Contacts of the helix formed by residues 295 - 312 (chain F) in PDB entry 5WUA
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 PHE 295 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262F ASN* 2.9 32.8 - - - -
265F ARG* 6.1 6.5 - - + -
266F LEU* 4.2 20.0 - - + -
291F LEU* 3.0 24.4 + - + +
294F ALA* 1.3 84.1 - - + +
296F GLY* 1.3 64.9 + - - +
297F ARG* 3.0 4.4 + - - -
298F ARG* 3.2 11.1 + - + +
299F LEU* 3.0 34.6 + - + +
383F THR* 4.9 7.6 - - - -
386F ASN* 4.2 6.1 - - + -
387F LEU* 3.5 40.2 - - + -
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Residues in contact with GLY 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F CYS 2.8 26.2 + - - -
293F HIS* 4.3 1.5 - - - -
294F ALA 3.2 3.8 + - - -
295F PHE* 1.3 76.1 - - - +
297F ARG* 1.3 56.7 + - - +
299F LEU* 3.3 11.4 - - - +
300F ILE* 2.8 35.0 + - - +
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Residues in contact with ARG 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F ALA 4.6 4.3 + - - +
295F PHE* 3.0 2.7 + - - -
296F GLY* 1.3 75.6 - - - +
298F ARG* 1.3 64.7 + - - +
300F ILE* 3.0 9.4 - - - +
301F LEU* 2.9 24.9 + - - +
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Residues in contact with ARG 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F PHE* 3.2 10.3 + - + +
297F ARG* 1.3 78.1 - - - +
299F LEU* 1.3 64.0 + - - +
301F LEU* 3.5 13.3 - - + +
302F SER* 2.9 24.1 + - - -
379F VAL* 5.4 0.7 - - - +
383F THR* 5.1 15.3 - - - -
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Residues in contact with LEU 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F LEU* 6.3 0.7 - - + -
292F CYS* 3.8 32.1 - - + -
295F PHE* 3.0 26.2 + - + +
296F GLY* 3.3 25.8 - - - +
297F ARG 3.1 0.2 - - - -
298F ARG* 1.3 75.2 - - - +
300F ILE* 1.3 62.7 + - - +
302F SER* 2.1 31.6 + - - +
303F SER* 3.0 5.6 + - - -
383F THR* 4.5 19.1 - - - -
432F PHE* 5.5 15.7 - - + +
435F CYS* 6.5 0.9 - - + -
436F PRO* 5.3 0.7 - - - +
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Residues in contact with ILE 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296F GLY 2.8 17.5 + - - +
297F ARG* 3.0 20.0 - - - +
299F LEU* 1.3 72.8 - - - +
301F LEU* 1.3 57.9 + - + +
303F SER* 2.6 37.3 + - - +
304F THR* 2.9 24.0 + - + +
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Residues in contact with LEU 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297F ARG 2.9 19.1 + - - +
298F ARG* 3.5 12.8 - - + +
300F ILE* 1.3 79.5 - - + +
302F SER* 1.3 66.8 - - - +
304F THR* 3.8 9.5 - - + +
305F PHE* 3.6 20.6 + - + +
379F VAL* 5.1 9.0 - - + -
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Residues in contact with SER 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298F ARG 2.9 11.5 + - - -
299F LEU* 2.1 34.1 + - - +
301F LEU* 1.3 79.9 - - - +
303F SER* 1.3 68.4 + - - +
305F PHE* 3.4 3.6 + - - +
306F ARG* 2.9 30.9 + - - +
376F SER* 5.4 0.3 - - - -
379F VAL* 3.5 37.0 - - - -
380F ALA* 4.5 4.9 - - - -
383F THR* 6.2 1.3 - - - -
436F PRO* 4.4 8.2 - - - +
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Residues in contact with SER 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F LEU 3.8 6.7 - - - -
300F ILE* 2.6 31.1 + - - +
302F SER* 1.3 76.0 + - - +
304F THR* 1.3 56.4 + - - -
306F ARG* 2.7 27.2 + - - +
307F ILE* 2.9 12.1 + - - +
436F PRO* 4.1 19.7 + - - +
439F TRP* 4.4 16.3 - - - +
440F ALA* 5.5 4.9 - - - +
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Residues in contact with THR 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300F ILE* 2.9 26.7 + - + +
