Contacts of the helix formed by residues 320 - 338 (chain A) in PDB entry 5Y7G
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 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A PRO* 3.2 3.4 + - - +
319A GLU* 1.3 83.4 - - - +
321A ASP* 1.3 61.8 + - - +
322A ALA* 2.9 12.8 + - - +
323A GLU* 2.9 22.8 + - - +
324A ARG* 2.9 38.0 + - - +
497A ASP* 5.2 9.9 - - - -
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Residues in contact with ASP 321 (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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320A SER* 1.3 74.3 - - - +
322A ALA* 1.3 57.6 + - - +
324A ARG* 2.9 38.8 + - - +
325A GLN* 2.9 26.7 + - - +
493A ARG* 4.5 13.0 + - - +
536A ARG* 4.0 21.5 - - + +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 4.7 2.9 - - - +
320A SER* 2.9 8.9 + - - +
321A ASP* 1.3 78.1 - - - +
323A GLU* 1.3 60.2 + - - +
325A GLN* 3.0 7.3 + - - +
326A GLY* 3.0 23.6 + - - -
532A ASP* 5.1 2.3 - - + +
536A ARG* 3.0 42.5 - - - +
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Residues in contact with GLU 323 (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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289A GLY* 4.5 5.4 - - - -
291A ARG* 2.6 50.1 + - - +
292A LEU* 4.0 25.2 + - + +
318A PRO* 3.8 1.8 - - + +
319A GLU* 3.0 36.1 + - + +
320A SER* 2.9 22.5 + - - +
322A ALA* 1.3 74.7 - - - +
324A ARG* 1.3 61.2 + - - +
326A GLY 3.3 0.3 + - - -
327A LEU* 2.8 51.9 + - + +
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Residues in contact with ARG 324 (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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318A PRO* 3.2 52.7 + - + +
320A SER* 2.9 15.0 + - - +
321A ASP* 2.9 42.4 + - - +
323A GLU* 1.3 74.3 - - - +
325A GLN* 1.3 63.3 + - - +
327A LEU* 3.8 7.9 - - - +
328A ALA* 3.0 24.6 + - - +
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Residues in contact with GLN 325 (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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321A ASP 2.9 11.5 + - - +
322A ALA* 3.0 9.4 + - - +
324A ARG* 1.3 78.9 - - - +
326A GLY* 1.3 61.5 + - - +
328A ALA* 3.5 14.9 + - - +
329A ARG* 3.8 19.6 + - - +
345A ARG* 5.4 0.7 + - - -
532A ASP* 3.1 52.9 + - - +
535A LEU* 3.7 19.8 - - - +
536A ARG* 3.0 35.9 + - + +
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Residues in contact with GLY 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 4.1 18.6 - - - -
322A ALA 3.0 12.1 + - - -
323A GLU 3.8 1.1 - - - -
325A GLN* 1.3 75.1 - - - +
327A LEU* 1.3 60.4 + - - +
328A ALA 3.0 1.8 - - - -
329A ARG* 2.9 23.3 + - - +
330A LEU* 2.9 28.2 + - - +
532A ASP* 4.8 1.5 + - - -
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Residues in contact with LEU 327 (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* 3.9 17.8 - - + +
295A ILE* 4.0 19.5 - - + -
311A ALA* 4.1 16.6 - - + +
314A ALA* 3.6 26.9 - - + +
315A SER* 4.0 20.6 - - - +
318A PRO* 4.4 4.5 - - + -
323A GLU* 2.8 46.4 + - + +
324A ARG* 3.8 6.7 - - - +
326A GLY* 1.3 76.4 - - - +
328A ALA* 1.3 58.2 + - - +
330A LEU* 4.2 6.3 - - + +
331A LEU* 3.0 34.2 + - + +
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Residues in contact with ALA 328 (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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324A ARG 3.0 17.6 + - - +
325A GLN* 3.5 10.5 - - - +
326A GLY 3.0 0.6 - - - -
327A LEU* 1.3 76.8 - - - +
329A ARG* 1.3 58.1 + - - +
331A LEU* 5.5 0.2 - - - -
332A PRO* 3.4 21.2 - - - +
345A ARG* 3.9 28.6 + - + +
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Residues in contact with ARG 329 (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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325A GLN* 3.8 21.2 + - - +
326A GLY* 2.9 16.8 + - - +
328A ALA* 1.3 78.6 - - - +
330A LEU* 1.3 66.4 + - + +
331A LEU 3.5 0.2 - - - -
332A PRO* 3.4 8.9 - - - +
333A ARG* 3.6 29.4 + - - +
