Contacts of the helix formed by residues 289 - 303 (chain A) in PDB entry 5E2Q
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 SER 289 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ASP* 5.2 2.7 - - - -
229A GLU* 3.3 23.4 + - - -
230A VAL* 3.7 19.3 - - - -
283A GLU* 6.1 0.2 - - - -
284A SER* 2.7 34.5 + - - +
287A GLN* 4.7 5.6 - - - -
288A GLY* 1.3 77.8 - - - +
290A ILE* 1.3 60.2 + - - +
291A GLU 3.3 4.5 + - - -
292A ALA* 2.9 29.1 + - - +
293A HIS 3.3 2.3 + - - -
295A ARG* 5.3 0.7 - - - -
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 6.3 1.8 - - + -
194A SER* 3.6 34.1 - - - +
196A TYR* 3.9 18.6 - - + -
197A ASN* 3.5 38.8 - - + +
229A GLU* 5.3 0.2 + - - -
284A SER* 5.1 1.8 - - - +
288A GLY 3.8 1.8 + - - +
289A SER* 1.3 70.5 - - - +
291A GLU* 1.3 54.5 + - - +
293A HIS* 2.9 10.0 + - + +
294A LYS* 2.5 41.7 + - + +
314A PHE* 5.8 2.2 - - + +
395A TYR* 3.8 31.6 - - + +
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A ASN* 5.1 7.1 - - - +
229A GLU* 3.2 26.4 + - - +
289A SER* 3.3 0.6 + - - +
290A ILE* 1.3 79.7 - - + +
292A ALA* 1.3 52.1 + - - +
294A LYS* 3.0 29.1 + - + +
295A ARG* 2.6 56.9 + - - +
298A ARG* 4.3 14.7 + - - -
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Residues in contact with ALA 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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280A GLN* 3.2 34.7 - - - +
283A GLU* 3.9 9.4 - - + +
284A SER 3.7 10.1 - - - +
289A SER* 2.9 27.9 + - - +
290A ILE 3.2 0.2 - - - -
291A GLU* 1.3 76.0 - - - +
293A HIS* 1.3 58.3 + - - +
295A ARG* 3.4 23.0 - - - +
296A GLY 3.0 20.3 + - - -
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Residues in contact with HIS 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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281A TYR* 3.7 23.9 - + - -
284A SER* 3.3 19.0 - - - +
285A PHE* 4.2 18.6 - + - -
289A SER 3.3 2.5 + - - +
290A ILE* 2.9 15.7 + - + +
292A ALA* 1.3 76.7 - - - +
294A LYS* 1.3 56.4 + - - +
296A GLY* 3.7 0.7 - - - +
297A SER* 2.8 40.3 + - - -
311A TYR* 3.2 31.0 - + - -
312A ILE 2.8 26.7 + - - -
313A GLY* 4.0 4.0 - - - -
314A PHE 5.4 2.2 - - - -
315A ILE* 3.9 10.3 - - + -
395A TYR* 2.6 24.8 + - - +
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Residues in contact with LYS 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 ILE* 2.5 30.4 + - + +
291A GLU* 3.3 35.6 + - + +
293A HIS* 1.3 71.4 - - - +
295A ARG* 1.3 59.2 + - - +
297A SER* 3.3 3.0 + - - -
298A ARG* 2.9 39.3 + - - +
395A TYR* 3.5 38.8 - - + -
397A ASP* 2.8 33.5 + - - -
398A LEU* 3.8 18.1 - - + +
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Residues in contact with ARG 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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227A ASP* 6.0 0.2 + - - -
229A GLU* 4.1 13.9 + - - -
280A GLN* 2.9 34.7 + - + +
283A GLU* 5.3 5.5 + - - +
289A SER* 5.3 0.2 - - - -
291A GLU* 2.6 40.6 + - - +
292A ALA* 3.4 28.9 - - - +
294A LYS* 1.3 72.1 - - - +
296A GLY* 1.3 62.5 + - - +
298A ARG* 3.3 30.2 + - - +
299A PHE* 3.2 27.8 + - + -
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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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277A MET* 3.2 20.2 - - - +
280A GLN* 3.5 20.4 - - - +
281A TYR* 3.7 19.7 - - - -
292A ALA 3.0 10.5 + - - -
293A HIS 3.4 0.4 + - - -
294A LYS 3.2 0.4 - - - -
295A ARG* 1.3 74.5 - - - +
297A SER* 1.3 58.5 + - - +
299A PHE 3.3 1.4 + - - -
