Contacts of the strand formed by residues 314 - 320 (chain E) in PDB entry 4OMD
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274E PHE* 3.7 31.6 - - + -
289E PHE* 3.2 15.0 - - + -
291E TRP* 4.0 17.4 - - + +
308E TYR 2.6 25.0 + - - +
309E THR* 3.6 3.8 + - - -
311E SER* 3.4 7.9 + - - +
312E ILE* 3.2 4.0 - - - +
313E TYR* 1.3 85.2 - - - +
315E LEU* 1.3 59.8 + - - +
316E SER 3.5 1.4 + - - -
394E GLN* 4.3 6.2 + - - +
534E MET* 5.4 1.2 - - - +
606E NA 2.4 44.7 - - - -
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Residues in contact with LEU 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E ILE* 3.7 28.0 - - + -
289E PHE 2.8 23.3 + - - +
290E VAL* 3.8 3.0 - - + -
291E TRP 3.0 21.6 + - - +
313E TYR 5.2 1.3 - - - +
314E THR* 1.3 71.4 - - - +
316E SER* 1.3 63.8 + - - +
317E ILE* 3.5 15.6 + - + +
337E LEU* 3.8 21.3 - - + -
378E ILE* 4.0 22.0 - - + -
390E TRP 5.6 1.1 - - - +
393E MET* 4.5 6.5 - - + -
394E GLN* 3.8 34.5 - - + +
397E VAL* 4.1 17.5 - - + -
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Residues in contact with SER 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E TRP* 3.5 8.3 - - - -
293E SER* 3.4 18.5 - - - -
303E CYS* 5.4 0.3 - - - +
309E THR* 3.3 44.1 - - - +
314E THR 3.5 4.8 + - - -
315E LEU* 1.3 71.6 - - - +
317E ILE* 1.3 64.2 + - - +
335E SER* 4.1 3.7 + - - -
336E THR* 3.6 20.2 + - - +
337E LEU* 3.0 28.2 + - - +
338E ALA 3.6 1.2 + - - -
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Residues in contact with ILE 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290E VAL* 4.0 6.3 - - + -
291E TRP 2.8 15.1 + - - +
292E ALA* 3.9 4.0 - - - -
293E SER* 3.2 20.5 + - - -
315E LEU* 3.6 22.4 - - + +
316E SER* 1.3 82.3 + - - +
318E SER* 1.3 74.7 + - - +
337E LEU* 5.2 1.1 - - + -
338E ALA* 3.4 27.4 - - + +
340E THR* 3.9 28.3 - - + +
367E THR* 4.1 4.2 + - - -
370E SER* 4.1 11.0 - - - +
371E ALA* 4.4 5.2 - - - -
374E ALA* 3.6 24.5 - - + -
378E ILE* 6.2 0.4 - - + -
397E VAL* 5.7 1.1 - - + -
429E LEU* 4.9 4.5 - - + -
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Residues in contact with SER 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293E SER* 3.0 19.4 + - - -
317E ILE* 1.3 77.2 - - - +
319E SER* 1.3 66.3 + - - +
330E SER* 4.9 4.3 - - - -
331E GLU 4.2 6.4 + - - -
336E THR* 3.1 26.2 + - - +
338E ALA 2.9 7.5 + - - -
339E THR* 3.2 8.9 - - - +
340E THR 3.1 24.3 + - - +
367E THR* 5.4 0.4 - - - -
370E SER* 3.6 1.9 + - - -
423E SER 3.2 24.7 + - - -
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Residues in contact with SER 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318E SER* 1.3 74.7 - - - +
320E ALA* 1.3 61.6 + - - +
327E PRO* 3.3 16.6 - - - +
329E TYR* 3.7 30.5 - - - -
330E SER* 4.6 6.5 + - - -
339E THR* 3.5 4.6 - - - +
340E THR 3.3 4.3 - - - -
342E SER* 3.7 7.3 - - - -
367E THR* 3.7 17.2 - - - -
370E SER* 2.6 24.7 + - - -
423E SER 4.5 2.3 - - - +
424E TYR* 3.6 14.9 - - - -
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Residues in contact with ALA 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E SER* 1.3 77.7 - - - +
321E THR* 1.3 66.0 + - - +
324E GLY* 5.1 0.7 - - - -
325E ASN 3.5 8.3 - - - +
327E PRO* 4.0 3.4 - - - -
339E THR* 3.8 14.6 - - + -
340E THR 3.4 4.8 + - - +
341E TYR* 3.4 12.8 - - + -
342E SER 2.9 23.8 + - - +
406E LEU* 4.0 21.5 - - + -
424E TYR* 4.0 12.1 - - + -
428E LEU* 4.4 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