Contacts of the helix formed by residues 370 - 390 (chain A) in PDB entry 2FY5
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 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A VAL* 4.6 2.1 - - - +
368A LYS 5.2 1.3 - - - -
369A CYS* 1.3 76.3 - - - +
371A PRO* 1.3 77.0 - - - +
372A GLU* 3.0 27.6 + - - +
373A ILE* 3.2 12.6 + - - +
374A GLN* 3.1 20.0 + - - +
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Residues in contact with PRO 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A SER* 1.3 88.7 - - - +
372A GLU* 1.3 62.6 + - + +
374A GLN* 3.6 9.6 - - + +
375A GLY* 3.4 12.8 + - - -
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Residues in contact with GLU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A VAL* 3.4 36.4 - - + +
252A LYS* 3.6 22.4 + - - +
370A SER* 3.0 11.9 + - - +
371A PRO* 1.3 75.9 - - + +
373A ILE* 1.3 58.8 + - - +
375A GLY* 2.7 24.9 + - - -
376A HIS* 3.2 22.3 + - + +
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ILE* 4.1 17.9 - - + -
235A LEU* 4.6 7.0 - - + -
246A ALA 4.1 4.0 - - - +
249A VAL* 3.4 29.6 - - + -
250A LEU* 3.3 34.3 - - + -
368A LYS 5.2 1.6 - - - +
369A CYS* 4.3 11.9 - - + -
370A SER* 3.2 27.5 + - - +
372A GLU* 1.3 77.9 - - - +
374A GLN* 1.3 57.7 + - - +
376A HIS* 3.1 9.4 + - + +
377A LEU* 2.9 48.6 + - + +
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Residues in contact with GLN 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PRO* 5.3 7.6 - - - +
369A CYS* 5.5 5.6 - - + +
370A SER 3.1 11.9 + - - +
371A PRO* 3.6 14.6 - - + +
372A GLU 3.0 0.6 + - - -
373A ILE* 1.3 76.3 - - - +
375A GLY* 1.3 60.8 + - - +
377A LEU* 3.7 18.8 + - - +
378A ALA* 3.3 20.7 + - - +
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Residues in contact with GLY 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PRO 3.4 5.6 + - - -
372A GLU 2.7 15.3 + - - -
374A GLN* 1.3 72.8 - - - +
376A HIS* 1.3 61.6 + - - -
378A ALA* 3.1 18.4 + - - +
379A SER* 3.1 14.3 + - - -
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Residues in contact with HIS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 3.8 17.0 - - + -
242A GLU 5.0 2.0 + - - -
245A GLU* 3.5 26.0 - - + -
246A ALA* 3.7 28.5 - - + +
249A VAL* 4.1 19.1 - - + +
372A GLU* 3.2 31.7 + - + +
373A ILE* 3.1 12.9 + - + +
375A GLY* 1.3 73.0 - - - +
377A LEU* 1.3 66.0 + - - +
379A SER* 3.2 8.5 + - - +
380A SER* 3.0 26.5 + - - -
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PRO* 4.0 25.4 - - + -
231A PRO* 3.2 37.2 - - + +
232A ILE* 4.1 3.4 - - + -
234A LEU* 3.0 23.8 - - + +
235A LEU* 3.7 25.3 - - + +
369A CYS* 5.1 1.1 - - - -
373A ILE* 2.9 36.3 + - + +
374A GLN* 3.9 20.2 - - - +
376A HIS* 1.3 76.0 - - - +
378A ALA* 1.3 58.1 + - - +
380A SER* 3.6 0.6 + - - -
381A ALA* 3.0 24.6 + - - +
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLN* 3.3 12.7 + - - +
375A GLY* 3.1 14.4 + - - +
377A LEU* 1.3 76.9 - - - +
379A SER* 1.3 65.4 + - - +
381A ALA* 3.2 8.6 + - - +
382A GLU* 3.1 21.5 + - - +
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Residues in contact with SER 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ASP* 4.6 6.1 - - - -
375A GLY 3.1 12.6 + - - -
376A HIS* 3.2 10.7 + - - -
378A ALA* 1.3 75.0 - - - +
380A SER* 1.3 54.5 + - - +
382A GLU* 2.9 11.6 + - - +
383A LYS* 2.7 50.9 + - - +
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Residues in contact with SER 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 3.6 29.8 - - - -
235A LEU* 3.8 14.5 - - - +
237A SER* 4.4 1.1 + - - +
238A ASP* 2.9 32.1 + - - +
376A HIS 3.0 17.0 + - - -
377A LEU* 3.8 5.2 - - - -
379A SER* 1.3 74.8 - - - +
381A ALA* 1.3 58.2 + - - +
383A LYS* 3.7 1.1 - - - +
384A LEU* 2.8 34.8 + - - +
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Residues in contact with ALA 381 (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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234A LEU* 3.5 19.9 - - + +
