Contacts of the strand formed by residues 388 - 395 (chain A) in PDB entry 2W8B
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 MET 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASN 3.5 13.5 - - - +
65A SER 3.4 26.7 - - - +
382A LEU* 3.5 7.2 - - - +
383A ALA* 2.9 31.3 + - + +
386A GLY 3.6 1.2 - - - -
387A THR* 1.3 89.5 - - - +
389A VAL* 1.3 65.1 + - - +
403A LEU* 4.4 7.9 - - + -
404A VAL 3.7 9.0 - - - +
405A SER* 3.6 26.2 - - - +
406A THR* 3.8 0.8 - - - +
410A PHE* 3.9 19.1 - - + -
426A TRP* 3.4 28.0 - - + -
1431A SO4 3.4 27.4 - - - +
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Residues in contact with VAL 389 (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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347A VAL* 4.0 14.1 - - + -
358A ILE* 4.5 5.4 - - + -
371A LEU* 4.2 10.8 - - + -
380A PRO* 3.7 23.1 - - + -
381A SER 3.6 7.6 - - - +
382A LEU* 3.8 19.5 - - + -
388A MET* 1.3 77.6 - - - +
390A LEU* 1.3 75.2 + - - +
391A TYR* 4.2 8.9 - - + -
402A ASN 3.7 0.5 - - - +
403A LEU* 3.3 9.2 - - - +
404A VAL* 2.9 43.0 + - + +
406A THR* 3.9 10.8 - - + -
426A TRP* 4.0 4.0 - - - -
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Residues in contact with LEU 390 (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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167A ILE* 3.6 42.0 - - + -
168A ALA 4.6 0.4 - - - +
187A TYR 6.1 0.4 - - - +
379A THR 3.6 1.0 - - - +
380A PRO* 3.3 0.3 - - - +
381A SER* 2.6 42.5 + - - +
389A VAL* 1.3 72.0 - - - +
391A TYR* 1.3 61.1 + - - +
401A LEU* 4.8 6.7 - - + -
402A ASN 3.6 7.0 - - - +
403A LEU* 3.7 20.4 - - + -
414A LEU* 4.3 14.6 - - + -
424A PRO* 2.9 33.4 - - + +
425A ALA 3.6 16.2 - - - +
426A TRP* 3.5 16.1 - - + +
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Residues in contact with TYR 391 (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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358A ILE* 3.7 19.7 - - + -
372A SER* 3.3 16.1 - - - -
374A THR* 2.7 23.2 + - - +
377A ASP* 3.4 26.9 - - + -
378A GLU 3.4 9.6 - - - +
379A THR 3.7 2.2 - - - -
380A PRO* 3.7 14.4 - - + -
389A VAL* 4.2 4.0 - - + -
390A LEU* 1.3 77.7 - - - +
392A SER* 1.3 68.6 + - - +
401A LEU* 3.4 6.2 - - - +
402A ASN* 2.8 70.7 + - + +
403A LEU 4.5 0.2 - - - -
404A VAL* 3.6 32.6 - - + +
424A PRO* 3.6 13.6 - - - +
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Residues in contact with SER 392 (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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376A LEU 3.6 0.9 - - - +
377A ASP* 3.4 2.6 - - - -
378A GLU* 2.8 45.7 + - - +
379A THR* 4.0 7.4 - - - -
391A TYR* 1.3 81.4 - - - +
393A SER* 1.3 64.9 + - - +
399A SER* 3.8 6.2 + - - -
400A VAL 2.9 17.9 + - - -
401A LEU* 4.3 0.7 - - - -
421A VAL 3.6 10.0 + - - -
422A LYS* 3.7 12.9 - - - +
424A PRO* 4.0 19.2 - - - +
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Residues in contact with SER 393 (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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374A THR* 3.9 9.8 - - - +
375A PHE 3.1 12.3 - - - -
376A LEU 3.5 9.2 - - - -
377A ASP* 3.3 20.0 - - - -
378A GLU* 5.7 0.2 - - - -
392A SER* 1.3 73.9 + - - +
394A SER* 1.3 66.5 + - - +
395A GLN* 5.6 0.7 + - - +
399A SER* 3.2 6.6 - - - -
400A VAL* 2.9 36.1 + - - +
402A ASN* 2.6 27.8 + - - +
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Residues in contact with SER 394 (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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375A PHE* 2.8 42.2 + - - +
376A LEU* 3.8 12.3 + - - +
393A SER* 1.3 79.6 + - - +
395A GLN* 1.3 62.2 + - - +
396A GLY 4.3 0.4 + - - -
398A GLY 3.4 10.0 + - - -
399A SER* 4.4 7.3 + - - -
111H GLU* 4.2 5.5 + - - -
158H HIS* 3.8 29.4 - - - -
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Residues in contact with GLN 395 (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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393A SER* 4.2 1.9 + - - +
394A SER* 1.3 73.3 - - - +
396A GLY* 1.3 66.4 + - - +
397A MET 3.4 1.6 + - - -
398A GLY* 3.0 16.4 + - - +
400A VAL* 4.0 33.8 - - + +
402A ASN* 5.1 1.6 + - - -
413A ARG* 3.6 35.5 + - - +
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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