Contacts of the strand formed by residues 314 - 320 (chain C) in PDB entry 4OMC
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 THR 314 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274C PHE* 3.6 32.5 - - + -
289C PHE* 3.2 9.4 - - + -
291C TRP* 3.8 23.6 - - + +
308C TYR 2.7 26.0 + - - +
309C THR* 3.5 3.1 + - - -
311C SER* 3.4 8.0 + - - +
312C ILE* 3.2 4.4 - - - +
313C TYR* 1.3 81.2 - - - +
315C LEU* 1.3 61.8 + - - +
316C SER 3.5 0.3 + - - -
394C GLN* 4.2 6.0 + - - +
534C MET* 5.5 0.5 - - - +
608C NA 2.3 49.4 - - - -
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Residues in contact with LEU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C ILE* 3.5 28.0 - - + -
289C PHE 2.8 24.4 + - - +
290C VAL* 3.7 7.6 - - + -
291C TRP 3.0 21.5 + - - +
313C TYR 5.2 0.9 - - - +
314C THR* 1.3 71.6 - - - +
316C SER* 1.3 64.2 + - - +
317C ILE* 3.5 15.7 + - + +
337C LEU* 4.0 15.0 - - + -
378C ILE* 4.0 14.4 - - + -
390C TRP 5.6 1.3 - - - +
393C MET* 4.4 9.0 - - + -
394C GLN* 3.9 29.2 - - + +
397C VAL* 4.0 28.3 - - + -
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Residues in contact with SER 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C TRP* 3.5 7.0 - - - -
293C SER* 3.4 17.0 - - - -
303C CYS* 5.4 0.2 - - - +
309C THR* 3.4 45.3 - - - +
314C THR 3.5 4.6 + - - -
315C LEU* 1.3 71.6 - - - +
317C ILE* 1.3 60.5 + - - +
335C SER* 4.2 2.6 + - - -
336C THR* 3.7 19.6 + - - +
337C LEU* 3.0 28.7 + - - +
338C ALA 3.6 5.9 + - - -
608C NA 3.8 2.0 - - - -
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Residues in contact with ILE 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C VAL* 3.9 7.4 - - + -
291C TRP 2.8 15.9 + - - +
292C ALA* 3.9 2.8 - - - -
293C SER* 3.0 24.2 + - - -
315C LEU* 3.7 23.3 - - + +
316C SER* 1.3 83.2 + - - +
318C SER* 1.3 73.7 + - - +
337C LEU* 5.3 1.1 - - + -
338C ALA* 3.4 24.9 - - + +
339C THR* 4.2 0.4 - - - -
340C THR* 3.7 28.3 - - + +
367C THR* 4.3 2.9 + - - -
370C SER* 4.0 10.6 - - - +
371C ALA* 4.4 5.6 - - - -
374C ALA* 3.7 23.1 - - + -
378C ILE* 6.0 1.1 - - + -
397C VAL* 5.8 1.6 - - + -
429C LEU* 4.9 5.2 - - + -
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Residues in contact with SER 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C SER* 2.9 19.4 + - - -
317C ILE* 1.3 76.7 - - - +
319C SER* 1.3 65.9 + - - +
330C SER* 5.0 4.3 - - - -
331C GLU 4.2 6.8 + - - -
336C THR* 3.2 25.3 + - - +
338C ALA 2.9 8.5 + - - -
339C THR* 3.3 9.1 - - - +
340C THR 3.1 23.7 + - - +
367C THR* 5.6 0.4 - - - -
370C SER* 3.5 1.8 + - - -
422C HIS 5.2 0.2 + - - -
423C SER 3.2 25.1 + - - -
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Residues in contact with SER 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C SER* 1.3 75.6 - - - +
320C ALA* 1.3 62.4 + - - +
327C PRO* 3.2 18.2 - - - +
329C TYR* 3.5 30.7 - - - -
330C SER* 4.8 5.5 + - - -
339C THR* 3.5 4.4 - - - +
340C THR 3.3 4.3 - - - -
342C SER* 3.7 7.1 - - - -
367C THR* 3.7 16.5 - - - -
370C SER* 2.6 24.7 + - - -
423C SER 4.7 1.2 - - - +
424C TYR* 3.7 12.6 - - - -
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C SER* 1.3 76.1 - - - +
321C THR* 1.3 68.7 + - - +
324C GLY* 5.1 0.9 - - - -
325C ASN 3.5 6.7 - - - +
327C PRO* 4.0 4.3 - - - -
339C THR* 3.8 15.3 - - + -
340C THR 3.3 5.7 + - - +
341C TYR* 3.4 14.6 - - + -
342C SER 3.0 23.5 + - - +
406C LEU* 4.1 17.7 - - + -
424C TYR* 4.0 12.3 - - + +
428C LEU* 4.5 2.0 - - + -
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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
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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