Contacts of the helix formed by residues 322 - 340 (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 PRO 322 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A TRP* 3.5 45.1 - - + +
320A CYS 3.3 3.5 - - - +
321A PHE* 1.4 83.1 - - + +
323A LYS* 1.4 65.3 + - - +
324A GLN* 4.7 2.9 - - + +
325A THR* 3.2 17.6 + - - +
326A ALA* 3.0 20.4 + - - +
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Residues in contact with LYS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE 5.7 2.0 + - - -
316A SER* 5.0 14.5 - - - -
321A PHE 3.4 4.3 + - - +
322A PRO* 1.4 71.1 - - - +
324A GLN* 1.4 56.3 + - - +
326A ALA* 3.4 6.4 + - - +
327A ALA* 3.0 31.4 + - - +
355A ASP* 4.4 9.0 + - - +
357A GLU* 4.6 12.6 - - - +
358A SER* 3.2 31.5 + - - +
361A ILE* 3.5 30.1 - - + +
362A TYR* 5.6 0.5 - - - -
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Residues in contact with GLN 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A PRO* 3.4 3.1 - - + +
323A LYS* 1.4 75.8 - - - +
325A THR* 1.4 57.8 + - - +
327A ALA* 3.5 1.7 + - - +
328A GLN* 3.0 38.5 + - - +
361A ILE* 3.8 21.0 - - + +
365A GLU* 3.6 23.3 + - + +
368A LYS* 4.8 5.7 - - - +
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Residues in contact with THR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A TRP* 4.0 13.0 - - + -
287A GLU* 3.6 41.1 - - + +
321A PHE* 4.4 4.3 - - + -
322A PRO* 3.2 26.4 + - - +
324A GLN* 1.4 73.7 - - - +
326A ALA* 1.3 60.4 + - - +
328A GLN* 3.3 11.0 + - - +
329A VAL* 2.9 38.5 + - + +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 3.9 13.0 - - + +
314A PHE* 3.8 38.6 - - + -
321A PHE* 4.2 6.4 - - + +
322A PRO 3.0 15.4 + - - +
323A LYS* 3.8 6.7 - - - +
325A THR* 1.3 75.3 - - - +
327A ALA* 1.3 56.5 + - - +
329A VAL* 4.0 0.2 - - - -
330A THR* 2.7 38.3 + - - +
362A TYR* 4.8 0.9 - - - -
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Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LYS 3.0 17.6 + - - +
324A GLN 3.9 1.8 - - - +
326A ALA* 1.3 75.4 - - - +
328A GLN* 1.3 64.6 + - - +
330A THR* 4.0 0.3 - - - -
331A LEU* 3.1 30.3 + - - +
361A ILE* 3.8 18.2 - - + -
362A TYR* 3.7 37.1 + - + -
365A GLU* 4.0 13.7 - - + -
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Residues in contact with GLN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLN* 3.0 28.3 + - - +
325A THR* 3.6 11.5 + - - +
327A ALA* 1.3 75.0 - - - +
329A VAL* 1.3 65.9 + - + +
331A LEU* 3.6 3.5 + - - +
332A LYS* 3.1 26.8 + - + +
365A GLU* 3.6 26.7 - - - +
368A LYS* 6.0 0.9 - - - -
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Residues in contact with VAL 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLU* 3.5 36.6 - - + +
290A LEU* 3.8 17.7 - - + -
291A GLU* 3.6 23.9 - - + +
325A THR* 2.9 23.8 + - + +
328A GLN* 1.3 76.1 - - + +
330A THR* 1.3 65.7 + - - +
332A LYS* 3.3 7.7 + - + +
333A ALA* 2.9 21.8 + - - +
1000A ACT 4.0 28.7 - - + +
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 4.3 7.3 - - - +
294A ILE* 4.0 36.3 - - + +
311A PHE* 5.3 5.4 - - + -
314A PHE* 5.7 2.9 - - - -
326A ALA* 2.7 24.9 + - - +
327A ALA 4.0 0.9 - - - -
329A VAL* 1.3 75.8 - - - +
331A LEU* 1.3 57.1 + - - +
333A ALA* 3.2 2.6 + - - +
334A ILE* 3.0 50.7 + - + +
351A PHE* 4.1 8.5 - - + -
362A TYR* 3.8 21.1 + - + +
1001A EDO 5.7 1.3 - - - -
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Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 4.0 16.3 - - + +
327A ALA 3.1 21.2 + - - +
328A GLN* 4.1 2.7 - - - +
330A THR* 1.3 74.2 - - - +
332A LYS* 1.3 60.9 + - - +
334A ILE* 3.4 4.3 + - + +
335A SER* 3.1 28.4 + - - -
351A PHE* 3.6 35.7 - - + -
362A TYR* 4.2 14.8 - - + -
365A GLU* 3.7 28.5 - - + +
366A MET* 3.8 29.6 - - + +
369A LEU* 4.1 18.0 - - + +
