Contacts of the helix formed by residues 292 - 308 (chain A) in PDB entry 2IHM
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 ARG 292 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A ARG* 1.3 73.2 - - - +
293A ALA* 1.3 56.9 + - - +
295A ALA* 3.0 7.6 + - - +
296A GLU* 2.8 44.3 + - + +
317A LEU* 4.1 20.1 - - - +
321A PHE* 3.2 48.5 + - + -
322A ARG* 5.7 0.6 - - - +
324A GLY* 4.3 6.1 + - - -
325A LYS 3.0 24.6 + - - +
326A LEU* 3.7 27.5 + - + +
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Residues in contact with ALA 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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291A ARG* 3.0 12.4 - - + +
292A ARG* 1.3 77.5 - - - +
294A ASP* 1.3 66.7 + - - +
296A GLU* 3.5 10.8 - - - +
297A ALA* 3.1 23.9 + - - +
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Residues in contact with ASP 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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290A VAL* 3.6 14.0 - - + -
291A ARG* 2.7 58.8 + - - +
293A ALA* 1.3 75.8 - - - +
295A ALA* 1.3 63.7 + - - +
297A ALA* 3.5 2.0 + - - +
298A LEU* 3.1 30.7 + - + +
396A LEU* 3.6 23.7 - - + +
398A GLN* 3.8 3.1 - - - +
415A LYS* 2.7 30.0 + - - +
417A VAL* 5.2 1.8 - - + -
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A VAL* 4.5 1.0 - - - +
291A ARG 3.0 9.9 + - - +
292A ARG* 3.0 12.3 + - - +
294A ASP* 1.3 77.4 - - - +
296A GLU* 1.3 55.8 + - - +
298A LEU* 3.3 1.3 + - - +
299A GLN* 2.9 30.2 + - - +
317A LEU* 4.2 17.5 - - + -
321A PHE* 4.1 19.3 - - + -
331A VAL* 4.1 27.8 - - + -
333A PHE* 3.5 7.2 - - - -
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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
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292A ARG* 2.8 32.2 + - + +
293A ALA* 3.5 11.4 - - - +
295A ALA* 1.3 77.1 - - - +
297A ALA* 1.3 59.4 + - - +
299A GLN* 2.8 31.0 + - - +
300A GLN* 3.0 28.7 + - + +
317A LEU* 5.8 4.1 - - + +
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Residues in contact with ALA 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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293A ALA 3.1 13.9 + - - +
294A ASP* 3.8 5.6 - - - +
296A GLU* 1.3 78.8 - - - +
298A LEU* 1.3 62.7 + - - +
300A GLN* 3.0 22.0 + - - +
301A LEU* 3.1 18.7 + - + +
396A LEU* 4.0 18.6 - - + -
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Residues in contact with LEU 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 ASP 3.1 22.1 + - - +
295A ALA 3.7 4.3 - - - +
297A ALA* 1.3 76.7 - - - +
299A GLN* 1.3 57.4 - - - +
301A LEU* 3.2 11.5 + - + +
302A ILE* 2.9 36.1 + - + +
331A VAL* 3.8 25.4 - - + -
333A PHE* 3.8 13.9 - - + -
394A LEU* 4.3 26.9 - - + -
396A LEU* 3.8 30.3 - - + -
417A VAL* 3.8 22.0 - - + -
419A VAL* 3.9 12.3 - - + -
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Residues in contact with GLN 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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295A ALA 2.9 12.3 + - - +
296A GLU* 2.8 19.6 + - - +
298A LEU* 1.3 77.3 - - - +
300A GLN* 1.3 59.9 + - - +
302A ILE* 4.5 2.2 - - - -
303A GLU* 2.9 58.6 + - + +
315A VAL* 3.0 32.7 + - + +
317A LEU* 4.1 25.2 - - - +
333A PHE* 3.5 22.0 - - + -
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Residues in contact with GLN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLU* 3.0 34.8 + - + +
297A ALA* 3.0 13.9 + - - +
299A GLN* 1.3 80.5 - - - +
301A LEU* 1.3 69.6 + - + +
303A GLU* 4.1 14.6 + - - +
304A ALA* 3.1 24.9 + - - +
