Contacts of the strand formed by residues 372 - 384 (chain A) in PDB entry 4H3T
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 THR 372 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A PHE* 3.1 8.1 - - - -
367A GLY 2.7 36.7 + - - -
368A ASN* 3.0 27.2 + - + +
371A THR* 1.4 89.8 - - - +
373A LEU* 1.3 60.9 + - - +
374A ASP* 2.9 17.7 + - - -
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Residues in contact with LEU 373 (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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46A PHE* 5.1 5.4 - - + -
48A THR* 5.6 2.9 - - + -
130A ALA* 6.0 3.4 - - + -
131A TYR 4.4 11.7 - - - +
133A PRO* 3.7 44.7 - - + +
169A SER* 5.7 0.2 - - - -
364A ALA* 3.7 23.1 - - + -
365A LYS 3.7 5.6 - - - +
366A PHE* 3.8 23.1 - - + -
371A THR 4.3 0.6 + - - -
372A THR* 1.3 70.2 - - - +
374A ASP* 1.3 59.7 + - - +
375A ASP 3.7 19.3 - - - +
376A LEU* 4.6 14.8 - - + -
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Residues in contact with ASP 374 (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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133A PRO* 3.6 15.9 - - - +
365A LYS* 2.7 23.1 + - + +
366A PHE 4.2 1.6 - - - +
367A GLY* 3.5 23.4 - - - +
368A ASN* 4.6 1.8 - - - +
372A THR* 2.9 24.9 + - - -
373A LEU* 1.3 74.5 - - - +
375A ASP* 1.3 66.3 + - + +
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Residues in contact with ASP 375 (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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133A PRO* 4.0 7.5 - - - +
319A PRO* 3.3 30.6 - - + +
320A GLY* 4.6 4.6 + - - -
364A ALA* 3.5 2.8 - - - -
365A LYS* 2.9 49.3 + - + +
373A LEU* 3.6 4.8 - - - +
374A ASP* 1.3 82.1 - - + +
376A LEU* 1.3 71.9 + - - +
377A ALA 4.3 0.2 - - - -
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Residues in contact with LEU 376 (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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46A PHE* 4.3 14.8 - - + -
47A PRO* 4.1 32.3 - - + -
48A THR* 4.1 26.5 - - + -
133A PRO* 3.5 24.5 - - + +
167A PHE* 5.3 3.6 - - + -
319A PRO* 4.4 1.4 - - - +
362A THR* 5.6 3.6 - - - -
363A SER 3.5 16.6 - - - +
364A ALA* 4.1 15.5 - - + -
373A LEU* 4.6 8.5 - - + -
375A ASP* 1.3 86.6 + - - +
377A ALA* 1.3 66.5 + - - +
378A TYR* 4.0 3.5 + - + +
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Residues in contact with ALA 377 (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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317A ALA* 3.9 14.8 - - + +
318A ARG 4.3 3.1 - - - +
319A PRO* 3.8 26.4 - - + +
361A VAL* 4.3 0.9 - - + -
362A THR* 3.2 8.7 - - - -
363A SER* 2.8 50.9 + - - +
376A LEU* 1.3 72.6 - - - +
378A TYR* 1.3 62.2 + - - +
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Residues in contact with TYR 378 (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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47A PRO* 3.7 45.3 - - + -
50A GLU* 5.0 9.6 + - + -
360A LEU* 3.8 26.2 - - + -
361A VAL 3.3 4.9 - - - -
362A THR* 4.3 8.5 - - + +
376A LEU* 4.0 7.3 + - + +
377A ALA* 1.3 76.0 - - - +
379A ASP* 1.3 75.8 + - - +
380A ARG* 5.3 6.5 - - + +
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Residues in contact with ASP 379 (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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321A GLN 4.7 1.6 - - - +
322A GLN* 4.0 3.8 - - - -
323A VAL* 3.1 52.3 + - + +
359A LEU 4.3 0.7 - - - -
360A LEU* 3.5 7.8 - - - +
361A VAL* 2.8 36.5 + - + +
378A TYR* 1.3 85.8 - - - +
380A ARG* 1.4 73.6 + - - +
465A ARG* 3.2 20.6 + - - -
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Residues in contact with ARG 380 (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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50A GLU* 4.3 14.8 + - - -
203A VAL* 3.5 30.0 - - - +
204A GLY 5.1 1.8 + - - -
323A VAL* 4.6 0.4 - - - -
358A SER* 2.3 37.1 + - - +
359A LEU 3.2 4.3 - - - -
360A LEU* 3.6 37.7 - - + +
378A TYR* 5.3 7.0 - - + +
379A ASP* 1.4 82.3 + - - +
381A LEU* 1.3 60.0 + - - +
382A ASP* 4.2 1.1 + - - -
465A ARG* 2.9 21.5 + - - -
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Residues in contact with LEU 381 (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 VAL* 3.9 21.5 - - + +
324A TRP* 4.2 29.4 - - + -
327A LEU* 4.3 20.0 - - + -
330A VAL* 5.8 4.0 - - + -
358A SER* 4.2 1.6 - - - -
359A LEU* 2.9 41.9 + - + +
361A VAL* 5.9 0.9 - - + -
380A ARG* 1.3 73.0 - - - +
382A ASP* 1.3 61.8 + - - +
383A THR* 3.1 24.9 + - - +
464A TYR* 5.2 0.4 - - + -
465A ARG* 3.9 28.3 - - + +
468A LEU* 3.8 25.6 - - + -
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Residues in contact with ASP 382 (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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356A LEU* 4.7 8.7 - - + -
357A VAL 3.7 4.3 - - - +
358A SER* 3.4 25.5 + - - -
380A ARG 4.2 1.6 + - - -
381A LEU* 1.3 70.7 - - - +
383A THR* 1.3 58.0 + - - +
384A PRO* 4.1 1.3 - - - +
465A ARG* 4.9 6.6 - - + +
468A LEU* 3.4 23.0 - - - +
469A THR* 3.6 25.2 + - + +
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Residues in contact with THR 383 (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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327A LEU* 5.5 3.1 - - + -
331A LEU* 5.4 2.7 - - + -
356A LEU* 4.0 4.4 - - - +
357A VAL* 2.8 39.9 + - - +
359A LEU* 3.6 27.6 - - + +
381A LEU* 3.1 28.2 + - + +
382A ASP* 1.3 73.4 - - - +
384A PRO* 1.3 82.6 - - + +
385A LEU 3.6 0.5 + - - -
387A VAL* 4.3 16.6 - - + -
388A LEU* 4.4 11.8 - - + +
468A LEU* 4.3 5.1 - - + +
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Residues in contact with PRO 384 (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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355A ALA 3.3 7.9 - - - +
356A LEU* 3.9 12.3 - - + -
382A ASP 4.1 1.3 - - - +
383A THR* 1.3 94.0 - - + +
385A LEU* 1.3 66.3 + - - +
386A ALA* 3.9 8.1 - - + +
387A VAL* 3.0 33.0 + - + +
388A LEU* 3.6 4.4 + - - +
468A LEU* 3.1 38.1 - - + +
471A LEU 4.3 0.4 - - - -
472A ALA* 3.8 30.5 - - + +
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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