Contacts of the helix formed by residues 323 - 339 (chain A) in PDB entry 5EO3
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 VAL 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A ASP* 1.3 78.2 + - - +
324A ALA* 1.3 56.6 + - - +
326A ARG* 3.3 6.3 + - - +
327A SER* 2.9 38.1 + - - +
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Residues in contact with ALA 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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322A ASP* 3.4 9.2 + - - +
323A VAL* 1.3 79.1 - - - +
325A THR* 1.3 64.0 + - - +
327A SER* 3.2 7.9 + - - -
328A ARG* 3.0 23.4 + - - +
331A ARG* 4.6 2.6 + - - -
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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
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296A LEU* 6.1 0.5 - - - +
317A LEU 5.4 0.5 + - - -
322A ASP* 2.9 50.5 - - + +
324A ALA* 1.3 77.1 - - - +
326A ARG* 1.3 60.1 + - - +
328A ARG* 3.1 12.7 + - - +
329A TYR* 3.1 41.8 + - - -
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Residues in contact with ARG 326 (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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317A LEU 4.5 2.7 - - - +
318A PHE* 2.6 69.7 + - + +
319A ARG 5.1 0.2 + - - -
322A ASP 2.9 22.4 + - - +
323A VAL* 3.7 6.1 - - - +
325A THR* 1.3 76.7 + - - +
327A SER* 1.3 57.2 + - - +
329A TYR* 3.2 10.5 + - - +
330A VAL* 3.0 47.6 + - - +
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Residues in contact with SER 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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323A VAL* 2.9 27.1 + - - +
324A ALA* 3.4 7.9 - - - -
326A ARG* 1.3 73.3 - - - +
328A ARG* 1.3 60.4 + - - +
330A VAL* 3.2 7.7 + - - +
331A ARG* 2.9 51.9 + - - +
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Residues in contact with ARG 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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296A LEU* 3.5 21.8 - - + +
297A LYS* 3.3 43.2 - - - +
300A GLU* 2.7 40.2 + - - +
324A ALA 3.0 13.1 + - - +
325A THR* 3.1 13.4 + - - +
327A SER* 1.3 77.3 - - - +
329A TYR* 1.3 62.3 + - + +
331A ARG* 3.5 24.6 + - - +
332A LEU* 3.1 22.9 + - - +
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Residues in contact with TYR 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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296A LEU* 3.6 44.1 - - + +
313A ILE* 4.0 15.8 - - + +
317A LEU* 3.6 60.7 - - + +
318A PHE* 4.0 20.4 - - + -
325A THR* 3.1 38.7 + - - -
326A ARG* 3.6 6.5 - - - +
328A ARG* 1.3 77.0 - - - +
330A VAL* 1.3 57.0 + - - +
332A LEU* 3.4 6.8 + - + +
333A VAL* 3.1 31.4 + - - +
360A THR 5.0 1.2 + - - -
362A VAL* 4.1 9.4 - - + +
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Residues in contact with VAL 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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318A PHE* 4.1 20.0 - - + -
326A ARG* 3.0 38.4 + - - +
327A SER* 3.2 7.2 + - - +
329A TYR* 1.3 73.3 - - - +
331A ARG* 1.3 67.0 + - + +
333A VAL* 3.4 7.2 + - + +
334A ASP* 3.1 37.2 + - - +
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Residues in contact with ARG 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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324A ALA 4.6 2.6 + - - -
327A SER* 2.9 39.6 + - - +
328A ARG* 3.6 32.7 - - - +
330A VAL* 1.3 76.0 - - + +
332A LEU* 1.3 55.0 + - - +
334A ASP* 3.3 5.8 + - - +
335A SER* 2.8 38.4 + - - -
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Residues in contact with LEU 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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296A LEU* 3.7 28.7 - - + -
299A VAL* 4.1 22.4 - - + +
300A GLU* 4.0 20.6 + - + +
303A ASN* 4.0 29.8 - - + +
311A LEU* 4.2 17.7 - - + -
313A ILE* 5.2 1.1 - - + -
328A ARG 3.1 10.7 + - - +
329A TYR* 3.5 13.7 - - + +
331A ARG* 1.3 79.5 - - - +
333A VAL* 1.3 63.8 + - - +
335A SER* 3.3 2.8 + - - -
336A VAL* 2.9 34.9 + - + +
362A VAL* 4.5 6.1 - - + -
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Residues in contact with VAL 333 (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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311A LEU* 4.3 9.4 - - + -
313A ILE* 4.4 4.5 - - + -
318A PHE* 4.1 22.9 - - + -
329A TYR 3.1 16.4 + - - +
330A VAL* 3.7 9.2 - - + +
331A ARG 3.3 0.2 - - - -
332A LEU* 1.3 76.2 - - - +
334A ASP* 1.3 69.3 + - - +
336A VAL 3.6 0.3 + - - -
337A LYS* 3.3 45.4 + - - +
343A VAL* 3.7 29.9 - - + +
345A ILE* 5.3 7.4 - - + -
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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
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330A VAL* 3.1 30.5 + - - +
331A ARG* 3.9 5.0 - - - +
333A VAL* 1.3 84.6 - - - +
335A SER* 1.3 64.2 + - - +
337A LYS* 3.2 13.6 + - - +
338A GLU* 3.0 35.6 + - - +
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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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303A ASN* 2.8 26.1 + - - -
331A ARG* 2.8 24.8 + - - -
332A LEU* 3.8 2.5 - - - -
334A ASP* 1.3 72.1 - - - +
336A VAL* 1.3 60.2 + - - +
338A GLU* 3.0 16.4 + - - +
339A ASN* 2.9 36.7 + - - +
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A ASN* 3.5 24.7 - - - +
308A ILE* 4.0 29.4 - - + -
311A LEU* 4.2 11.9 - - + -
332A LEU* 2.9 27.7 + - + +
333A VAL 3.8 4.5 - - - +
335A SER* 1.3 76.5 - - - +
337A LYS* 1.3 58.8 + - - +
339A ASN* 3.3 8.7 + - - +
341A GLY* 2.9 43.6 + - - -
342A THR 4.0 6.1 - - - +
343A VAL* 3.8 19.5 - - + -
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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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333A VAL* 3.3 38.0 + - - +
334A ASP* 3.2 15.1 + - - +
335A SER 3.2 0.8 - - - -
336A VAL* 1.3 74.4 - - - +
338A GLU* 1.3 65.1 + - - +
340A ALA* 3.2 13.0 + - - -
341A GLY 3.8 13.2 + - - +
342A THR* 5.4 0.4 - - - -
343A VAL* 3.9 24.1 + - + +
345A ILE* 5.7 4.0 - - - +
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Residues in contact with GLU 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* 3.0 25.4 + - - +
335A SER* 3.3 19.9 + - - +
337A LYS* 1.3 75.5 - - - +
339A ASN* 1.3 65.1 + - - +
340A ALA* 3.3 3.4 + - - +
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Residues in contact with ASN 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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303A ASN* 2.9 35.1 + - - +
306A MET* 3.6 47.7 - - + +
308A ILE* 4.8 5.4 - - + +
335A SER* 2.9 23.1 + - - +
336A VAL* 3.3 4.9 + - - +
337A LYS 3.2 0.6 - - - -
338A GLU* 1.3 83.5 + - - +
340A ALA* 1.3 68.4 + - - +
341A GLY* 3.3 2.7 + - - -
367A ARG* 4.2 5.9 + - - -
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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
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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