Contacts of the helix formed by residues 285 - 303 (chain A) in PDB entry 6FY5
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 LYS 285 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A SER 3.2 1.6 + - - -
284A ASP* 1.3 95.4 + - - +
286A CYS* 1.3 64.3 + - - +
287A GLU* 3.2 4.3 - - - -
288A GLU* 3.0 40.2 + - + +
289A GLN* 3.0 25.0 + - + +
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Residues in contact with CYS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PRO* 3.7 3.1 - - + +
280A GLN 3.4 8.7 - - - +
281A TRP* 3.7 25.8 - - - -
282A GLY* 3.6 20.0 - - - -
283A SER* 3.0 37.2 + - - +
284A ASP 3.2 1.0 - - - -
285A LYS* 1.3 76.5 - - - +
287A GLU* 1.3 60.6 + - - +
289A GLN* 3.3 9.5 + - - +
290A LEU 2.8 24.4 + - - -
321A PHE* 3.5 15.4 - - + -
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A TRP* 3.7 28.8 - - + -
285A LYS* 3.2 1.7 - - - -
286A CYS* 1.3 79.0 - - - +
288A GLU* 1.3 56.2 + - + +
290A LEU* 3.2 1.9 + - - -
291A GLU 3.0 22.9 + - - -
321A PHE* 4.3 7.6 - - + -
325A THR* 3.6 28.1 - - + +
329A VAL* 3.5 12.5 - - + +
1000A ACT 3.2 37.5 - - + +
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Residues in contact with GLU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A LYS* 3.0 43.0 + - + +
287A GLU* 1.3 77.3 - - + +
289A GLN* 1.3 57.8 + - + +
291A GLU* 3.3 11.6 + - - +
292A GLU* 3.0 31.5 + - + +
1000A ACT 3.5 15.9 - - + +
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 3.6 29.6 + - + +
258A ALA* 3.6 18.2 - - - +
279A PRO* 3.7 17.9 - - + -
283A SER* 6.1 0.4 - - - +
284A ASP 4.6 6.6 + - - +
285A LYS* 3.0 21.7 + - + +
286A CYS* 3.6 8.5 - - - +
288A GLU* 1.3 74.5 - - + +
290A LEU* 1.4 53.2 + - - +
292A GLU* 3.3 9.3 + - - +
293A THR* 2.7 38.4 + - - -
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Residues in contact with LEU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A PRO* 3.5 7.8 - - + +
286A CYS 2.8 12.7 + - - +
287A GLU 3.5 8.7 - - - +
289A GLN* 1.4 71.6 - - - +
291A GLU* 1.3 65.2 + - - +
293A THR* 3.1 14.5 + - + -
294A ILE* 3.0 43.7 + - + +
314A PHE* 3.3 35.4 - - + -
321A PHE* 3.7 28.9 - - + -
326A ALA* 3.9 27.8 - - + +
329A VAL* 3.8 18.6 - - + -
330A THR* 4.3 2.5 - - - +
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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
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287A GLU 3.0 12.5 + - - +
288A GLU* 3.3 14.4 - - - +
290A LEU* 1.3 76.2 - - - +
292A GLU* 1.4 69.6 + - - +
294A ILE* 3.3 0.7 + - - -
295A LYS* 3.1 53.5 + - - +
329A VAL* 3.6 14.5 - - + +
332A LYS* 2.8 35.5 + - - +
333A ALA* 3.7 23.0 - - + +
336A ALA* 4.3 4.5 - - - +
1000A ACT 3.6 8.9 - - - +
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Residues in contact with GLU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ALA* 4.1 12.6 - - + -
288A GLU* 3.0 17.0 + - + +
289A GLN* 3.3 15.2 + - - +
291A GLU* 1.4 78.6 - - - +
293A THR* 1.3 61.0 + - - +
295A LYS* 3.4 23.5 + - - +
296A ASN* 2.9 41.6 + - - +
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Residues in contact with THR 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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258A ALA* 3.4 19.8 - - - +
276A CYS* 3.8 33.5 - - + +
277A HIS 4.4 5.8 - - - +
278A ILE* 4.0 15.0 - - + -
279A PRO* 3.3 18.1 - - - +
289A GLN 2.7 19.7 + - - -
290A LEU* 3.1 11.4 + - + -
292A GLU* 1.3 77.6 - - - +
294A ILE* 1.3 68.1 + - + +
296A ASN* 3.2 3.8 + - - +
297A CYS* 3.1 24.0 + - - -
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Residues in contact with ILE 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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278A ILE* 6.3 0.4 - - + -
290A LEU* 3.0 28.6 + - + +
291A GLU* 3.8 0.9 - - - +
293A THR* 1.3 84.9 - - + +
295A LYS* 1.3 61.3 + - - +
297A CYS* 3.4 7.1 + - - +
298A LEU* 3.2 24.9 + - + +
311A PHE* 3.9 27.8 - - + -
314A PHE* 5.5 5.4 - - + -
330A THR* 4.0 35.0 - - + +
333A ALA* 3.6 25.6 - - + -
334A ILE* 3.8 24.9 - - + +
