Contacts of the strand formed by residues 325 - 331 (chain B) in PDB entry 2EHQ
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 ALA 325 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B ASP 3.5 9.4 - - - +
295B ILE* 3.6 22.4 - - + -
310B VAL* 4.6 3.4 - - + +
313B SER* 3.1 32.5 + - - -
314B ALA* 3.2 28.6 - - + +
323B SER 3.5 2.6 + - - -
324B ALA* 1.3 69.9 - - - +
326B SER* 1.3 60.3 + - - +
327B ARG 3.5 5.8 - - - +
422B VAL 5.1 0.3 - - - +
423B LEU* 3.6 7.4 - - + +
475B ILE* 3.8 8.1 - - + +
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Residues in contact with SER 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLY 4.8 1.2 + - - -
292B LYS* 3.4 38.1 + - - +
293B ASP 2.9 16.5 + - - -
324B ALA* 3.1 8.0 + - - -
325B ALA* 1.3 72.1 - - - +
327B ARG* 1.3 61.8 + - - +
418B ILE* 6.0 2.9 - - - -
419B PHE 6.4 0.4 - - - -
422B VAL 3.9 15.0 - - - +
423B LEU* 3.7 6.3 - - - -
424B SER* 2.9 28.1 + - - -
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Residues in contact with ARG 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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292B LYS* 3.0 42.4 + - + +
293B ASP 3.1 2.9 + - - +
294B ALA* 3.3 31.3 - - + +
295B ILE* 3.0 25.6 + - - +
325B ALA* 4.5 2.4 - - - +
326B SER* 1.3 87.6 + - - +
328B LEU* 1.3 60.9 + - - +
329B ILE* 4.0 5.6 - - + +
409B PRO 5.8 1.0 + - - -
414B ALA* 3.4 23.6 + - - +
415B GLN* 5.4 0.8 - - - +
423B LEU* 3.9 4.0 - - - +
424B SER* 3.3 6.7 - - - +
426B ILE* 4.2 20.1 - - + +
437B VAL* 2.9 33.7 + - - +
438B ALA* 2.9 22.2 + - - +
440B ASP 4.8 0.6 + - - -
441B THR* 3.3 18.5 + - - +
464B PHE* 5.5 1.8 - - - -
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Residues in contact with LEU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ILE* 3.5 16.4 - - + +
297B VAL* 3.9 7.0 - - + -
310B VAL* 3.7 32.1 - - + -
327B ARG* 1.3 73.3 - - - +
329B ILE* 1.3 59.9 + - - +
330B LEU* 3.7 38.1 - - + -
338B VAL* 4.4 1.6 - - + -
339B LEU* 5.4 2.2 - - + -
342B VAL* 4.1 26.2 - - + -
423B LEU* 3.9 16.6 - - + +
424B SER 2.8 12.0 + - - +
425B VAL* 3.4 19.1 - - + +
426B ILE* 2.8 27.9 + - - +
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Residues in contact with ILE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ALA* 3.5 29.4 - - + -
295B ILE 2.8 11.4 + - - +
296B ILE* 3.3 8.0 - - + +
297B VAL 2.9 26.9 + - - +
327B ARG* 4.2 4.7 - - + +
328B LEU* 1.3 74.0 - - - +
330B LEU* 1.3 61.2 + - - +
426B ILE* 3.4 14.6 - - + +
428B VAL* 3.8 19.7 - - + -
434B ALA* 3.8 32.5 - - + +
437B VAL* 3.8 15.0 - - + -
438B ALA* 3.6 33.4 - - + +
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Residues in contact with LEU 330 (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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297B VAL* 3.7 28.0 - - + +
328B LEU* 3.7 31.6 - - + -
329B ILE* 1.3 74.0 - - - +
331B THR* 1.3 63.0 + - - +
334B ALA* 4.4 1.1 - - + -
335B TYR* 3.6 46.4 - - + +
338B VAL* 3.7 13.5 - - + -
339B LEU* 4.1 11.2 - - + +
425B VAL* 3.8 25.1 - - + -
426B ILE 2.9 7.5 + - - +
427B ARG* 3.5 5.4 - - - +
428B VAL* 2.9 28.1 + - - -
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Residues in contact with THR 331 (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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297B VAL 3.2 12.8 + - - +
298B ASP* 3.4 30.8 - - + +
299B GLU* 3.5 10.7 + - - +
329B ILE 4.2 0.2 + - - -
330B LEU* 1.3 74.3 - - - +
332B GLN* 1.3 66.3 + - - +
333B GLY 4.0 2.6 + - - -
334B ALA* 2.9 15.6 + - - +
335B TYR* 3.0 10.0 + - - +
428B VAL* 3.3 12.3 - - + +
429B LYS 4.4 1.1 - - - -
430B ASP* 3.7 34.8 - - - +
431B PHE* 3.9 7.2 - - + +
434B ALA* 4.5 5.8 - - + -
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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