Contacts of the helix formed by residues 323 - 339 (chain A) in PDB entry 1EUQ
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 GLU 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 3.6 2.6 - - - +
264A GLU* 3.2 29.7 - - - +
321A THR 3.6 0.2 + - - -
322A ILE* 1.3 93.4 - - - +
324A MET* 1.3 64.2 + - - +
325A ALA* 4.2 12.5 - - + +
326A SER* 3.3 10.9 + - - +
327A LEU 4.0 0.5 + - - -
910B G 3.1 31.5 + - - +
911B C 3.3 37.3 + - - +
925B C 4.4 4.6 + - - +
926B A 4.7 6.9 + - - +
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Residues in contact with MET 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 4.1 17.7 - - + -
264A GLU* 3.1 30.9 + - - +
265A TYR* 3.7 22.7 - - + +
266A THR* 4.9 7.4 - - + -
322A ILE 4.0 0.2 + - - -
323A GLU* 1.3 69.1 - - - +
325A ALA* 1.3 53.6 + - - +
326A SER 2.7 16.6 + - - -
327A LEU* 2.9 12.5 + - - +
328A GLU* 2.8 39.4 + - + +
474A ARG* 3.5 46.2 - - + +
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A GLU* 3.4 9.8 - - + +
324A MET* 1.3 77.9 - - - +
326A SER* 1.3 57.6 + - - +
328A GLU* 3.7 17.8 + - - +
329A SER* 2.8 28.2 + - - -
332A ARG* 5.5 1.2 + - - +
925B C 3.5 7.9 + - - +
926B A 3.6 33.3 + - - +
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Residues in contact with SER 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A PHE* 3.9 11.5 - - - -
312A ARG* 4.6 8.5 + - - +
313A ILE* 4.9 6.2 - - - +
322A ILE* 3.6 15.7 - - - +
323A GLU* 3.3 17.7 + - - +
324A MET 2.7 4.9 + - - -
325A ALA* 1.3 70.8 - - - +
327A LEU* 1.3 67.7 + - - -
328A GLU 2.8 1.8 + - - -
329A SER* 2.9 16.4 + - - -
330A CYS* 3.1 14.3 + - - -
924B G 4.5 12.5 + - - -
925B C 3.6 17.8 + - - -
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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
----------------------------------------------------------
41A ILE* 4.7 10.1 - - + -
263A LEU* 3.7 27.1 - - + -
296A LEU* 4.3 18.8 - - + -
301A TYR* 3.0 38.7 - - + +
305A SER 5.4 0.7 - - - +
306A ILE* 5.3 2.9 - - + -
309A PHE* 3.7 39.6 - - + -
323A GLU 4.0 1.1 + - - +
324A MET* 2.9 16.4 + - - +
326A SER* 1.3 77.5 - - - +
328A GLU* 1.3 64.7 + - + +
330A CYS* 3.4 13.9 + - + +
331A ILE 3.4 4.5 + - - -
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Residues in contact with GLU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A TYR* 4.1 11.2 - - - +
324A MET* 2.8 37.6 + - + +
325A ALA* 3.8 14.9 + - - +
326A SER 2.8 0.8 + - - -
327A LEU* 1.3 74.4 - - + +
329A SER* 1.3 68.3 + - - +
330A CYS 2.8 2.9 + - - -
331A ILE* 3.1 24.5 + - - +
332A ARG* 3.2 30.5 + - - +
474A ARG* 4.9 5.1 + - - -
542A VAL* 4.4 18.9 - - + +
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Residues in contact with SER 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ARG* 3.4 10.6 + - - -
325A ALA 2.8 23.2 + - - -
326A SER 3.4 4.7 - - - -
328A GLU* 1.3 72.9 - - - +
330A CYS* 1.3 55.7 + - - +
332A ARG* 3.3 11.3 + - - +
333A GLU* 2.9 29.8 + - - +
925B C 3.3 40.0 + - - -
926B A 4.3 7.5 + - - -
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Residues in contact with CYS 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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305A SER* 3.6 23.7 - - - +
308A GLU* 3.9 9.1 - - + +
309A PHE* 3.8 28.7 - - + -
312A ARG* 2.9 35.2 - - - +
326A SER* 3.1 14.7 + - - -
327A LEU* 3.4 10.8 - - + +
328A GLU 2.8 2.0 + - - -
329A SER* 1.3 74.4 - - - +
331A ILE* 1.3 66.4 + - - +
333A GLU* 3.2 7.8 + - - +
334A ASP* 3.2 20.4 + - - +
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Residues in contact with ILE 331 (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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300A GLY 3.7 13.0 - - - +
301A TYR* 3.4 31.4 - - + +
302A THR* 3.7 24.2 - - - +
305A SER* 3.7 8.6 - - - +
327A LEU 3.4 2.2 + - - -
328A GLU 3.1 11.0 + - - +
330A CYS* 1.3 75.5 - - - +
