Contacts of the strand formed by residues 314 - 320 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B PHE* 3.7 30.5 - - + -
289B PHE* 3.2 11.4 - - + -
291B TRP* 3.9 21.9 - - + +
308B TYR 2.7 26.6 + - - +
309B THR* 3.5 3.3 + - - -
311B SER* 3.4 7.8 + - - +
312B ILE 3.2 4.4 - - - +
313B TYR* 1.3 83.8 - - - +
315B LEU* 1.3 60.3 + - - +
316B SER 3.4 1.4 + - - -
337B LEU* 5.7 0.3 - - - +
394B GLN* 4.3 6.2 + - - +
534B MET* 5.4 0.7 - - - +
608B NA 2.4 47.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 3.6 27.8 - - + -
289B PHE 2.8 24.2 + - - +
290B VAL* 3.7 7.6 - - + -
291B TRP 3.0 20.6 + - - +
313B TYR 5.1 1.1 - - - +
314B THR* 1.3 73.4 - - - +
316B SER* 1.3 63.0 + - - +
317B ILE* 3.5 15.2 + - + +
337B LEU* 3.9 22.7 - - + -
378B ILE* 3.9 18.4 - - + -
390B TRP 5.6 1.1 - - - +
393B MET* 4.3 9.4 - - + -
394B GLN* 3.9 32.8 - - + +
397B VAL* 4.1 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TRP* 3.5 7.6 - - - -
293B SER* 3.4 22.0 - - - -
303B CYS* 5.4 0.3 - - - +
309B THR* 3.4 41.0 - - - +
314B THR 3.4 4.6 + - - -
315B LEU* 1.3 72.0 - - - +
317B ILE* 1.3 66.6 + - - +
335B SER* 4.2 2.3 + - - -
336B THR* 3.7 18.9 + - - +
337B LEU* 3.0 28.7 + - - +
338B ALA 3.6 1.2 + - - -
608B NA 3.8 1.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL* 3.9 7.2 - - + -
291B TRP 2.8 14.9 + - - +
292B ALA* 3.9 2.9 - - - -
293B SER* 3.0 24.1 + - - -
315B LEU* 3.6 22.2 - - + +
316B SER* 1.3 82.0 + - - +
318B SER* 1.3 72.5 + - - +
337B LEU* 5.3 1.3 - - + -
338B ALA* 3.4 25.4 - - + +
339B THR* 4.2 0.2 - - - -
340B THR* 3.9 26.0 - - + +
367B THR* 4.3 2.9 + - - -
370B SER* 4.0 13.6 - - - +
371B ALA* 4.3 6.1 - - - -
374B ALA* 3.7 22.7 - - + -
378B ILE* 6.1 1.3 - - + -
397B VAL* 5.9 1.8 - - + -
429B LEU* 4.9 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B SER* 2.9 19.7 + - - -
317B ILE* 1.3 76.3 - - - +
319B SER* 1.3 64.1 - - - +
330B SER* 5.0 4.0 - - - -
331B GLU 4.1 7.3 + - - -
336B THR* 3.3 24.3 + - - +
338B ALA 2.9 7.9 + - - -
339B THR* 3.4 8.0 - - - +
340B THR 3.1 23.2 + - - +
367B THR* 5.5 0.4 - - - -
370B SER* 3.5 5.3 + - - -
423B SER 3.2 25.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B SER* 1.3 77.6 - - - +
320B ALA* 1.3 61.1 + - - +
326B VAL* 4.8 0.2 - - - -
327B PRO* 3.2 18.0 - - - +
329B TYR* 3.5 38.7 - - - -
330B SER* 4.8 5.7 + - - -
339B THR* 3.5 4.4 - - - +
340B THR 3.3 4.5 - - - -
342B SER* 3.7 6.1 - - - -
367B THR* 3.7 10.0 - - - -
370B SER* 2.7 22.6 + - - -
423B SER 4.6 1.2 - - - +
424B TYR* 3.6 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B SER* 1.3 76.8 - - - +
321B THR* 1.3 64.3 + - - +
324B GLY* 5.1 1.1 - - - -
325B ASN 3.5 7.9 - - - +
327B PRO* 4.0 4.3 - - - -
339B THR* 3.7 15.7 - - + -
340B THR 3.3 5.2 + - - +
341B TYR* 3.4 19.1 - - + -
342B SER 2.9 23.8 + - - -
406B LEU* 4.3 14.4 - - + -
424B TYR* 4.0 12.1 - - + -
428B LEU* 4.3 2.9 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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