4 4.4 + - - +
311A GLY 3.3 5.2 + - - -
312A ALA* 3.1 28.5 + - - +
315A ILE* 3.7 34.5 - - + -
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Residues in contact with LYS 308 (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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29A ASN* 4.1 16.0 - - + +
30A THR 2.8 27.7 + - - +
31A LEU* 3.8 25.4 - - + -
32A THR* 4.9 1.0 + - - +
35A ASP* 2.8 44.1 + - + +
304A LEU 3.3 3.7 + - - +
305A LEU* 3.1 16.0 + - + +
307A MET* 1.3 76.0 - - - +
309A ARG* 1.3 62.8 + - - +
311A GLY* 3.3 12.6 + - - -
312A ALA 3.3 26.8 + - - +
313A ASP* 4.7 4.9 - - - +
315A ILE* 4.3 5.6 - - + -
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Residues in contact with ARG 309 (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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29A ASN* 3.5 13.3 + - + +
259A LEU* 3.8 4.0 - - - +
263A TRP* 4.0 10.9 - - - -
305A LEU 2.8 15.4 + - - +
306A CYS* 3.4 20.6 - - - +
308A LYS* 1.3 78.3 - - - +
310A ALA* 1.3 59.4 + - - +
311A GLY* 3.1 1.8 + - - -
201B TYR* 4.4 0.7 - - - -
229B PRO 2.6 37.6 + - - +
230B ALA* 3.7 11.2 - - - +
231B ASN 3.3 25.6 - - - -
232B THR* 3.1 28.5 + - - +
257B ALA 3.0 22.8 + - - -
258B TYR* 3.3 31.9 - - - +
260B ASP* 2.8 34.9 + - - +
261B ILE* 3.6 9.2 - - - +
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Residues in contact with ALA 310 (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 LEU* 3.4 48.0 - - + +
262A VAL* 3.8 8.4 - - + -
263A TRP* 3.3 34.6 + - - -
306A CYS 3.0 9.1 + - - +
307A MET 3.7 6.3 - - - +
308A LYS 3.3 0.6 - - - -
309A ARG* 1.3 75.5 - - - +
311A GLY* 1.3 58.0 + - - +
260B ASP* 3.6 14.1 + - - -
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Residues in contact with GLY 311 (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 VAL* 4.1 5.2 - - - -
263A TRP* 4.9 3.6 - - - -
266A LYS* 3.3 42.8 - - - +
273A VAL* 3.8 4.3 - - - +
308A LYS 3.3 8.1 + - - -
309A ARG 3.1 6.1 - - - -
310A ALA* 1.3 80.4 - - - +
312A ALA* 1.3 65.3 + - - +
313A ASP 3.8 0.9 + - - -
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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