Contacts of the helix formed by residues 292 - 308 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B ARG* 1.3 71.3 - - - +
293B ALA* 1.3 58.1 + - - +
295B ALA* 2.9 23.9 + - - +
296B GLU* 3.1 38.2 + - - +
317B LEU* 4.2 16.3 - - - +
321B PHE* 3.2 54.1 + - + -
322B ARG* 5.2 1.4 - - - +
324B GLY* 4.5 7.7 + - - -
325B LYS 3.5 16.3 + - - +
326B LEU* 3.3 21.0 + - + +
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG* 4.0 17.6 - - + +
292B ARG* 1.3 79.5 - - - +
294B ASP* 1.3 60.9 + - - +
296B GLU* 3.8 12.4 + - - +
297B ALA* 3.7 18.4 + - - +
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Residues in contact with ASP 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL* 3.8 13.9 - - + -
291B ARG* 2.8 50.0 + - - +
293B ALA* 1.3 74.0 - - - +
295B ALA* 1.3 64.2 + - - +
297B ALA* 3.5 3.8 + - - +
298B LEU* 3.2 31.4 + - + +
396B LEU* 2.9 28.3 - - + +
398B GLN* 3.8 3.1 + - - -
415B LYS* 2.6 30.4 + - - +
417B VAL* 5.4 0.2 - - + -
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL* 4.5 0.4 - - - +
291B ARG 3.1 5.1 + - - +
292B ARG* 2.9 16.9 + - - +
294B ASP* 1.3 79.3 - - - +
296B GLU* 1.3 55.8 + - - +
298B LEU* 3.5 1.3 + - - -
299B GLN* 2.9 27.1 + - - +
317B LEU* 4.8 9.4 - - + +
321B PHE* 3.8 36.8 - - + -
331B VAL* 4.2 17.7 - - + -
333B PHE* 3.9 6.9 - - - -
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Residues in contact with GLU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ARG* 3.1 36.9 + - + +
293B ALA* 4.3 10.5 - - - +
294B ASP 3.3 0.4 - - - -
295B ALA* 1.3 76.0 - - + +
297B ALA* 1.3 64.2 + - - +
299B GLN* 3.2 21.4 + - + +
300B GLN* 3.3 20.2 + - - +
317B LEU* 5.8 3.6 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA 3.7 11.6 + - - +
294B ASP* 3.5 9.1 + - - +
295B ALA 3.4 0.2 - - - -
296B GLU* 1.3 78.9 - - - +
298B LEU* 1.3 63.0 + - - +
300B GLN* 3.5 11.5 + - - +
301B LEU* 3.3 28.4 + - + +
396B LEU* 4.0 18.2 - - + -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ASP* 3.2 20.5 + - + +
295B ALA* 4.0 3.4 - - - +
297B ALA* 1.3 74.3 - - - +
299B GLN* 1.3 63.0 + - - +
301B LEU* 3.7 16.4 + - + +
302B ILE* 2.9 34.8 + - + +
331B VAL* 4.0 13.2 - - + -
333B PHE* 4.0 10.1 - - + -
394B LEU* 5.1 14.4 - - + -
395B GLY 5.4 0.4 - - - +
396B LEU* 3.7 31.0 - - + +
417B VAL* 3.5 39.3 - - + -
419B VAL* 4.1 15.5 - - + -
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Residues in contact with GLN 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 2.9 17.9 + - - +
296B GLU* 3.2 14.2 - - + +
297B ALA 3.2 0.2 - - - -
298B LEU* 1.3 79.8 - - - +
300B GLN* 1.3 62.3 + - + +
302B ILE* 3.5 4.3 - - - +
303B GLU* 3.1 40.9 + - - +
315B VAL* 3.1 46.7 + - - +
317B LEU* 3.5 30.4 - - - +
333B PHE* 3.4 22.4 - - + -
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Residues in contact with GLN 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLU* 3.3 43.5 + - + +
227A GLN* 3.6 26.1 + - + +
296B GLU* 3.3 17.1 + - - +
297B ALA* 3.9 10.4 + - - +
298B LEU 3.2 0.4 - - - -
299B GLN* 1.3 75.3 - - + +
301B LEU* 1.3 58.7 + - + +
302B ILE 2.9 4.5 - - - -
303B GLU* 2.6 41.0 + - - +
304B ALA* 2.8 12.3 + - - +
