Contacts of the helix formed by residues 283 - 296 (chain A) in PDB entry 5E92
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 GLU 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A ARG 4.5 5.5 - - - +
255A PHE* 3.4 56.3 - - - +
279A PHE* 3.7 11.3 - - + -
280A PRO* 3.1 27.8 + - + +
282A GLU* 1.4 85.3 - - + +
284A TYR* 1.4 62.2 + - - +
285A ALA* 3.3 3.1 - - - -
286A SER* 3.2 17.3 + - - -
287A TRP* 3.2 10.0 + - - +
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Residues in contact with TYR 284 (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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280A PRO 3.8 2.6 + - - -
281A TYR* 3.0 26.1 + + + +
282A GLU 3.4 1.8 - - - -
283A GLU* 1.4 75.5 - - - +
285A ALA* 1.4 61.4 + - - +
287A TRP* 3.2 34.6 + + - +
288A LYS* 2.8 51.0 + - + +
312A GLU* 5.1 4.4 + - - -
321A TYR* 3.5 39.7 - + + -
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU 5.1 1.0 + - - -
283A GLU* 3.3 0.8 - - - -
284A TYR* 1.4 84.7 - - + +
286A SER* 1.4 56.6 + - - +
288A LYS* 3.3 4.4 + - - +
289A THR* 2.9 36.8 + - - +
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PHE* 3.5 36.8 - - - +
279A PHE* 3.5 17.8 - - - -
283A GLU* 3.2 13.3 + - - -
285A ALA* 1.4 75.4 - - - +
287A TRP* 1.4 60.8 + - - +
289A THR* 3.3 3.9 + - - -
290A GLU* 3.1 35.2 + - - +
399A GLY* 3.8 18.0 + - - -
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Residues in contact with TRP 287 (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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279A PHE* 3.5 44.1 - + + -
283A GLU 3.2 8.0 + - - +
284A TYR* 3.2 46.4 + + - +
286A SER* 1.4 73.9 - - - +
288A LYS* 1.3 74.0 + - + +
290A GLU* 3.5 2.1 + - - +
291A LYS* 2.9 61.1 + - + +
310A ALA* 3.9 13.5 - - + -
311A GLU 4.0 14.6 - - - -
312A GLU* 4.0 14.8 - - + -
321A TYR* 3.5 31.0 - + + -
322A TRP 3.0 21.6 + - - +
323A LEU* 3.7 18.1 - - + +
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Residues in contact with LYS 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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284A TYR* 2.8 46.1 + - + +
285A ALA* 3.9 4.9 - - - +
287A TRP* 1.3 86.4 - - + +
289A THR* 1.4 59.8 + - - +
291A LYS* 3.8 11.7 - - + +
292A ASP* 2.9 68.2 + - - +
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Residues in contact with THR 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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285A ALA* 2.9 22.3 + - - +
286A SER 3.7 4.5 - - - -
288A LYS* 1.4 76.3 - - - +
290A GLU* 1.4 59.8 + - - +
292A ASP* 3.5 7.1 + - - +
293A ILE* 3.2 31.1 + - + +
398A PHE 3.7 13.2 - - - +
399A GLY 3.8 14.3 + - - +
400A LEU 5.0 0.2 - - - -
401A SER 3.6 23.6 - - - +
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Residues in contact with GLU 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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277A LYS* 2.8 37.4 + - - +
279A PHE* 3.3 20.8 - - + -
286A SER* 3.1 17.8 + - - +
287A TRP 3.9 0.4 - - - +
289A THR* 1.4 71.1 - - - +
291A LYS* 1.4 56.3 + - - +
293A ILE* 3.2 3.5 + - - +
294A PHE* 2.9 49.0 + - + -
323A LEU* 3.7 16.1 - - + +
397A ASP* 3.7 3.1 + - - +
398A PHE* 3.2 23.4 + - + -
399A GLY* 3.3 29.3 - - - +
601A ANP 4.3 1.2 + - - -
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Residues in contact with LYS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A TRP* 2.9 52.1 + - + +
288A LYS* 3.8 12.6 - - + +
289A THR 3.4 0.2 - - - -
290A GLU* 1.4 75.6 - - - +
292A ASP* 1.4 63.1 + - - +
294A PHE* 3.4 4.8 + - - +
295A SER* 2.7 50.8 + - - +
307A PHE* 4.8 2.4 - - + -
310A ALA* 3.7 24.2 - - + -
323A LEU* 3.9 15.4 - - + +
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Residues in contact with ASP 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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288A LYS* 2.9 58.5 + - - +
289A THR* 3.7 6.9 - - - +
291A LYS* 1.4 83.3 + - - +
293A ILE* 1.4 61.7 + - + +
295A SER* 3.4 14.0 + - - -
296A ASP 3.4 6.6 + - - -
403A ARG* 2.9 22.4 + - - +
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Residues in contact with ILE 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 THR* 3.2 26.6 + - + +
290A GLU 3.7 5.6 - - - +
292A ASP* 1.4 79.7 - - + +
294A PHE* 1.4 60.8 + - - +
295A SER 3.4 0.2 + - - -
296A ASP* 3.4 15.8 + - - +
299A LEU* 3.5 34.4 - - + +
375A ILE* 4.3 19.7 - - + -
398A PHE* 3.5 49.1 - - + +
401A SER* 3.5 22.9 - - - +
403A ARG* 3.8 17.0 + - + +
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Residues in contact with PHE 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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277A LYS* 6.4 0.4 - - + -
290A GLU* 2.9 41.7 + - + +
291A LYS 3.9 3.1 - - - +
293A ILE* 1.4 72.2 - - - +
295A SER* 1.3 61.1 + - - +
296A ASP 3.4 5.8 + - - +
299A LEU* 3.8 17.6 - - + +
305A LEU* 3.3 46.7 - - + -
307A PHE* 3.6 54.8 - + + +
323A LEU* 4.5 11.0 - - + -
325A THR* 4.4 9.4 - - + -
397A ASP 5.3 2.0 - - - -
398A PHE* 3.7 35.0 - + - -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LYS* 2.7 45.5 + - - +
292A ASP* 3.7 8.5 - - - -
293A ILE 3.3 0.2 - - - -
294A PHE* 1.3 72.5 - - - +
296A ASP* 1.4 63.2 + - - +
297A ILE* 3.4 4.5 + - - +
307A PHE* 4.5 11.1 - - - -
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP 3.4 5.4 + - - +
293A ILE 3.4 11.1 + - - +
294A PHE 3.9 4.9 - - - +
295A SER* 1.4 76.1 - - - +
297A ILE* 1.3 74.4 + - - +
298A ASN* 3.0 32.0 + - - +
299A LEU* 3.3 21.7 + - + +
300A LYS* 4.4 1.9 + - - +
372A LYS* 5.9 0.3 - - - +
373A MET* 5.0 10.2 + - - +
375A ILE* 4.8 3.7 - - + +
403A ARG* 2.8 34.0 + - - +
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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