332A ARG* 1.3 63.3 + - - +
334A ASP* 3.1 2.6 + - - +
335A LEU* 2.8 68.9 + - + +
541A THR* 3.7 13.7 - - + -
542A VAL* 3.5 25.6 - - + -
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Residues in contact with ARG 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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325A ALA* 5.5 1.2 + - - +
328A GLU* 3.2 35.2 + - - +
329A SER* 3.4 13.7 - - - +
330A CYS 3.1 0.4 - - - -
331A ILE* 1.3 80.0 - - - +
333A GLU* 1.3 61.2 + - - +
336A ASN* 2.7 37.1 + - + +
523A TYR* 3.9 19.3 - - + +
542A VAL* 3.5 32.3 - - + +
543A GLY* 2.6 35.5 + - - +
544A LEU* 3.7 17.2 + - - +
545A ARG* 4.3 14.1 - - - +
926B A 5.1 6.5 + - - -
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Residues in contact with GLU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A GLU* 4.2 17.2 - - - +
312A ARG* 3.0 30.1 + - - +
329A SER* 2.9 18.0 + - - +
330A CYS 3.2 8.4 + - - +
332A ARG* 1.3 71.4 - - - +
334A ASP* 1.3 65.5 + - - +
336A ASN* 4.2 5.5 + - - +
337A GLU* 3.6 16.6 + - - +
925B C 5.4 0.5 + - - -
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Residues in contact with ASP 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A THR* 2.5 37.2 + - - +
304A ALA* 4.1 11.6 - - + +
305A SER* 4.7 4.0 - - - +
330A CYS 3.2 8.0 + - - +
331A ILE 3.1 8.6 + - - +
333A GLU* 1.3 84.3 + - - +
335A LEU* 1.3 74.0 + - + +
337A GLU* 3.0 10.0 + - - +
338A ASN* 2.7 44.8 + - - +
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Residues in contact with LEU 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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300A GLY 4.3 5.4 - - - +
302A THR* 3.8 14.1 - - + -
331A ILE* 2.8 50.5 + - + +
334A ASP* 1.3 82.6 - - - +
336A ASN* 1.3 67.5 + - - +
338A ASN* 4.2 4.0 - - + +
339A ALA* 2.8 35.7 + - + +
341A ARG* 3.4 4.2 + - - -
515A ALA* 4.1 21.5 - - + +
523A TYR* 3.4 42.8 - - + -
541A THR* 4.5 2.2 - - + -
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Residues in contact with ASN 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 ARG* 2.7 22.6 + - + +
333A GLU* 4.2 4.8 + - - +
335A LEU* 1.3 71.5 - - - +
337A GLU* 1.3 71.1 + - - +
341A ARG* 2.5 28.3 + - - +
368A HIS* 2.8 14.2 + - - -
517A GLN* 5.7 0.7 + - - -
523A TYR* 2.9 23.8 + - - +
937B A 4.8 2.8 + - - +
938B U 2.8 56.1 + - - +
939B U 4.9 3.4 + - - -
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Residues in contact with GLU 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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333A GLU 3.6 9.6 + - - +
334A ASP* 3.0 9.9 + - - +
335A LEU 3.0 0.4 - - - -
336A ASN* 1.3 90.0 - - - +
338A ASN* 1.3 67.2 + - - +
368A HIS* 3.8 5.4 - - - -
371A LYS* 3.0 53.8 + - + +
374A MET* 4.9 0.3 - - - +
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Residues in contact with ASN 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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334A ASP* 2.7 35.9 + - - +
335A LEU* 3.0 4.9 + - + -
337A GLU* 1.3 94.6 - - - +
339A ALA* 1.3 67.2 + - - +
340A PRO* 3.4 3.1 - - - +
368A HIS* 4.7 0.2 - - - -
371A LYS* 4.5 3.9 + - - +
374A MET* 3.2 20.3 - - - +
514A LYS* 4.2 14.5 + - - +
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Residues in contact with ALA 339 (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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335A LEU* 2.8 26.7 + - + +
338A ASN* 1.3 73.8 - - - +
340A PRO* 1.3 60.3 - - - +
341A ARG* 2.7 31.1 + - - -
368A HIS* 3.1 8.1 + - - -
514A LYS* 4.8 2.0 - - - +
515A ALA 2.9 28.5 - - - +
516A PHE 4.0 10.1 - - - -
517A GLN* 4.1 1.6 - - + +
523A TYR* 4.2 13.0 - - + -
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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
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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