Contacts of the helix formed by residues 314 - 324 (chain A) in PDB entry 5CEO
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 ASP 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A ASP 3.8 3.2 + - - -
313A VAL* 1.4 73.9 - - - +
315A SER* 1.3 65.3 + - - +
316A SER* 4.6 11.1 + - - -
317A ALA* 3.2 20.2 + - + +
318A ILE* 3.1 19.6 + - - +
398A LYS* 5.6 1.8 - - - +
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Residues in contact with SER 315 (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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271A ALA* 4.1 32.5 + - - +
274A VAL* 4.4 1.6 - - - -
313A VAL 3.5 2.2 + - - -
314A ASP* 1.3 74.0 + - - +
316A SER* 1.4 51.1 + - - +
318A ILE* 3.0 16.0 + - - +
319A ILE* 2.7 52.4 + - - +
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Residues in contact with SER 316 (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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314A ASP* 3.3 12.0 + - - +
315A SER* 1.4 75.8 - - - +
317A ALA* 1.4 56.2 + - - +
319A ILE* 3.9 8.6 - - - +
320A TRP* 2.9 31.7 + - - +
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Residues in contact with ALA 317 (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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313A VAL* 4.3 11.4 - - + -
314A ASP* 3.2 21.6 + - + +
316A SER* 1.4 75.2 - - - +
318A ILE* 1.4 60.0 + - - +
320A TRP* 4.4 3.3 - - - +
321A GLY* 3.0 26.2 + - - -
327A LEU* 4.4 5.3 - - - +
397A ILE* 4.7 12.7 - - + +
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Residues in contact with ILE 318 (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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271A ALA 5.8 0.2 - - - +
274A VAL* 3.9 32.3 - - + +
275A ALA* 5.3 3.4 - - + -
282A ILE* 4.3 0.6 - - + +
309A PRO 5.4 0.4 - - - +
310A TYR* 3.7 48.9 - - + +
313A VAL* 3.6 33.7 - - + +
314A ASP 3.1 13.2 + - - +
315A SER* 3.0 14.1 + - - +
317A ALA* 1.4 72.8 - - - +
319A ILE* 1.3 62.0 + - - +
322A VAL* 2.9 39.6 + - + +
327A LEU* 4.7 6.1 - - - -
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Residues in contact with ILE 319 (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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270A PHE* 6.1 1.3 - - + -
271A ALA* 5.4 3.4 - - + -
274A VAL* 3.8 32.8 - - + -
282A ILE* 3.4 28.2 - - + +
315A SER* 2.7 38.1 + - - +
316A SER* 3.9 7.4 - - - +
318A ILE* 1.3 71.8 - - - +
320A TRP* 1.4 57.6 + - - +
323A GLY* 3.0 28.6 + - - -
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Residues in contact with TRP 320 (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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316A SER 2.9 21.6 + - - +
317A ALA* 4.4 3.6 - - - +
319A ILE* 1.4 73.4 - - - +
321A GLY* 1.3 60.6 + - - +
323A GLY* 3.7 0.6 - - - -
324A SER* 2.9 51.9 + - - -
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Residues in contact with GLY 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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317A ALA 3.0 18.6 + - - -
320A TRP* 1.3 77.0 - - - +
322A VAL* 1.3 63.5 + - - +
324A SER* 3.4 8.4 + - - -
326A SER* 3.2 27.5 + - - -
327A LEU* 3.2 21.3 + - - -
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Residues in contact with VAL 322 (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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274A VAL 5.6 0.7 - - - +
277A MET 3.9 10.1 - - - +
279A PRO* 3.4 21.5 - - + +
282A ILE* 3.7 19.5 - - + -
294A TRP* 3.7 26.0 - - + -
310A TYR* 3.7 21.1 - - + +
318A ILE* 2.9 35.5 + - + +
321A GLY* 1.3 70.4 - - - -
323A GLY* 1.3 56.7 + - - +
325A ASN* 2.9 20.6 + - - -
327A LEU* 3.6 23.3 - - + +
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Residues in contact with GLY 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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279A PRO 4.4 2.5 - - - -
282A ILE* 3.8 16.9 - - - +
283A ARG* 2.4 43.4 + - - -
319A ILE 3.0 21.7 + - - -
320A TRP* 3.7 1.3 - - - -
322A VAL* 1.3 77.6 - - - +
324A SER* 1.3 54.3 + - - +
325A ASN 3.3 0.4 - - - -
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Residues in contact with SER 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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320A TRP* 2.9 39.6 + - - -
321A GLY* 3.4 2.8 + - - -
322A VAL 3.2 0.2 - - - -
323A GLY* 1.3 74.0 - - - +
325A ASN* 1.4 62.6 + - - +
326A SER* 3.0 30.7 + - - -
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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
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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