Contacts of the strand formed by residues 316 - 325 (chain A) in PDB entry 2BTO
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 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A PHE* 4.8 5.2 - + - -
311A PRO* 3.8 24.0 - - + -
312A MET* 3.9 26.5 - - + -
315A ARG* 1.3 71.4 - - - +
317A LEU* 1.3 63.6 + - - +
318A SER* 4.4 2.2 - - - +
319A THR* 3.4 24.9 - - - +
344A LEU* 3.7 31.2 - - + -
345A PRO* 2.7 23.8 + - + +
346A LEU* 3.7 14.1 - - + +
347A THR* 3.3 20.0 + - - -
352A THR* 3.9 5.2 - - - +
372A LEU* 4.9 9.6 - - + -
374A ALA* 4.0 25.4 - - + -
375A ASN 3.5 5.2 - - - -
376A ASN* 3.7 17.9 - - - -
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A PRO* 3.8 25.1 - - + -
269A LEU* 3.7 38.4 - - + -
315A ARG 4.2 1.1 - - - +
316A PHE* 1.3 74.8 - - - +
318A SER* 1.3 61.9 + - - +
347A THR* 3.7 31.9 - - + +
350A ILE* 4.3 4.5 - - + -
351A PRO 3.6 3.6 - - - +
352A THR* 3.0 32.0 - - - +
375A ASN* 2.7 36.6 + - + +
377A THR* 3.9 21.3 - - + +
427A TYR* 4.5 6.1 - - + -
430A ALA* 4.6 2.9 - - + -
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ASN 2.9 26.7 + - - -
263A LEU* 3.2 30.2 - - - +
265A PRO* 5.5 2.7 - - - -
316A PHE* 3.5 2.2 - - - -
317A LEU* 1.3 83.9 - - - +
319A THR* 1.3 71.8 + - - +
351A PRO 5.4 1.1 - - - -
352A THR* 5.0 0.7 - - - -
353A ALA 3.4 15.4 + - - -
374A ALA* 3.6 1.9 - - - +
375A ASN* 3.0 28.0 + - - +
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Residues in contact with THR 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A ASN 5.5 0.2 - - - +
263A LEU* 4.1 3.7 - - - +
300A PHE* 4.4 3.8 - - + -
316A PHE* 3.4 24.6 - - - +
318A SER* 1.3 82.1 + - - +
320A ALA* 1.3 69.9 + - - +
321A VAL* 4.3 5.6 - - + +
344A LEU* 4.1 5.5 - - - +
353A ALA* 2.8 9.3 + - - +
354A PHE* 3.7 35.2 - - + -
355A LYS* 2.9 25.2 + - - +
372A LEU* 3.5 24.2 - - + -
373A LEU 3.5 4.5 - - - -
374A ALA* 4.7 0.3 - - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU* 4.7 8.7 - - + -
262A ASN* 6.4 0.7 - - + -
263A LEU* 3.9 20.6 - - + -
319A THR* 1.3 75.8 - - - +
321A VAL* 1.3 62.1 + - - +
322A LEU* 4.1 14.9 - - + +
355A LYS* 3.2 17.7 - - + +
371A VAL 3.8 1.2 - - - +
372A LEU* 3.5 2.9 - - - +
373A LEU* 2.8 44.9 + - + +
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A LEU* 4.2 14.1 - - + -
300A PHE* 3.8 33.4 - - + -
319A THR* 4.3 7.6 - - + -
320A ALA* 1.3 75.8 - - - +
322A LEU* 1.3 65.1 + - - +
323A TYR* 4.5 8.7 - - + +
337A LEU* 3.8 29.8 - - + -
354A PHE* 4.5 4.9 - - + -
355A LYS 2.9 9.1 + - - +
356A ILE* 3.4 8.2 - - + +
357A GLY 2.8 26.3 + - - +
370A MET* 4.7 12.8 - - + -
371A VAL 3.5 6.5 - - - +
372A LEU* 4.3 2.0 - - + -
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Residues in contact with LEU 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A GLY 3.8 11.0 - - - +
240A ILE* 3.7 37.5 - - + +
243A SER* 4.0 22.4 - - - +
254A ILE* 5.7 1.6 - - + -
259A LEU* 4.7 16.2 - - + -
320A ALA* 4.6 16.4 - - + +
321A VAL* 1.3 81.7 - - - +
323A TYR* 1.3 63.0 + - - +
324A ARG* 4.0 4.6 + - - +
355A LYS* 5.3 1.6 - - + +
356A ILE 5.2 0.7 - - - -
357A GLY* 3.7 17.5 - - - +
359A VAL* 6.1 3.1 - - + -
369A SER 4.1 0.3 - - - +
370A MET* 3.7 2.0 - - - -
371A VAL* 3.0 46.6 + - + +
373A LEU* 5.5 3.4 - - + -
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Residues in contact with TYR 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A ILE* 4.5 18.6 - - + +
295A MET* 5.0 4.0 - - - -
321A VAL* 3.9 5.5 - - + -
322A LEU* 1.3 73.5 - - - +
324A ARG* 1.3 67.5 + - - +
325A GLY 4.2 0.9 - - - -
326A ILE* 3.4 19.7 + - - +
333A ALA* 5.9 11.7 - - + -
337A LEU* 6.0 4.0 - - + -
356A ILE* 5.9 2.9 - - + -
357A GLY 2.9 13.1 + - - +
358A TYR* 3.3 39.1 - + + -
359A VAL* 3.1 26.2 + - - +
368A LYS* 3.3 42.6 - - + +
369A SER 3.6 4.3 - - - -
370A MET* 3.4 38.6 - - + -
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Residues in contact with ARG 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU* 2.6 44.0 + - - +
238A ALA* 3.6 23.2 + - - +
239A GLY* 4.4 7.5 - - - +
242A ALA* 3.8 22.3 - - + +
246A PHE* 4.0 9.9 - - - -
322A LEU 4.6 4.9 - - - +
323A TYR* 1.3 81.6 - - - +
325A GLY* 1.3 57.4 + - - +
359A VAL* 3.6 15.7 - - + -
361A GLN* 2.8 30.5 + - - +
362A PRO* 3.6 6.5 + - - +
363A GLY* 3.2 24.3 - - - +
368A LYS* 3.1 4.7 - - - +
369A SER* 2.7 53.9 + - - +
371A VAL* 6.5 0.2 - - + -
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Residues in contact with GLY 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A TYR* 4.2 3.2 - - - -
324A ARG* 1.3 76.4 - - - +
326A ILE* 1.3 58.7 + - - -
358A TYR* 2.7 32.2 + - - -
359A VAL 3.1 9.7 + - - -
360A GLU* 3.4 19.8 + - - +
362A PRO* 4.2 6.7 - - - -
367A ARG 3.6 13.9 - - - -
368A LYS* 4.1 0.9 - - - -
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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