Contacts of the strand formed by residues 326 - 335 (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 PHE 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B PHE* 3.7 14.6 - + - +
237B VAL* 3.2 2.8 - - - -
238B GLU* 2.9 60.1 + - + +
325B GLY* 1.3 71.0 - - - -
327B TYR* 1.3 74.1 + - - +
328B GLY* 3.8 17.3 - - - -
376B ARG* 3.5 44.6 - - + +
378B PRO* 4.2 20.0 - - + -
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Residues in contact with TYR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B PHE 3.3 4.0 - - - -
237B VAL* 3.7 16.8 - - + +
251B PHE* 3.7 35.9 - + - -
308B TRP* 3.5 26.1 + + - -
325B GLY 3.6 22.2 + - - -
326B PHE* 1.3 79.9 - - - +
328B GLY* 1.3 58.8 + - - +
378B PRO* 3.7 4.9 - - - +
379B MET* 2.9 37.3 + - + +
384B VAL* 3.6 46.4 - - + -
387B LEU* 4.4 7.4 - - + -
388B HIS* 5.4 5.7 + - - +
391B ARG* 4.8 4.0 + - - -
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Residues in contact with GLY 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ALA* 3.4 3.5 - - - +
236B PHE* 2.9 46.4 + - - -
326B PHE* 3.8 19.1 + - - -
327B TYR* 1.3 74.2 - - - +
329B VAL* 1.3 66.4 + - - +
376B ARG 5.0 0.2 - - - -
377B SER 3.3 9.0 - - - -
379B MET* 4.1 2.3 - - - +
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Residues in contact with VAL 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B PHE* 3.8 24.7 - - + -
234B SER 3.4 10.1 - - - +
235B ALA* 4.3 2.7 - - + -
236B PHE* 4.2 0.2 - - - -
328B GLY* 1.3 79.2 - - - +
330B SER* 1.3 65.6 + - - +
331B SER* 4.4 4.7 - - - +
374B LEU 3.7 2.3 - - - +
376B ARG 3.5 0.3 + - - -
377B SER* 2.7 47.4 + - - +
379B MET* 4.0 22.9 - - + -
380B P1L 4.1 41.1 - - + +
410B GLN* 5.5 0.7 - - - +
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Residues in contact with SER 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B GLU* 4.5 1.7 - - - +
233B PHE* 3.4 4.7 - - - -
234B SER* 2.9 45.2 + - - +
236B PHE* 3.6 14.6 - - - -
248B ARG* 5.2 2.7 + - - -
329B VAL* 1.3 71.2 - - - +
331B SER* 1.3 65.3 + - - +
374B LEU 3.5 3.1 - - - -
375B LEU* 3.5 18.3 - - - +
376B ARG* 2.8 24.9 + - - +
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Residues in contact with SER 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 5.2 0.7 - - - -
232B GLU 3.5 6.3 - - - -
233B PHE* 3.2 27.6 - - - -
329B VAL* 4.4 4.3 - - - +
330B SER* 1.3 73.2 - - - +
332B GLN* 1.3 63.4 + - - +
333B TYR* 3.9 26.1 + - - -
343B CYS* 6.2 1.3 - - - -
372B TYR 4.0 0.4 - - - +
374B LEU* 2.9 46.6 + - - +
375B LEU* 3.8 4.3 - - - +
410B GLN* 4.6 5.0 + - - -
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Residues in contact with GLN 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LEU* 3.7 4.8 - - - +
231B VAL* 2.8 49.3 + - + +
232B GLU* 2.9 18.8 + - + +
331B SER* 1.3 77.3 - - - +
333B TYR* 1.3 65.9 + - - +
371B VAL* 3.5 24.2 - - + +
372B TYR 3.2 11.4 - - - +
373B ARG* 3.8 31.3 + - + +
375B LEU* 4.4 13.3 - - + +
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Residues in contact with TYR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LEU* 3.8 28.3 - - + -
229B GLN 3.2 16.2 - - - +
230B LEU* 3.7 27.2 - - + +
231B VAL* 4.2 3.4 - - - +
233B PHE* 5.7 0.3 - - - -
331B SER* 3.9 24.6 + - - -
332B GLN* 1.3 76.1 - - - +
334B GLU* 1.3 63.0 + - - +
341B LEU* 4.4 10.3 - - + -
343B CYS* 4.3 11.7 - - + -
371B VAL* 3.6 5.2 - - - +
372B TYR* 2.9 37.0 + - + -
374B LEU* 4.3 19.3 - - + -
410B GLN* 4.2 14.0 + - - -
412B VAL* 3.8 24.5 - - + +
422B LEU* 4.2 17.3 - - + -
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Residues in contact with GLU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LEU* 3.6 2.8 - - - -
229B GLN* 2.9 55.7 + - + +
231B VAL* 3.5 24.8 - - + +
333B TYR* 1.3 75.1 - - - +
335B SER* 1.3 65.4 + - - +
369B ARG* 5.3 7.4 - - + +
370B PHE 3.3 11.2 - - - +
371B VAL* 4.8 11.7 - - + +
372B TYR* 4.3 0.4 - - - -
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Residues in contact with SER 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ARG 2.9 24.2 + - - -
228B LEU* 4.0 5.4 - - - -
229B GLN* 4.5 6.5 - - - +
334B GLU* 1.3 78.0 - - - +
336B LEU* 1.3 73.9 + - - +
337B GLU* 3.0 18.7 + - - +
339B MET* 3.5 6.9 - - - +
369B ARG* 3.6 6.4 - - - +
370B PHE 2.9 29.7 + - - -
372B TYR* 3.8 20.6 - - - -
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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