345A ARG* 3.3 34.7 - - - +
532A ASP* 2.4 43.9 + - - -
535A LEU* 6.2 1.2 - - - +
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Residues in contact with LEU 330 (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* 3.8 32.5 - - + -
295A ILE* 4.3 26.0 - - + -
296A ARG* 4.4 21.1 - - + -
299A GLU* 3.7 15.5 - - + +
311A ALA* 5.3 1.1 - - + -
326A GLY 2.9 15.7 + - - +
327A LEU* 3.2 8.3 + - + +
329A ARG* 1.3 75.2 - - + +
331A LEU* 1.3 70.6 + - - +
333A ARG* 3.3 30.3 + - - +
334A LEU* 3.1 29.2 + - + +
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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
----------------------------------------------------------
308A HIS* 3.8 22.9 - - + +
311A ALA* 3.6 30.0 - - + +
312A ARG* 3.4 37.2 - - - +
315A SER* 4.1 16.4 - - - +
327A LEU* 3.0 17.9 + - + +
328A ALA* 5.5 0.4 - - - -
330A LEU* 1.3 77.6 - - - +
332A PRO* 1.3 64.0 - - + +
334A LEU* 3.1 3.5 + - + +
335A GLN* 2.7 37.0 + - - +
343A GLN* 3.5 29.2 - - - +
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Residues in contact with PRO 332 (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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327A LEU 4.0 0.2 - - - +
328A ALA* 3.4 28.5 - - - +
329A ARG* 3.4 9.4 - - - +
331A LEU* 1.3 94.5 - - + +
333A ARG* 1.3 55.4 + - - +
335A GLN* 3.7 10.5 - - + +
336A GLY 2.9 20.4 + - - -
342A ARG* 3.2 29.1 + - + +
343A GLN* 3.8 32.1 - - + +
345A ARG* 5.2 8.1 - - + +
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Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ARG* 3.9 13.9 - - - +
299A GLU* 3.3 21.6 + - - +
329A ARG* 3.6 26.7 + - - +
330A LEU* 3.3 32.3 + - - +
331A LEU 3.3 0.6 - - - -
332A PRO* 1.3 79.9 - - - +
334A LEU* 1.3 60.8 + - + +
336A GLY* 3.0 3.8 + - - -
337A LYS* 3.0 54.6 + - - +
342A ARG* 5.1 4.3 - - - +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 4.1 13.9 - - + -
299A GLU* 4.1 24.9 - - + -
304A PHE* 4.2 20.9 - - + +
307A ALA* 3.6 26.9 - - + +
308A HIS* 3.6 37.2 - - + +
311A ALA* 4.3 8.7 - - + -
330A LEU* 3.1 21.8 + - + +
331A LEU* 3.5 6.3 - - - +
333A ARG* 1.3 74.0 - - + +
335A GLN* 1.3 59.6 + - - +
336A GLY 3.0 1.1 - - - -
337A LYS* 3.2 3.8 + - + +
338A LEU* 2.8 36.1 + - - +
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Residues in contact with GLN 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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308A HIS* 3.5 29.0 + - + +
312A ARG* 4.7 5.7 - - - +
331A LEU* 2.7 31.1 + - - +
332A PRO* 3.6 9.2 - - + +
334A LEU* 1.3 72.1 - - - +
336A GLY* 1.3 52.8 + - - +
338A LEU* 2.7 22.3 - - - +
340A LEU* 2.8 34.7 + - + +
341A PRO 3.6 21.8 + - - +
342A ARG* 4.1 4.3 - - - -
343A GLN* 3.2 53.1 + - - +
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Residues in contact with GLY 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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332A PRO 2.9 11.1 + - - -
333A ARG 3.2 5.6 - - - -
334A LEU 3.0 1.4 - - - -
335A GLN* 1.3 73.2 - - - +
337A LYS* 1.3 58.9 + - - -
338A LEU 2.8 14.3 - - - +
342A ARG* 3.3 27.4 - - - -
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Residues in contact with LYS 337 (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 GLU* 2.4 32.7 + - - -
304A PHE* 3.6 36.6 - - + -
333A ARG* 3.0 40.6 + - + +
334A LEU* 3.2 4.0 + - - +
336A GLY* 1.3 73.0 - - - +
338A LEU* 1.3 65.8 + - - +
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Residues in contact with LEU 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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304A PHE* 3.6 35.4 - - + +
305A ALA* 4.2 11.0 - - + +
308A HIS* 3.6 34.5 - - + +
334A LEU* 2.8 20.8 + - - +
335A GLN* 2.7 19.6 - - - +
336A GLY 2.8 10.1 - - - +
337A LYS* 1.3 86.4 - - - +
339A GLY* 1.3 61.1 + - - +
340A LEU* 3.0 13.7 - - + +
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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