Contacts of the strand formed by residues 366 - 380 (chain A) in PDB entry 3M8D
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 GLY 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360A ASP 3.5 0.2 - - - +
361A ASP* 3.4 15.6 - - - -
362A ASN 2.7 43.9 + - - -
363A SER 5.0 0.2 + - - -
364A GLN 3.5 1.8 + - - -
365A PHE* 1.3 82.6 - - - +
367A ARG* 1.3 60.2 + - - -
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Residues in contact with ARG 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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359A SER* 3.4 25.0 + - - +
360A ASP 3.1 11.0 - - - +
361A ASP* 4.4 7.9 - - + +
365A PHE* 3.5 7.6 + - - +
366A GLY* 1.3 73.6 - - - -
368A HIS* 1.3 66.9 + - - +
369A GLY* 5.3 4.2 - - - +
702A C8E 3.7 57.1 + - - +
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Residues in contact with HIS 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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358A ARG 4.1 0.3 - - - +
360A ASP* 2.9 36.1 + - + +
365A PHE* 3.9 20.4 - - + -
366A GLY 3.9 0.6 + - - -
367A ARG* 1.3 79.0 + - - +
369A GLY* 1.3 81.0 + - - +
370A THR* 3.8 4.8 - - + +
391A THR* 6.2 0.6 - - - -
392A SER 4.6 1.8 + - - -
393A TYR* 3.6 44.8 - + + +
412A PRO* 4.6 12.6 - - + +
414A LYS* 4.1 30.4 - - + +
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Residues in contact with GLY 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ARG 3.3 10.5 - - - -
359A SER* 4.4 4.5 - - - -
367A ARG* 5.2 4.2 - - - +
368A HIS* 1.3 88.5 + - - +
370A THR* 1.3 68.9 + - - +
391A THR* 4.6 1.4 + - - -
702A C8E 3.8 36.5 + - - +
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Residues in contact with THR 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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115A SER* 3.5 6.6 + - - -
116A ALA* 3.4 22.5 + - - -
357A ALA* 3.4 0.5 - - - -
358A ARG* 2.9 33.5 + - - +
360A ASP* 5.1 0.7 + - - -
368A HIS* 3.8 6.9 + - + +
369A GLY* 1.3 80.0 - - - +
371A TRP* 1.3 68.9 + - - +
391A THR* 3.4 23.1 - - - +
392A SER* 3.8 14.6 - - - +
393A TYR* 3.7 30.8 - - + -
702A C8E 3.5 5.9 - - - +
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Residues in contact with TRP 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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116A ALA* 3.9 5.4 - - - +
356A ALA 3.3 12.1 - - - +
357A ALA* 4.0 9.9 - - + -
370A THR* 1.3 81.7 - - - +
372A GLN* 1.3 71.8 + - - +
373A THR* 4.0 22.4 - - + -
389A TYR* 3.5 30.9 + + - -
390A GLY* 3.5 1.2 - - - -
391A THR* 3.1 46.7 + - + +
702A C8E 4.2 10.6 - - - -
705A C8E 4.4 20.4 - - - -
707A C8E 3.7 55.8 - - + +
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Residues in contact with GLN 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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113A PRO* 3.1 33.6 + - + +
114A ARG* 3.3 41.0 + - - +
115A SER 4.1 0.2 + - - -
116A ALA* 3.4 18.5 + - + +
117A VAL* 5.4 0.9 - - - +
355A GLY* 3.3 4.0 - - - -
356A ALA* 2.9 43.4 + - + +
371A TRP* 1.3 78.5 - - - +
373A THR* 1.3 68.3 + - - +
389A TYR 3.3 14.1 - - - +
390A GLY* 3.9 6.5 - - - -
391A THR 5.1 1.1 - - - +
705A C8E 3.9 5.5 - - - +
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Residues in contact with THR 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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354A GLU 3.2 12.3 + - - -
371A TRP* 4.0 19.3 - - + -
372A GLN* 1.3 80.6 - - - +
374A SER* 1.3 64.4 + - - +
388A SER* 3.5 2.1 - - - -
389A TYR* 3.0 40.2 + - + +
705A C8E 3.2 40.7 + - - +
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Residues in contact with SER 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.6 29.5 - - - +
24A ALA* 5.0 3.6 + - - +
353A PHE* 3.4 4.9 - - - +
354A GLU* 2.8 45.1 + - - +
373A THR* 1.3 75.1 + - - +
375A ALA* 1.3 61.7 + - - +
386A ILE* 5.1 0.2 - - - -
387A ALA 3.3 6.1 - - - -
388A SER* 2.7 23.1 + - - -
705A C8E 5.3 1.1 - - - +
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Residues in contact with ALA 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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23A LEU* 3.8 4.5 - - - -
351A PHE* 6.0 2.0 - - + -
352A THR 3.3 4.9 - - - -
353A PHE* 3.9 24.7 - - + -
374A SER* 1.3 75.9 - - - +
376A GLY* 1.3 58.7 + - - +
385A PHE* 3.9 0.9 - - - +
386A ILE* 3.2 2.8 - - - +
387A ALA* 2.8 41.3 + - + +
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Residues in contact with GLY 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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23A LEU* 3.6 13.2 - - - +
350A ASP 3.9 0.3 - - - +
351A PHE* 3.4 8.7 - - - -
352A THR* 2.8 33.8 + - - +
375A ALA* 1.3 76.7 - - - +
377A TRP* 1.3 61.7 + - - +
378A GLU 4.3 0.2 - - - -
384A ARG* 4.3 7.0 - - - -
385A PHE 3.1 8.7 - - - -
386A ILE* 4.1 7.6 - - - -
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Residues in contact with TRP 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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350A ASP* 3.7 15.1 + - + +
351A PHE* 3.5 44.9 - + + -
376A GLY* 1.3 73.2 - - - -
378A GLU* 1.3 66.0 + - - +
379A PHE* 3.0 47.3 + + + +
384A ARG* 3.3 5.2 - - - +
385A PHE* 2.7 49.3 + + + +
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Residues in contact with GLU 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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350A ASP* 2.8 46.7 + - + +
377A TRP* 1.3 71.2 - - - +
379A PHE* 1.3 60.9 + - - +
380A ILE* 3.3 18.3 + - - +
381A GLU* 3.1 22.6 - - - +
382A GLY* 2.7 27.4 + - - +
383A TYR 3.3 10.3 - - - +
384A ARG* 4.2 12.9 - - + +
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Residues in contact with PHE 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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350A ASP* 5.4 0.7 - - - +
377A TRP* 3.0 57.1 + + + +
378A GLU* 1.3 71.9 - - - +
380A ILE* 1.3 85.1 + - + +
383A TYR* 3.3 20.8 + - + -
384A ARG* 3.9 21.1 - - - -
385A PHE* 3.9 7.9 - - + -
422A PHE* 4.1 26.2 - + - -
423A GLU 5.8 0.2 - - - -
703A C8E 4.5 19.5 - - + -
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Residues in contact with ILE 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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378A GLU* 3.3 7.0 - - - +
379A PHE* 1.3 100.2 - - + +
381A GLU* 1.3 77.6 + - + +
382A GLY 3.2 0.5 + - - -
383A TYR* 2.9 28.8 + - + +
703A C8E 3.8 45.5 - - + +
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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