Contacts of the helix formed by residues 291 - 305 (chain A) in PDB entry 4UEL
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 TYR 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A MET* 4.9 3.0 - - - +
286A ARG* 2.7 50.2 + - - +
287A ARG 5.4 0.4 - - - -
289A HIS* 3.2 44.4 - + + +
290A ASN* 1.3 71.3 + - - +
292A LEU* 1.3 64.8 + - - +
293A PRO* 3.4 1.8 - - - -
294A PHE* 3.2 11.9 + - + +
295A ILE* 3.0 28.3 + - + +
315C PRO* 4.0 7.1 - - + +
330C THR* 3.9 23.6 - - + -
333C SER* 4.4 2.8 + - - -
335C GLN* 3.9 14.2 - - + +
336C PHE* 3.8 31.6 - + + -
339C ALA* 3.7 32.0 - - + +
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Residues in contact with LEU 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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148A MET* 4.0 28.6 - - + +
149A PHE* 4.7 5.8 - - + -
290A ASN* 2.8 19.6 + - - +
291A TYR* 1.3 76.4 - - - +
293A PRO* 1.3 58.5 - - + +
295A ILE* 3.1 6.6 + - - +
296A MET* 2.8 41.1 + - + +
343C PHE* 3.5 37.9 - - + -
352C LEU* 5.4 0.4 - - + -
355C LEU* 3.9 25.8 - - + -
359C PHE* 3.7 27.8 - - + -
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Residues in contact with PRO 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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290A ASN* 3.4 25.8 - - + +
291A TYR 3.6 0.2 - - - -
292A LEU* 1.3 96.3 - - + +
294A PHE* 1.3 56.4 + - - +
296A MET* 3.3 1.0 + - - +
297A GLU* 2.9 30.8 + - - +
313C TYR* 3.5 32.5 - - + +
359C PHE* 4.0 26.4 - - + -
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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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291A TYR* 3.2 15.1 + + + +
293A PRO* 1.3 79.3 - - - +
295A ILE* 1.3 59.2 + - - +
297A GLU* 3.5 2.6 + - - +
298A LEU* 2.8 53.1 + - + +
310C LEU* 4.2 31.6 - - + +
313C TYR* 3.6 27.6 + - + +
314C LEU* 3.5 32.3 - - + -
327C ILE* 4.6 11.0 - - + -
330C THR* 4.2 12.8 - - + -
331C LEU* 4.0 17.9 - - + -
336C PHE* 3.6 33.2 - + - -
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Residues in contact with ILE 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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148A MET* 5.1 1.6 - - - -
291A TYR* 3.0 23.9 + - + +
292A LEU* 3.5 8.5 - - - +
294A PHE* 1.3 77.2 - - - +
296A MET* 1.3 63.9 + - - +
298A LEU* 3.3 7.4 + - - +
299A LEU* 3.0 32.6 + - + +
292C LEU* 4.6 10.5 - - + -
336C PHE* 3.8 24.0 - - + -
339C ALA* 4.4 4.3 - - + +
340C LEU* 4.0 31.9 - - + +
343C PHE* 3.9 46.4 - - + -
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Residues in contact with MET 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 LEU* 2.8 35.7 + - + +
293A PRO 3.7 4.0 - - - +
295A ILE* 1.3 73.5 - - - +
297A GLU* 1.3 61.9 + - - +
299A LEU* 3.3 9.5 + - - +
300A LYS* 3.1 33.1 + - - +
343C PHE* 4.0 26.5 - - + -
352C LEU* 5.5 0.9 - - + -
355C LEU* 4.3 9.9 - - + +
356C MET* 3.4 44.6 - - + +
359C PHE* 3.7 37.5 - - + -
361C LEU* 4.6 12.7 - - - +
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Residues in contact with GLU 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 PRO 2.9 16.6 + - - +
294A PHE 3.9 2.5 - - - +
296A MET* 1.3 76.2 - - - +
298A LEU* 1.3 54.2 + - - +
300A LYS* 3.4 20.6 + - - +
301A THR* 2.6 40.7 + - - +
309C ARG* 2.7 67.0 + - - +
310C LEU* 4.0 7.6 - - + -
313C TYR* 3.7 27.0 + - + -