300A TRP* 3.0 23.4 + - - +
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Residues in contact with SER 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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281A TYR* 3.8 3.2 + - - -
293A HIS* 2.8 22.9 + - - -
294A LYS 3.6 4.9 - - - -
296A GLY* 1.3 75.9 - - - +
298A ARG* 1.3 62.1 + - - +
300A TRP* 3.2 10.5 + - - +
301A ILE* 3.1 32.1 + - - +
311A TYR* 2.8 32.4 + - - -
393A PRO* 4.2 8.1 - - - -
395A TYR* 3.6 13.7 - - - -
398A LEU* 4.2 8.1 - - - -
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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
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291A GLU* 4.3 11.7 + - - -
294A LYS* 2.9 37.5 + - - +
295A ARG* 3.3 23.9 - - - +
296A GLY 3.1 0.2 - - - -
297A SER* 1.3 78.8 - - - +
299A PHE* 1.3 62.9 + - + +
301A ILE* 3.7 9.9 + - + +
302A GLN* 3.7 22.8 + - - +
397A ASP* 5.3 1.4 + - - -
398A LEU* 3.8 24.7 - - + +
402A GLU* 2.3 58.6 + - + +
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Residues in contact with PHE 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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273A HIS* 3.7 33.0 - + - +
276A GLN* 3.4 59.5 - - + -
277A MET* 3.9 2.5 - - + -
280A GLN* 4.3 15.5 - - + -
295A ARG* 3.2 26.4 + - + -
296A GLY 3.3 6.3 + - - +
298A ARG* 1.3 76.7 - - + +
300A TRP* 1.3 66.2 + - - +
302A GLN* 3.1 30.4 + - - +
303A ASP 3.4 7.8 + - - -
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Residues in contact with TRP 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 MET* 3.5 29.1 - - + +
281A TYR* 3.6 12.6 - - - +
296A GLY 3.0 13.6 + - - +
297A SER* 3.2 13.0 + - - +
299A PHE* 1.3 77.8 - - - +
301A ILE* 1.3 67.1 + - + +
303A ASP* 3.1 12.7 + - + +
309A GLU* 2.8 26.8 + - + -
310A SER 2.8 27.6 + - - -
311A TYR* 3.9 25.6 - + + -
331A PHE* 4.9 1.6 - + - -
392A ILE* 3.5 55.9 - - + -
393A PRO* 3.9 6.5 - - + -
405A LYS* 3.0 53.3 + - + +
407A VAL* 5.9 2.5 - - + -
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Residues in contact with ILE 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 SER 3.1 17.2 + - - +
298A ARG* 4.0 8.3 - - + +
299A PHE 3.3 0.4 - - - -
300A TRP* 1.3 81.9 - - + +
302A GLN* 1.3 61.5 + - + +
303A ASP 3.2 1.1 + - - -
304A LYS* 3.7 17.2 - - + +
393A PRO* 3.8 30.1 - - + -
398A LEU* 4.1 14.1 - - + -
402A GLU* 5.2 4.7 - - + +
403A GLY* 3.3 31.0 - - - +
404A PHE* 3.5 30.3 - - - +
405A LYS* 3.8 14.7 - - + +
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Residues in contact with GLN 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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273A HIS* 3.2 41.4 + - - +
298A ARG* 3.7 17.9 + - - +
299A PHE* 3.1 20.1 + - - +
301A ILE* 1.3 76.2 - - + +
303A ASP* 1.3 60.1 + - - +
304A LYS* 3.0 18.2 + - - +
402A GLU* 5.4 5.3 + - - -
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Residues in contact with ASP 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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271A ASN* 2.8 30.0 + - - +
273A HIS* 4.0 14.5 - - + -
274A GLN* 2.9 36.8 + - + +
277A MET* 5.0 3.8 - - - +
299A PHE 3.4 4.2 + - - +
300A TRP* 3.1 18.2 + - + +
302A GLN* 1.3 73.9 - - - +
304A LYS* 1.3 63.5 + - - +
305A GLY 3.5 0.7 + - - -
306A PRO* 3.6 17.5 - - - +
309A GLU* 4.7 2.8 - - - +
405A LYS* 2.8 25.0 + - - +
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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