Contacts of the strand formed by residues 362 - 372 (chain A) in PDB entry 5WWT
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 LEU 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A GLU* 3.3 6.9 - - - +
317A PHE 3.8 5.6 - - - +
318A ASP 3.8 19.1 - - - +
320A ILE* 4.0 16.6 - - + +
358A ALA 3.2 13.4 + - - +
359A VAL* 3.6 8.1 - - - +
360A GLN 3.2 2.6 - - - -
361A LEU* 1.3 78.4 - - - +
363A LYS* 1.3 68.3 + - - +
366A GLY 3.9 16.4 - - - +
367A VAL 3.7 20.4 - - - +
368A LEU* 3.8 26.2 - - + +
394A LEU* 4.6 9.4 - - + -
463A PHE 5.3 0.2 - - - +
465A LYS* 2.7 45.2 + - + +
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Residues in contact with LYS 363 (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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237A LYS* 5.4 3.6 - - - +
315A GLU* 3.3 21.6 - - - +
316A SER* 3.6 25.8 + - - +
317A PHE 3.0 21.1 + - - +
318A ASP* 3.2 35.2 + - - +
362A LEU* 1.3 79.1 - - - +
364A PRO* 1.3 79.9 - - + +
366A GLY* 3.1 16.8 + - - -
465A LYS* 3.7 3.2 - - - +
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Residues in contact with PRO 364 (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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315A GLU* 3.6 32.1 - - + +
363A LYS* 1.3 89.0 - - + +
365A GLU* 1.3 74.8 + - + +
366A GLY* 3.0 5.8 + - - -
465A LYS* 4.2 11.9 - - + -
466A CYS 3.7 18.8 - - - +
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Residues in contact with GLU 365 (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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363A LYS 3.7 0.2 + - - -
364A PRO* 1.3 78.7 - - + +
366A GLY* 1.3 61.6 + - - +
367A VAL* 4.8 3.8 - - - +
464A VAL* 4.2 12.3 - - - +
465A LYS 2.9 24.4 + - - +
466A CYS* 5.1 4.0 - - - +
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Residues in contact with GLY 366 (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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318A ASP 3.5 15.5 - - - -
362A LEU* 3.9 8.0 - - - +
363A LYS* 3.1 15.4 + - - -
364A PRO 3.0 6.2 - - - -
365A GLU* 1.3 80.6 - - - +
367A VAL* 1.3 62.0 + - - -
463A PHE 3.7 0.2 - - - +
464A VAL* 3.3 8.1 - - - +
465A LYS 3.2 22.0 + - - +
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Residues in contact with VAL 367 (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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230A LEU* 4.1 17.5 - - + +
318A ASP 3.5 7.3 + - - -
319A ARG* 3.4 40.4 - - + +
320A ILE 2.9 26.2 + - - +
362A LEU* 3.7 3.2 - - - +
365A GLU 4.8 4.7 - - - +
366A GLY* 1.3 78.4 - - - +
368A LEU* 1.3 61.4 + - - +
369A VAL* 4.1 3.8 - - + -
397A GLN* 6.1 0.7 - - - +
462A LYS* 3.7 38.1 - - + +
463A PHE 3.3 10.8 - - - +
464A VAL* 5.2 5.2 - - + -
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Residues in contact with LEU 368 (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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320A ILE* 3.2 36.1 - - + +
322A LEU* 4.4 13.5 - - + -
355A PHE* 3.5 39.9 - - + -
358A ALA* 3.8 14.1 - - + -
359A VAL* 4.0 17.7 - - + +
362A LEU* 3.8 16.3 - - + +
367A VAL* 1.3 72.5 - - - +
369A VAL* 1.3 65.1 + - - +
394A LEU* 4.3 9.0 - - + -
463A PHE* 2.9 49.0 + - + +
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Residues in contact with VAL 369 (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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226A VAL* 4.0 16.8 - - + +
229A VAL* 4.5 3.1 - - + -
230A LEU* 3.7 39.7 - - + +
320A ILE 2.9 9.5 + - - -
321A LEU* 3.3 24.5 - - + +
322A LEU 2.9 27.2 + - - -
367A VAL* 4.2 8.7 - - + -
368A LEU* 1.3 76.6 - - - +
370A TYR* 1.3 62.6 + - - +
371A SER* 4.7 0.2 - - - -
460A ILE* 4.0 17.5 - - + -
461A ALA 3.4 7.2 - - - +
462A LYS* 4.4 12.6 - - + -
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Residues in contact with TYR 370 (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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322A LEU* 3.5 33.4 - - + -
324A ALA* 3.7 19.3 - - + -
351A GLN* 3.1 28.1 + - + +
355A PHE* 3.7 29.4 - + + -
368A LEU* 3.9 1.9 + - + -
369A VAL* 1.3 71.4 - - - +
371A SER* 1.3 60.5 + - - +
372A THR* 3.5 15.8 - - + +
379A GLU 2.7 28.9 + - - -
383A GLN* 3.8 16.9 - - + +
384A VAL* 5.1 3.8 - - + -
459A PHE* 3.8 20.0 - + - +
460A ILE* 3.6 1.2 - - - -
461A ALA* 2.9 39.4 + - + +
463A PHE* 4.4 7.2 - - + -
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Residues in contact with SER 371 (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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226A VAL* 4.0 22.6 - - - +
321A LEU* 4.2 1.6 - - - +
322A LEU 2.9 7.8 + - - -
323A ASP* 2.8 35.7 + - - +
324A ALA 3.2 22.7 + - - -
369A VAL* 4.0 3.1 + - - -
370A TYR* 1.3 77.2 - - - +
372A THR* 1.3 65.0 + - - +
458A PHE* 3.9 14.6 - - - -
459A PHE 3.1 11.7 - - - -
460A ILE* 4.3 4.7 - - - -
72C C 3.4 0.7 + - - -
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Residues in contact with THR 372 (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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324A ALA* 4.6 5.2 - - + +
326A CYS* 4.1 12.1 - - + -
351A GLN* 4.6 4.3 - - - +
370A TYR* 3.5 35.4 - - + +
371A SER* 1.3 79.7 - - - +
373A CYS* 1.3 59.2 + - - +
374A THR* 3.3 18.3 + - + +
379A GLU 3.9 5.8 - - - +
380A ASN* 2.6 22.4 + - - +
458A PHE* 3.3 12.8 - - - -
459A PHE* 2.9 32.6 + - - +
72C C 4.0 6.5 - - - +
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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