Contacts of the helix formed by residues 287 - 296 (chain A) in PDB entry 2EIN
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 VAL 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A HIS* 3.5 33.7 - - + +
283A LEU* 3.4 20.6 - - + +
284A GLY* 4.0 2.2 - - - -
285A PHE 3.7 1.2 - - - -
286A ILE* 1.3 82.1 - - + +
288A TRP* 1.3 66.1 + - - +
289A ALA 3.3 2.9 - - - -
290A HIS* 2.9 29.3 + - + +
305A PHE* 3.7 10.1 - - - +
308A ALA* 3.8 9.0 - - + +
309A THR* 3.3 40.8 - - - +
312A ILE* 4.3 7.9 - - + -
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Residues in contact with TRP 288 (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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233A HIS* 3.0 42.6 + - - +
236A TRP* 3.0 40.8 - - + +
237A PHE* 3.8 14.8 - + - +
240A HIS* 4.2 12.5 - - + +
241A PRO* 5.6 0.2 - - + -
284A GLY 5.6 0.2 + - - -
285A PHE 4.0 17.4 + - - -
286A ILE* 4.4 7.2 - - + -
287A VAL* 1.3 83.8 - - - +
289A ALA* 1.3 65.6 + - - +
290A HIS 2.9 5.8 + - - -
291A HIS* 3.1 24.5 + - - +
292A MET* 4.2 2.2 - - - +
304A TYR* 6.2 0.2 - + - -
305A PHE* 3.9 20.6 - + - -
99C TRP* 3.7 28.5 - + - -
268C PGV 4.5 11.7 - - + -
525C CHD 4.0 31.0 - - + -
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Residues in contact with ALA 289 (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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233A HIS* 4.8 2.7 - - + -
287A VAL 3.2 2.2 + - - -
288A TRP* 1.3 85.7 - - - +
290A HIS* 1.3 55.6 + - - +
291A HIS 2.9 6.3 - - - -
292A MET* 2.9 35.0 + - - +
293A PHE* 3.7 7.6 - - - -
297A MET* 4.0 20.4 - - + +
305A PHE* 3.4 38.9 - - + -
525C CHD 5.5 0.2 - - + -
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Residues in contact with HIS 290 (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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240A HIS* 2.9 21.0 + + - -
244A TYR* 5.0 0.4 - - - -
287A VAL* 2.9 20.8 + - + +
288A TRP 2.9 3.0 + - - -
289A ALA* 1.3 76.4 - - - +
291A HIS* 1.3 85.6 + + - +
292A MET 3.2 1.9 + - - -
293A PHE* 3.7 37.4 - - + -
305A PHE* 4.2 3.2 - - - +
309A THR* 2.7 39.2 + - + +
364A ASP* 4.1 4.2 - - - +
516A HEA 3.3 44.5 - + + +
517A CU 2.0 30.6 - - - -
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Residues in contact with HIS 291 (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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129A TYR* 4.5 4.2 + - - -
232A GLN* 5.3 0.5 - - - +
236A TRP* 3.4 66.3 + + + +
240A HIS* 4.3 2.3 - - + +
243A VAL* 5.5 1.8 - - + -
288A TRP* 3.2 18.8 - - - +
289A ALA 2.9 0.4 - - - -
290A HIS* 1.3 99.6 + + - +
292A MET* 1.3 60.0 + - - +
293A PHE 3.8 1.1 - - - -
368A HIS* 3.9 20.7 - - - -
516A HEA 3.5 48.8 + + + +
517A CU 2.0 30.8 - - - -
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Residues in contact with MET 292 (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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229A ILE* 3.7 12.3 - - + +
232A GLN* 3.1 47.1 - - + +
233A HIS* 3.5 46.7 - - + +
236A TRP* 4.1 11.7 - - + -
288A TRP* 4.2 5.2 - - - -
289A ALA* 2.9 24.9 + - + +
291A HIS* 1.3 87.3 - - - +
293A PHE* 1.3 64.5 + - - +
294A THR 3.1 4.2 + - - -
295A VAL* 3.2 32.1 + - + +
296A GLY 4.4 0.7 + - - -
297A MET* 3.9 11.2 - - + +
368A HIS* 5.7 0.7 - - - -
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Residues in contact with PHE 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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289A ALA 3.7 14.1 - - - -
290A HIS* 3.7 27.1 + - + -
291A HIS 3.8 1.4 - - - -
292A MET* 1.3 76.5 - - - +
294A THR* 1.3 61.4 + - + +
295A VAL 3.8 0.2 + - - -
296A GLY* 3.9 4.3 + - - -
297A MET* 4.6 1.1 - - + -
302A ARG* 3.4 40.3 + - + +
305A PHE* 4.0 13.5 - - + -
306A THR* 3.5 24.7 - - - -
358A LEU 4.0 3.4 - - - -
359A ALA 3.2 24.5 - - - -
361A SER* 3.4 34.3 - - - +
364A ASP* 3.1 35.8 + - + +
365A ILE* 3.8 8.8 - - + +
368A HIS* 5.4 1.0 + - - -
23H GLN* 5.3 1.2 + - - +
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Residues in contact with THR 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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292A MET 3.2 1.0 - - - -
293A PHE* 1.3 76.3 - - + +
295A VAL* 1.3 58.4 + - - +
296A GLY* 2.8 10.4 + - - -
365A ILE* 3.6 35.4 - - + +
368A HIS* 3.6 43.0 + - + -
171B LYS* 3.9 19.1 - - + +
172B THR* 3.9 5.2 - - - +
173B ASP* 2.9 44.7 + - - -
23H GLN* 5.0 1.1 - - - +
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Residues in contact with VAL 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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229A ILE* 4.0 33.2 - - + -
232A GLN* 3.7 24.7 - - - +
292A MET* 3.2 32.3 + - + +
294A THR* 1.3 78.1 + - - +
296A GLY* 1.3 62.4 + - - +
297A MET* 4.4 14.1 - - + -
173B ASP* 3.2 26.7 - - + +
175B ILE* 4.2 2.2 - - + +
178B ARG* 3.4 12.3 + - - +
180B ASN* 3.3 17.7 + - - +
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Residues in contact with GLY 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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293A PHE 3.9 4.1 + - - -
294A THR* 2.8 7.8 - - - +
295A VAL* 1.3 76.7 - - - +
297A MET* 1.3 61.3 + - - +
178B ARG* 2.7 29.0 + - - -
180B ASN* 4.2 3.0 - - - +
23H GLN* 2.9 40.8 - - - +
24H ASN 4.8 1.7 + - - -
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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