307A ARG* 5.0 1.9 + - - -
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Residues in contact with LEU 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 ALA* 3.1 14.0 + - + +
298A LEU* 3.2 14.3 + - + +
300A GLN* 1.3 78.5 - - + +
302A ILE* 1.3 67.3 + - + +
304A ALA* 3.7 6.3 - - + +
305A ALA* 3.1 22.2 + - - +
354A LEU* 4.6 13.4 - - + +
357A GLN* 4.6 16.6 + - - +
359A LEU* 4.3 19.7 - - + -
394A LEU* 6.2 2.0 - - + -
396A LEU* 4.4 21.1 - - + -
397A PRO* 4.8 11.7 - - + -
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Residues in contact with ILE 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 LEU* 2.9 23.4 + - + +
299A GLN* 4.0 5.4 - - - +
301A LEU* 1.3 75.9 - - + +
303A GLU* 1.3 67.7 + - - +
305A ALA* 2.8 16.3 + - - +
306A VAL* 2.8 14.4 + - + +
315A VAL* 4.0 25.4 - - + -
333A PHE* 3.9 19.7 - - + -
335A ILE* 4.2 17.0 - - + -
350A VAL* 5.0 3.8 - - + -
354A LEU* 4.0 20.9 - - + -
394A LEU* 4.7 11.2 - - + -
419A VAL* 5.2 1.1 - - + -
421A LEU* 3.9 30.7 - - + -
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Residues in contact with GLU 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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299A GLN* 2.9 53.5 + - + +
300A GLN* 4.1 13.9 + - - +
302A ILE* 1.3 75.6 - - - +
304A ALA* 1.3 56.9 + - - +
306A VAL* 3.3 3.4 + - - +
307A ARG* 2.8 46.6 + - - +
315A VAL* 3.6 35.9 + - + +
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Residues in contact with ALA 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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300A GLN 3.1 20.4 + - - +
301A LEU* 3.7 7.6 - - + +
303A GLU* 1.3 75.1 - - - +
305A ALA* 1.3 64.8 + - - +
307A ARG* 3.1 34.0 + - - +
308A GLN* 3.0 28.1 + - - +
357A GLN* 6.3 1.1 - - - +
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Residues in contact with ALA 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 LEU 3.1 13.5 + - - +
302A ILE* 2.8 11.7 + - - +
304A ALA* 1.3 75.8 - - - +
306A VAL* 1.3 63.9 + - - +
308A GLN* 2.9 27.5 + - - +
309A THR* 3.9 4.0 + - - -
350A VAL* 4.1 28.3 - - + +
353A CYS* 4.0 25.5 - - + +
354A LEU* 4.6 6.7 - - + -
357A GLN* 5.0 1.9 - - - +
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Residues in contact with VAL 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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302A ILE* 2.8 20.6 + - + +
303A GLU* 3.7 9.4 - - - +
305A ALA* 1.3 73.2 - - - +
307A ARG* 1.3 57.2 + - - +
309A THR* 3.1 4.7 + - - -
310A LEU* 2.8 34.2 + - + +
313A ALA* 3.3 36.6 - - + +
315A VAL* 4.1 11.2 - - + -
335A ILE* 3.8 31.6 - - + -
346A LEU* 4.6 9.4 - - + +
350A VAL* 4.0 19.3 - - + -
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Residues in contact with ARG 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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300A GLN 5.0 2.0 + - - -
303A GLU* 2.8 35.5 + - - +
304A ALA* 3.2 31.6 - - - +
305A ALA 3.1 0.4 - - - -
306A VAL* 1.3 77.7 - - - +
308A GLN* 1.3 65.9 + - - +
309A THR* 3.1 3.0 + - - -
310A LEU 4.5 8.2 + - - -
311A PRO* 4.7 16.1 - - + +
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Residues in contact with GLN 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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304A ALA* 3.0 29.7 + - - +
305A ALA* 2.9 17.7 + - - +
307A ARG* 1.3 83.5 - - - +
309A THR* 1.3 63.2 + - - +
353A CYS* 4.4 15.0 - - + -
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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