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Residues in contact with LYS 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 2.8 34.9 + - - +
328A GLN* 3.1 19.6 + - + +
329A VAL* 3.5 5.4 - - + +
331A LEU* 1.3 74.2 - - - +
333A ALA* 1.3 64.0 + - - +
335A SER* 3.6 4.7 + - - -
336A ALA* 3.1 24.6 + - + +
369A LEU* 5.6 0.6 - - - +
1000A ACT 3.2 23.9 + - + +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 3.7 35.0 + - + +
294A ILE* 3.6 26.7 - - + -
295A LYS* 3.8 8.0 - - + +
329A VAL 2.9 12.8 + - - +
330A THR 3.4 8.5 - - - +
332A LYS* 1.3 72.9 - - - +
334A ILE* 1.4 61.4 + - - +
336A ALA* 3.5 1.7 + - - +
337A HIS* 2.9 30.2 + - - +
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Residues in contact with ILE 334 (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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191A LEU* 4.6 1.3 - - + -
197A LEU* 3.8 24.2 - - + -
294A ILE* 3.8 15.5 - - + -
298A LEU* 4.0 15.5 - - + -
311A PHE* 4.5 3.8 - - + -
330A THR* 3.0 29.7 + - + +
331A LEU* 3.8 5.8 - - - +
332A LYS 3.3 0.2 - - - -
333A ALA* 1.4 72.6 - - - +
335A SER* 1.3 66.6 + - - +
337A HIS* 3.2 3.6 + - - +
338A PHE* 3.1 47.4 + - + -
349A VAL* 4.2 10.5 - - + -
351A PHE* 3.5 38.6 - - + -
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Residues in contact with SER 335 (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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191A LEU* 4.2 27.9 - - - +
197A LEU* 5.4 0.5 - - - +
331A LEU 3.1 17.6 + - - -
332A LYS* 4.0 5.2 - - - -
334A ILE* 1.3 76.9 - - - +
336A ALA* 1.3 58.3 + - - +
338A PHE* 3.1 3.6 + - - +
339A ASP* 2.9 38.4 + - - +
369A LEU* 4.2 13.9 - - - +
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Residues in contact with ALA 336 (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 4.7 - - - +
295A LYS* 3.9 20.9 - - - +
332A LYS* 3.1 20.4 + - + +
333A ALA 3.7 4.0 - - - +
335A SER* 1.3 72.0 - - - +
337A HIS* 1.3 67.4 + - - +
339A ASP* 3.3 10.1 + - - +
340A ASP* 3.2 30.7 + - - +
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Residues in contact with HIS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LYS* 3.9 23.8 + - + +
298A LEU* 3.6 32.4 - - + +
299A SER* 3.4 23.7 + - - -
302A GLU* 2.5 37.9 + - - -
333A ALA 2.9 17.6 + - - +
334A ILE 3.2 4.9 + - - +
336A ALA* 1.3 74.9 - - - +
338A PHE* 1.4 73.5 + + - +
340A ASP* 3.1 21.4 + - - +
341A SER* 3.4 13.4 + - - -
372B LYS* 5.6 2.0 - - - -
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Residues in contact with PHE 338 (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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191A LEU* 4.0 11.2 - - + -
193A LEU* 3.9 10.2 - - + +
195A GLN* 3.4 52.6 + - + +
197A LEU* 5.0 0.2 - - + -
298A LEU* 4.6 5.6 - - + -
302A GLU* 4.3 0.2 - - - -
334A ILE* 3.1 40.6 + - + -
335A SER 3.8 5.2 - - - +
337A HIS* 1.4 88.0 - + - +
339A ASP* 1.3 66.7 + - - +
340A ASP 3.3 0.2 + - - -
341A SER* 3.0 23.9 + - - +
344A SER* 3.6 28.3 - - - -
346A LEU* 3.8 29.4 - - + -
349A VAL* 4.0 15.7 - - + -
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Residues in contact with ASP 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 4.8 11.4 - - - +
335A SER* 2.9 29.0 + - - +
336A ALA* 3.6 12.1 + - - +
338A PHE* 1.3 76.6 - - - +
340A ASP* 1.3 64.7 + - - +
341A SER 3.4 3.1 + - - +
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Residues in contact with ASP 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A LYS* 5.0 8.0 + - - -
336A ALA* 3.2 14.7 + - - +
337A HIS* 3.1 12.3 + - - +
339A ASP* 1.3 82.3 - - - +
341A SER* 1.3 58.1 + - - +
372B LYS* 5.0 2.1 - - - +
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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
------------------------------------------------------------
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