Contacts of the strand formed by residues 369 - 378 (chain B) in PDB entry 5EMV
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 ARG 369 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLU* 5.3 10.5 - - + +
335B SER 3.6 13.7 - - - +
336B LEU* 4.0 13.5 - - + -
364B GLN 3.5 0.3 - - - +
365B LEU* 3.7 2.2 - - - -
366B GLU* 2.8 35.8 + - - +
367B ASP 3.3 3.0 - - - +
368B GLY* 1.3 79.6 - - - +
370B PHE* 1.3 69.2 + - - +
371B VAL* 3.9 2.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 370 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B GLU* 3.3 5.9 - - - +
335B SER 2.9 32.1 + - - +
336B LEU* 3.2 24.5 - - - -
337B GLU* 3.2 27.1 - - - +
338B HIS* 3.4 44.6 - - + -
363B ALA* 3.9 15.0 - - + -
364B GLN 3.3 1.6 - - - -
365B LEU* 3.7 44.0 - - + -
368B GLY 5.1 4.0 - - - -
369B ARG* 1.3 74.1 - - - +
371B VAL* 1.3 61.1 + - - +
372B TYR* 3.7 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B GLN* 3.5 31.4 - - + +
333B TYR 3.6 7.6 - - - +
334B GLU* 4.9 12.6 - - + +
362B ARG 4.2 0.2 - - - +
363B ALA 3.7 2.8 - - - -
364B GLN* 2.8 36.6 + - + +
366B GLU* 3.8 29.4 - - + +
369B ARG* 4.3 4.5 - - + +
370B PHE* 1.3 79.6 - - - +
372B TYR* 1.3 65.1 + - - +
373B ARG* 3.6 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 372 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 4.0 5.4 - - + -
331B SER 4.0 0.2 - - - +
332B GLN* 3.2 8.3 - - - +
333B TYR* 2.9 53.5 + - + +
335B SER* 3.8 16.6 - - - -
337B GLU 3.0 22.6 + - - -
339B MET* 3.1 42.0 + - - +
341B LEU* 3.5 42.6 - - + -
361B GLU* 3.7 21.5 - - + -
362B ARG 4.1 0.4 - - - -
363B ALA* 3.4 19.6 - - + +
370B PHE 3.7 16.2 - - - -
371B VAL* 1.3 75.1 - - - +
373B ARG* 1.3 61.6 + - - +
374B LEU* 4.1 4.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 373 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B SER 3.9 2.9 - - - -
332B GLN* 3.8 32.7 + - - +
361B GLU* 3.1 29.9 + - - +
364B GLN* 4.8 11.0 - - + +
366B GLU* 2.7 43.7 + - - -
371B VAL* 3.6 18.5 + - + +
372B TYR* 1.3 73.9 - - - +
374B LEU* 1.3 62.3 + - - +
375B LEU* 3.6 27.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B VAL 3.7 4.2 - - - +
330B SER* 3.5 4.0 - - - -
331B SER* 2.9 42.2 + - - +
333B TYR* 4.3 24.7 - - + -
341B LEU* 5.6 2.9 - - + -
343B CYS* 4.3 19.3 - - + -
359B GLU* 3.9 40.8 - - + +
360B THR 5.3 0.7 - - - +
361B GLU* 3.8 30.3 - - + +
372B TYR* 4.3 5.6 - - + +
373B ARG* 1.3 76.8 - - - +
375B LEU* 1.3 60.9 + - - +
377B SER* 4.6 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B SER* 3.5 19.3 - - - +
331B SER 3.8 18.4 - - - +
332B GLN* 4.4 15.3 - - + +
373B ARG* 3.6 31.4 + - + +
374B LEU* 1.3 73.7 - - - +
376B ARG* 1.3 78.7 + - + +
377B SER* 3.1 5.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 376 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B PHE* 4.2 18.0 - - + -
238B GLU* 2.8 42.2 + - - -
246B TYR* 4.4 3.0 + - - -
248B ARG* 4.9 4.9 - - - +
326B PHE* 3.5 32.4 - - + -
329B VAL 3.5 2.2 + - - -
330B SER* 2.8 21.7 + - - +
375B LEU* 1.3 79.2 - - + +
377B SER* 1.3 65.4 + - - +
378B PRO* 3.3 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 377 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B GLY* 3.3 0.9 - - - -
329B VAL* 2.7 48.5 + - - +
357B LYS* 3.3 14.0 + - - +
359B GLU* 2.8 31.0 + - - -
374B LEU* 4.6 8.3 - - - -
375B LEU 3.1 4.0 + - - -
376B ARG* 1.3 75.4 - - - +
378B PRO* 1.3 71.4 + - - +
380B P1L 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B PHE* 4.2 17.3 - - + -
327B TYR 3.7 7.0 - - - +
329B VAL* 5.5 0.4 - - - +
357B LYS* 4.8 8.6 + - - +
376B ARG 3.3 7.4 - - - +
377B SER* 1.3 92.3 + - - +
379B MET* 1.3 67.3 + - - +
380B P1L 3.4 9.0 + - - +
----------------------------------------------------------
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