295A TYR* 4.8 18.4 - - + +
377A LEU 3.0 15.2 + - - +
378A ALA* 3.3 13.2 - - - +
380A SER* 1.3 77.6 - - - +
382A GLU* 1.3 60.4 + - - +
384A LEU* 3.5 3.3 + - - +
385A GLN* 3.2 25.8 + - - +
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Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ALA 3.1 10.6 + - - +
379A SER* 2.9 11.6 + - - +
381A ALA* 1.3 77.4 - - - +
383A LYS* 1.3 64.9 + - + +
385A GLN* 3.4 7.7 + - + +
386A ARG* 2.9 53.9 + - + +
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Residues in contact with LYS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A SER 5.6 0.7 - - - +
238A ASP* 3.8 29.2 - - - +
242A GLU* 5.3 12.8 + - - -
379A SER* 2.7 38.9 + - - +
380A SER* 3.7 4.9 - - - +
382A GLU* 1.3 74.6 - - + +
384A LEU* 1.3 62.8 + - - +
386A ARG* 3.4 44.1 + - - +
387A ILE* 3.4 19.3 + - + +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PRO* 4.8 8.3 - - + -
234A LEU* 4.7 7.4 - - + -
237A SER* 3.6 35.4 - - - +
291A HIS* 4.6 16.2 - - + +
294A GLY* 3.3 34.1 - - - +
295A TYR* 3.6 10.8 - - + +
299A GLY* 4.8 6.5 - - - +
304A TYR* 5.5 1.1 - - - +
380A SER 2.8 18.3 + - - +
381A ALA* 3.9 4.7 - - - +
383A LYS* 1.3 76.4 - - - +
385A GLN* 1.3 63.2 + - - +
387A ILE* 3.5 15.6 + - + +
388A VAL* 3.2 22.3 + - + +
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Residues in contact with GLN 385 (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 GLY 4.8 2.4 + - - -
294A GLY* 3.9 7.2 - - - -
295A TYR* 3.9 22.3 + - - +
296A SER* 5.1 4.7 + - - -
381A ALA 3.2 17.3 + - - +
382A GLU* 3.7 10.3 - - + +
383A LYS 3.2 0.6 - - - -
384A LEU* 1.3 74.7 - - - +
386A ARG* 1.3 60.9 + - + +
388A VAL* 3.4 17.4 + - - +
389A LYS* 2.8 34.7 + - + +
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Residues in contact with ARG 386 (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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382A GLU* 2.9 46.4 + - + +
383A LYS* 3.6 39.2 - - - +
384A LEU 3.3 0.6 - - - -
385A GLN* 1.3 75.5 - - + +
387A ILE* 1.3 56.0 + - + +
389A LYS* 3.2 6.3 + - - +
390A ASN* 2.7 40.2 + - + +
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Residues in contact with ILE 387 (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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91A ALA* 3.8 28.9 - - + -
93A PRO* 4.0 17.7 - - + +
94A VAL* 3.5 32.5 - - + -
95A ASN* 4.2 9.2 - - - +
237A SER 4.5 6.5 - - - +
291A HIS* 4.8 7.4 - - + -
383A LYS* 3.4 13.4 + - + +
384A LEU* 3.7 12.6 - - + +
385A GLN 3.3 0.6 - - - -
386A ARG* 1.3 76.8 - - + +
388A VAL* 1.3 63.4 + - - +
390A ASN* 3.9 4.1 - - - +
391A LEU* 3.2 23.7 + - - +
578A PHE* 5.9 3.4 - - + -
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Residues in contact with VAL 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A HIS* 3.0 52.3 + - + +
293A GLY* 4.2 11.9 - - - +
294A GLY* 3.4 19.1 - - - +
384A LEU* 3.2 15.9 + - + +
385A GLN* 3.7 19.5 - - - +
386A ARG 3.2 0.2 - - - -
387A ILE* 1.3 78.6 - - - +
389A LYS* 1.3 63.5 + - - +
390A ASN 3.5 0.2 + - - -
391A LEU* 3.7 13.0 + - - +
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Residues in contact with LYS 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLN* 2.8 22.4 + - + +
386A ARG* 3.6 8.1 - - - +
388A VAL* 1.3 81.7 - - - +
390A ASN* 1.3 57.6 + - - +
391A LEU 4.8 0.2 - - - +
579A HIS* 3.6 17.2 + - - +
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Residues in contact with ASN 390 (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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386A ARG* 2.7 22.5 + - + +
387A ILE* 4.1 4.7 - - - +
388A VAL 3.3 0.4 - - - -
389A LYS* 1.3 74.5 - - + +
391A LEU* 1.3 59.9 + - - +
578A PHE* 3.3 32.9 - - + +
579A HIS* 2.9 31.8 + - - +
580A SER* 2.8 45.0 - - - +
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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