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Residues in contact with LYS 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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291A GLU* 3.1 45.1 + - - +
292A GLU* 3.8 25.2 + - - +
294A ILE* 1.3 75.4 - - - +
296A ASN* 1.4 60.6 + - - +
298A LEU* 3.3 6.8 + - - +
299A SER* 2.9 32.3 + - - -
333A ALA* 3.8 24.7 - - + +
336A ALA* 3.9 16.4 - - - +
337A HIS* 3.9 19.9 + - + +
340A ASP* 5.0 7.7 + - - -
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Residues in contact with ASN 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A ALA* 2.7 34.9 + - - +
259A GLU* 4.2 4.4 - - - +
260A ALA* 3.7 15.1 - - + +
292A GLU* 2.9 27.1 + - - +
293A THR 3.2 2.4 + - - +
295A LYS* 1.4 76.3 - - - +
297A CYS* 1.4 57.9 + - - +
299A SER* 3.7 8.2 + - - -
300A ALA* 2.9 30.1 + - - +
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Residues in contact with CYS 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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216A VAL* 3.8 22.2 - - + -
260A ALA* 4.3 0.7 - - - -
274A ILE* 3.9 17.8 - - - +
276A CYS* 3.5 37.7 - - - -
293A THR* 3.1 18.8 + - - -
294A ILE* 3.4 9.8 + - - +
296A ASN* 1.4 70.8 - - - +
298A LEU* 1.3 66.7 + - - +
300A ALA* 3.3 3.1 + - - +
301A ALA* 3.0 23.2 + - - +
309A VAL* 5.1 1.2 - - - +
311A PHE* 3.8 20.0 - - + -
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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 ILE* 3.2 18.7 + - + +
295A LYS 3.3 5.8 + - - +
297A CYS* 1.3 77.2 - - - +
299A SER* 1.3 63.5 + - - +
301A ALA* 3.1 4.7 + - - +
302A GLU* 3.0 29.9 + - - +
309A VAL* 3.9 9.0 - - + -
311A PHE* 3.9 26.0 - - + -
333A ALA 4.6 0.4 - - - +
334A ILE* 4.0 27.6 - - + +
337A HIS* 3.6 42.4 - - + +
338A PHE* 4.6 3.4 - - + -
346A LEU* 3.9 21.3 - - + -
349A VAL* 4.3 10.5 - - + -
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Residues in contact with SER 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 LYS* 2.9 19.2 + - - +
296A ASN* 3.7 10.8 + - - -
298A LEU* 1.3 74.5 - - - +
300A ALA* 1.3 61.5 + - - +
302A GLU* 3.5 10.9 + - - +
303A ASP* 3.0 37.0 + - - +
337A HIS* 3.4 14.6 + - - -
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Residues in contact with ALA 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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260A ALA* 4.2 10.3 - - + +
262A VAL* 3.8 21.0 - - + +
274A ILE* 3.7 21.5 - - + +
296A ASN 2.9 20.7 + - - +
297A CYS 3.3 6.3 + - - +
299A SER* 1.3 72.5 - - - +
301A ALA* 1.4 58.9 + - - +
303A ASP* 3.5 14.8 + - - +
304A LYS* 3.6 18.4 + - - +
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Residues in contact with ALA 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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274A ILE* 3.8 16.1 - - + +
297A CYS 3.0 14.0 + - - +
298A LEU 3.1 8.0 + - - +
300A ALA* 1.4 72.2 - - - +
302A GLU* 1.3 63.8 + - - +
304A LYS 3.1 7.6 + - - -
306A LEU* 3.0 44.4 + - + +
309A VAL* 4.2 8.1 - - + -
346A LEU* 4.0 24.9 - - + -
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Residues in contact with GLU 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 11.2 + - - +
299A SER* 3.7 12.9 + - - +
301A ALA* 1.3 75.9 - - - +
303A ASP* 1.3 63.3 + - - +
304A LYS 3.1 0.9 - - - -
305A LYS* 2.9 17.2 + - - +
337A HIS* 2.5 40.5 + - - -
338A PHE* 4.3 0.9 - - - -
341A SER* 4.7 0.5 + - - -
344A SER* 2.6 40.4 + - - +
345A SER* 3.6 14.7 + - - +
346A LEU* 3.8 9.1 - - + +
192B VAL* 3.3 14.8 - - - +
371B ALA 4.7 9.5 - - - +
372B LYS* 4.2 15.5 - - - +
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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
----------------------------------------------------------
299A SER* 3.0 26.0 + - - +
300A ALA* 3.8 9.5 + - - +
301A ALA 3.2 0.6 - - - -
302A GLU* 1.3 80.2 - - - +
304A LYS* 1.4 67.9 + - - +
305A LYS 3.4 0.9 - - - -
192B VAL* 3.6 34.6 - - - +
193B LEU* 5.0 7.6 - - + +
372B LYS* 2.9 43.0 + - - +
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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
------------------------------------------------------------
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