Contacts of the strand formed by residues 325 - 332 (chain B) in PDB entry 2COJ
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 VAL 325 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B LEU* 3.9 21.3 - - + -
266B TYR 4.2 0.2 - - - +
267B TRP* 3.8 11.7 - - + -
316B LEU* 4.0 19.5 - - + -
319B ALA* 3.7 27.6 - - + -
320B LEU* 4.0 22.7 - - + +
323B ASN* 3.6 4.5 - - - +
324B ARG* 1.3 80.2 + - - +
326B ARG* 1.3 66.8 + - - +
327B GLU 4.1 7.2 - - - +
352B ILE* 4.3 21.8 - - + -
353B PRO* 3.2 18.0 - - + +
357B ASN* 4.0 2.3 + - - -
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Residues in contact with ARG 326 (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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266B TYR* 3.0 40.3 + - + +
267B TRP* 4.9 0.9 - - - +
268B ILE* 3.7 32.5 - - + +
274B GLU* 3.7 29.2 + - - +
324B ARG 5.0 0.2 - - - -
325B VAL* 1.3 80.8 - - - +
327B GLU* 1.3 71.2 + - + +
353B PRO 3.3 11.8 - - - +
354B THR* 3.4 2.4 - - - -
357B ASN* 3.1 31.6 + - + +
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B PHE 4.1 0.2 - - - +
265B LEU* 3.7 5.0 - - - +
266B TYR* 2.8 53.9 + - + +
325B VAL* 3.9 2.8 - - - +
326B ARG* 1.3 87.9 - - + +
328B MET* 1.3 61.9 + - - +
329B PHE* 4.3 8.6 - - + -
354B THR* 3.9 11.7 - - + +
357B ASN* 4.3 4.1 - - + +
359B PRO* 3.0 30.6 - - + +
360B LYS* 3.4 5.9 + - - +
361B LEU* 2.8 33.1 + - - +
362B ALA* 2.8 28.7 + - - +
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Residues in contact with MET 328 (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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204B LEU* 4.9 3.6 - - - -
246B LEU* 5.7 1.8 - - - -
255B ILE* 4.8 7.9 - - + -
263B LEU* 3.8 22.9 - - + -
264B PHE 3.5 11.4 - - - +
265B LEU* 3.7 24.7 - - + -
316B LEU* 3.5 33.4 - - + -
327B GLU* 1.3 76.8 - - - +
329B PHE* 1.3 58.0 + - - +
339B PRO* 3.7 1.2 - - - +
340B VAL* 2.7 47.8 + - + +
343B ILE* 4.1 9.9 - - - -
352B ILE* 3.7 31.6 - - + -
354B THR* 3.1 9.2 + - - +
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Residues in contact with PHE 329 (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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258B VAL* 4.4 5.6 - - - -
263B LEU* 3.7 4.5 - - - +
264B PHE* 3.0 62.9 + + + +
266B TYR* 4.8 2.5 - - + -
276B LEU* 4.2 15.5 - - + -
294B ILE* 4.3 3.1 - - + -
327B GLU* 4.4 28.3 - - + -
328B MET* 1.3 79.6 - - - +
330B GLY* 1.3 70.9 + - - +
337B VAL* 4.1 17.5 - - + -
338B CYS 3.4 15.7 - - - +
339B PRO* 3.8 10.3 - - + -
340B VAL* 4.2 2.5 - - - +
354B THR* 5.6 0.7 - - + -
361B LEU* 4.5 7.6 - - + -
362B ALA* 4.4 11.9 - - + -
365B ILE* 3.6 31.9 - - + -
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Residues in contact with GLY 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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258B VAL* 4.0 18.0 - - - +
261B MET* 4.3 9.2 - - - -
262B ASN 3.1 10.3 - - - -
264B PHE* 5.3 0.2 - - - -
329B PHE* 1.3 77.9 - - - +
331B SER* 1.3 60.8 + - - -
337B VAL* 3.1 8.1 - - - +
338B CYS 2.8 36.3 + - - -
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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
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261B MET* 3.2 11.3 - - - +
262B ASN* 2.9 44.5 + - - +
264B PHE* 3.7 12.5 - - - -
290B THR* 3.8 5.4 - - - -
291B ARG 3.7 10.6 + - - -
294B ILE* 3.7 25.4 - - - -
330B GLY* 1.3 75.8 - - - -
332B GLY* 1.3 59.0 + - - +
336B VAL 3.3 11.7 - - - -
337B VAL* 4.6 0.4 - - - -
410B PLP 4.2 2.8 - - - +
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Residues in contact with GLY 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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261B MET* 4.6 3.4 - - - +
290B THR* 3.1 13.6 + - - -
331B SER* 1.3 76.2 - - - +
333B THR* 1.3 57.2 + - - -
334B ALA 3.4 2.7 - - - -
335B CYS 4.2 0.4 - - - -
336B VAL* 2.5 43.3 + - - +
410B PLP 3.8 9.4 - - - -
420B GBN 3.4 15.7 - - - -
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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