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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 PHE* 2.8 43.2 + - + +
295A ILE* 3.6 6.1 - - - +
297A GLU* 1.3 77.2 - - - +
299A LEU* 1.3 56.3 + - + +
301A THR* 3.3 6.1 + - + -
302A LEU* 3.0 49.6 + - + +
292C LEU* 4.3 17.7 - - + -
297C MET* 3.6 30.7 - - + -
301C LEU* 5.4 5.4 - - + -
306C VAL* 5.7 1.8 - - + -
310C LEU* 3.9 27.3 - - + +
331C LEU* 4.4 2.9 - - + -
336C PHE* 5.0 1.8 - - + -
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Residues in contact with LEU 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 ILE* 3.0 28.2 + - + +
296A MET* 3.7 10.8 - - - +
297A GLU 3.3 0.2 - - - -
298A LEU* 1.3 74.8 - - - +
300A LYS* 1.3 66.5 + - - +
302A LEU* 3.4 2.7 + - - +
303A ALA* 3.0 23.4 + - - +
308A LEU* 3.7 30.8 - - + +
288C LEU* 4.6 11.9 - - + -
292C LEU* 4.1 23.8 - - + -
343C PHE* 3.9 31.4 - - + -
377C PHE* 4.2 20.6 - - + -
381C MET* 3.8 15.3 - - + -
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Residues in contact with LYS 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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296A MET* 3.1 21.9 + - - +
297A GLU* 3.6 24.6 + - - +
299A LEU* 1.3 75.8 - - - +
301A THR* 1.3 57.3 + - - +
303A ALA* 3.3 3.5 + - - +
304A GLU* 2.9 33.5 + - + +
309C ARG* 3.7 13.9 - - - +
359C PHE* 2.9 41.6 + - - +
360C GLY 5.1 2.5 - - - -
361C LEU* 3.8 19.7 - - + -
381C MET* 3.8 10.9 - - + +
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Residues in contact with THR 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 GLU* 2.6 31.1 + - - +
298A LEU* 3.6 12.0 - - + -
300A LYS* 1.3 73.2 - - - +
302A LEU* 1.3 65.6 + - + +
304A GLU* 3.5 0.5 + - - +
305A HIS* 3.1 34.9 + - + -
300C ILE* 5.4 1.6 - - + -
306C VAL* 3.7 47.6 - - + +
309C ARG* 3.3 32.3 + - - +
310C LEU* 4.4 2.4 - - - +
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Residues in contact with LEU 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* 3.0 35.3 + - + +
299A LEU* 3.9 3.8 - - - +
301A THR* 1.3 75.9 - - + +
303A ALA* 1.3 57.7 + - - +
305A HIS* 3.4 4.1 + - - +
306A GLN 3.1 6.6 + - - -
307A GLN* 2.8 38.0 + - + -
308A LEU* 4.0 26.9 - - + +
311A LEU* 3.7 25.4 - - + -
292C LEU* 3.3 33.7 - - + -
297C MET* 3.9 11.4 - - - -
300C ILE* 4.3 20.6 - - + -
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Residues in contact with ALA 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 LEU 3.0 17.5 + - - +
300A LYS* 3.6 7.6 - - - +
302A LEU* 1.3 74.1 - - - +
304A GLU* 1.3 65.6 + - - +
306A GLN* 3.0 25.6 + - - -
308A LEU* 4.0 11.1 - - + +
381C MET* 3.7 41.5 - - + +
382C GLN* 3.7 8.3 - - - +
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Residues in contact with GLU 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 LYS* 2.9 20.2 + - + +
301A THR 3.8 1.8 - - - +
303A ALA* 1.3 76.4 - - + +
305A HIS* 1.3 63.2 + - + +
306A GLN* 3.1 13.9 + - - +
309C ARG* 3.0 35.4 + - - +
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Residues in contact with HIS 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 THR* 3.1 31.4 + - + +
302A LEU* 4.1 3.6 - - - +
304A GLU* 1.3 80.2 - - + +
306A GLN* 1.3 69.7 + - - +
307A GLN* 3.2 24.2 + - + +
300C ILE* 4.8 5.9 - - + +
303C ASN* 3.2 31.6 + - - -
305C ASP* 4.9 8.2 - - + +
306C VAL* 3.3 27.8 + - + +
309C ARG* 4.8 5.4 + - - -
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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