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA* 3.3 18.7 + - + +
298B LEU* 4.1 22.9 - - + +
299B GLN 3.6 0.2 - - - -
300B GLN* 1.3 80.6 - - + +
302B ILE* 1.3 62.8 + - + +
304B ALA* 3.3 20.1 - - - +
305B ALA 3.5 5.0 + - - -
354B LEU* 3.6 14.5 - - + +
357B GLN* 5.4 3.2 - - - +
359B LEU* 3.7 31.6 - - + -
394B LEU* 6.5 1.3 - - + -
395B GLY 5.3 0.4 - - - +
396B LEU* 5.0 2.0 - - + -
397B PRO* 4.4 19.3 - - + -
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Residues in contact with ILE 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B LEU* 2.9 26.0 + - + +
299B GLN 3.5 5.2 - - - +
300B GLN 2.7 1.4 + - - -
301B LEU* 1.3 76.8 - - + +
303B GLU* 1.3 62.3 + - - +
304B ALA 3.1 1.5 + - - -
305B ALA* 3.3 4.9 + - - +
306B VAL* 2.8 29.4 + - + +
315B VAL* 4.0 14.6 - - + -
333B PHE* 3.9 16.4 - - + -
335B ILE* 4.0 25.6 - - + -
350B VAL* 4.6 1.5 - - + +
354B LEU* 3.9 26.7 - - + -
394B LEU* 4.4 15.7 - - + -
419B VAL* 4.7 1.8 - - + -
421B LEU* 4.0 25.6 - - + -
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLN* 6.1 0.5 - - - +
299B GLN* 3.1 28.1 + - - +
300B GLN* 2.6 35.1 + - - +
302B ILE* 1.3 73.7 - - - +
304B ALA* 1.3 51.4 + - - +
306B VAL* 3.7 0.7 - - - -
307B ARG* 2.7 73.8 + - + +
315B VAL* 3.4 36.2 + - + +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLN* 6.2 2.2 - - - +
300B GLN 2.8 9.3 + - - +
301B LEU* 3.3 17.0 - - + +
303B GLU* 1.3 73.7 - - - +
305B ALA* 1.3 58.1 + - - +
306B VAL 2.9 3.8 - - - -
307B ARG* 4.0 3.7 - - - +
308B GLN* 2.8 40.3 + - - +
357B GLN* 5.3 9.2 - - - +
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B LEU 3.5 0.4 + - - -
302B ILE 3.3 5.1 + - - +
304B ALA* 1.3 76.6 - - - +
306B VAL* 1.3 57.3 + - - +
308B GLN* 4.4 0.9 - - - -
309B THR* 2.6 27.4 + - - -
350B VAL* 3.4 24.6 - - + +
353B CYS* 3.4 37.4 - - + -
354B LEU* 3.8 23.1 - - + -
357B GLN* 4.5 0.7 - - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ILE* 2.8 24.5 - - + +
303B GLU* 3.4 7.6 - - - +
304B ALA 2.9 0.8 - - - -
305B ALA* 1.3 82.6 - - - +
307B ARG* 1.3 62.6 + - + +
309B THR* 3.9 1.3 - - - -
310B LEU* 2.9 32.2 + - - +
313B ALA* 3.2 33.4 - - + +
315B VAL* 3.7 19.1 - - + -
335B ILE* 3.5 35.4 - - + -
346B LEU* 4.9 3.4 - - + +
350B VAL* 4.2 9.9 - - + -
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLU* 6.2 0.2 - - - +
224A GLU* 3.7 38.9 + - - +
227A GLN* 3.7 30.5 - - - +
228A VAL* 4.3 10.6 - - - +
233A ARG* 5.8 3.3 - - - -
303B GLU* 2.7 56.4 + - + +
304B ALA* 4.2 2.7 - - - +
306B VAL* 1.3 74.9 - - + +
308B GLN* 1.3 65.5 + - - +
309B THR 3.1 1.1 + - - -
310B LEU 3.5 5.3 + - - -
311B PRO* 3.4 28.3 - - + +
312B GLY 5.7 1.3 - - - +
313B ALA* 5.3 5.8 - - - +
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Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A GLU* 6.1 1.3 - - - -
233A ARG* 6.1 7.0 - - - +
304B ALA* 2.8 22.3 + - - +
305B ALA* 4.4 1.8 - - - -
307B ARG* 1.3 79.6 - - - +
309B THR* 1.3 58.4 + - - +
311B PRO* 5.6 0.3 - - - +
353B CYS* 3.5 27.9 - - - +
357B GLN* 4.9 3.6 + - - -
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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