301F LEU* 3.8 10.3 - - + +
303F SER* 1.3 74.9 - - - +
305F PHE* 1.3 68.1 + - + +
307F ILE* 2.9 32.1 - - - +
308F LEU* 2.9 11.9 + - + +
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Residues in contact with PHE 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F LEU* 3.6 15.7 - - + +
302F SER* 3.4 3.7 + - - +
303F SER 3.2 0.4 - - - -
304F THR* 1.3 83.6 - - + +
306F ARG* 1.3 65.5 + - - +
308F LEU* 3.0 34.5 - - + +
309F ALA* 2.9 19.8 + - - +
372F PHE* 3.1 48.5 - - + -
375F ALA* 4.2 14.8 - - + -
376F SER* 4.3 10.8 - - - -
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Residues in contact with ARG 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F SER* 2.9 25.4 + - - +
303F SER* 2.7 15.1 + - - +
305F PHE* 1.3 73.7 - - - +
307F ILE* 1.3 55.4 + - - +
309F ALA* 3.4 2.4 + - - +
310F ASP* 2.9 49.3 + - - +
376F SER* 3.3 38.1 - - - -
377F TYR* 6.0 1.3 - - - -
380F ALA* 4.8 6.4 - - - +
433F PHE 4.0 13.3 + - - -
434F LEU* 4.7 0.4 - - - +
436F PRO* 3.3 24.8 - - + +
437F ASN* 2.6 56.2 - - - +
440F ALA* 5.5 4.3 - - + -
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Residues in contact with ILE 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F SER* 2.9 9.3 + - - +
304F THR* 2.9 32.2 + - - +
306F ARG* 1.3 75.3 - - - +
308F LEU* 1.3 62.1 + - + +
310F ASP* 4.3 11.0 - - + -
311F LEU* 2.9 41.6 + - + +
440F ALA* 3.5 30.7 - - + +
443F VAL* 4.4 19.1 - - + -
444F GLN* 5.0 4.5 - - + +
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Residues in contact with LEU 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304F THR* 2.9 12.1 + - + +
305F PHE* 3.0 51.8 + - + +
307F ILE* 1.3 79.7 - - + +
309F ALA* 1.3 67.2 + - - +
311F LEU* 4.8 3.8 - - - -
312F LEU* 3.7 26.8 + - + +
372F PHE* 4.0 16.6 - - + -
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Residues in contact with ALA 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305F PHE 2.9 14.1 + - - +
306F ARG* 3.6 7.0 - - - +
308F LEU* 1.3 82.6 - - - +
310F ASP* 1.3 65.2 + - - +
312F LEU* 3.8 3.5 + - - +
313F GLY* 3.2 15.6 + - - -
369F GLN* 4.4 11.6 - - - +
372F PHE* 3.5 29.6 - - + +
373F LEU* 3.5 24.5 - - + +
376F SER* 5.2 0.2 - - - -
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Residues in contact with ASP 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306F ARG* 2.9 44.3 + - - +
307F ILE* 4.0 11.9 - - + +
309F ALA* 1.3 79.6 - - - +
311F LEU* 1.3 59.5 + - - +
313F GLY* 2.5 26.9 + - - -
314F PHE* 4.0 1.4 + - - -
373F LEU* 5.2 6.2 - - - +
440F ALA* 4.2 14.9 - - - +
444F GLN* 4.8 17.7 - - + +
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Residues in contact with LEU 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F ILE* 2.9 28.7 + - + +
308F LEU* 4.5 4.0 - - - +
310F ASP* 1.3 78.0 - - - +
312F LEU* 1.3 70.2 + - + +
313F GLY 3.4 0.5 + - - -
314F PHE* 3.5 33.0 + - + +
443F VAL 5.8 1.3 - - - +
444F GLN* 6.4 2.5 - - - +
447F VAL* 5.2 10.1 - - + -
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Residues in contact with LEU 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F LEU* 3.7 19.9 + - + +
309F ALA* 3.8 3.4 - - - +
310F ASP 3.2 0.4 - - - -
311F LEU* 1.3 89.5 - - + +
313F GLY* 1.3 60.4 + - - +
314F PHE* 3.0 2.0 - - - +
315F ALA* 2.7 35.4 + - + +
365F ALA* 6.0 6.7 - - + +
368F LEU* 5.9 7.4 - - + -
369F GLN* 4.2 13.6 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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