Contacts of the strand formed by residues 383 - 394 (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 TYR 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A GLU* 3.3 15.8 + - - +
379A PHE* 3.3 26.1 + + + -
380A ILE* 2.9 26.9 + - + +
381A GLU 3.6 14.1 - - - -
382A GLY* 1.3 77.7 - - - +
384A ARG* 1.3 60.7 + - - +
423A GLU 3.5 3.6 - - - +
424A GLY* 3.8 13.0 - - - -
425A LEU 3.1 19.4 + - - -
426A THR* 2.7 39.0 + - - +
431A TRP* 3.8 15.7 - + - -
703A C8E 3.4 63.7 - - + +
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Residues in contact with ARG 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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20A SER* 2.8 36.3 + - - +
22A VAL 5.1 2.8 + - - -
23A LEU* 3.8 17.4 - - - +
347A GLN* 5.5 1.8 - - - +
350A ASP 5.6 0.7 - - - -
352A THR* 3.7 21.5 + - - -
376A GLY* 4.3 6.3 - - - -
377A TRP 3.3 24.7 - - - +
378A GLU* 4.2 12.3 - - + +
379A PHE* 3.9 5.8 - - - -
383A TYR* 1.3 76.9 - - - +
385A PHE* 1.3 71.7 + - - +
386A ILE* 3.9 9.9 - - + +
422A PHE* 3.5 5.7 - - - -
423A GLU* 2.8 71.0 + - + +
432A ARG* 5.8 0.2 - - - +
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Residues in contact with PHE 385 (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 ALA 3.9 0.6 - - - +
376A GLY* 3.1 2.9 - - - -
377A TRP* 2.7 55.7 + + + +
379A PHE* 3.9 8.4 - - + -
384A ARG* 1.3 72.3 - - - +
386A ILE* 1.3 73.4 + - - +
387A ALA* 4.4 20.6 - - + -
420A GLY* 4.8 4.3 - - - -
421A ALA 3.3 22.0 - - - -
422A PHE* 3.9 32.3 - + + -
706A C8E 4.8 9.6 - - + -
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Residues in contact with ILE 386 (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 58.6 - - + +
375A ALA 3.2 10.1 - - - +
376A GLY* 4.3 0.4 - - - -
384A ARG* 3.9 11.9 - - + +
385A PHE* 1.3 86.4 - - - +
387A ALA* 1.3 61.4 + - - +
388A SER* 4.1 13.9 - - - +
419A GLU 3.9 0.7 - - - +
420A GLY* 3.3 5.5 - - - -
421A ALA* 2.9 41.5 + - + +
423A GLU* 3.7 25.4 - - + +
432A ARG* 3.8 16.4 - - - +
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Residues in contact with ALA 387 (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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373A THR 4.3 0.2 - - - +
374A SER* 3.3 3.1 - - - -
375A ALA* 2.8 39.8 + - + +
385A PHE* 4.4 19.4 - - + -
386A ILE* 1.3 73.2 - - - +
388A SER* 1.3 62.5 + - - +
419A GLU 3.5 5.6 - - - +
420A GLY* 4.7 1.1 - - - -
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 5.3 1.9 + - - +
24A ALA* 5.6 2.4 - - - +
373A THR 3.5 6.7 - - - -
374A SER* 2.7 23.4 + - - -
386A ILE* 4.1 9.9 - - - +
387A ALA* 1.3 74.5 - - - +
389A TYR* 1.3 64.7 + - - +
418A TRP* 3.5 4.9 - - - +
419A GLU* 3.0 45.3 + - - +
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Residues in contact with TYR 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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113A PRO* 5.1 2.0 - - - -
371A TRP* 3.5 42.9 + + - -
372A GLN* 3.3 4.0 - - - +
373A THR* 3.0 38.3 + - + +
388A SER* 1.3 78.1 - - - +
390A GLY* 1.3 62.9 + - - +
391A THR* 3.7 18.3 - - + +
416A LYS* 3.7 27.1 - - + +
417A GLN 3.2 17.5 - - - -
418A TRP* 3.3 46.1 - + + -
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Residues in contact with GLY 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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113A PRO* 3.9 14.3 - - - +
371A TRP 3.5 11.4 - - - -
372A GLN* 3.9 8.5 - - - -
389A TYR* 1.3 82.9 - - - +
391A THR* 1.3 64.1 + - - -
415A SER* 3.9 0.3 + - - +
416A LYS* 3.5 1.4 - - - -
417A GLN* 2.8 41.2 + - - +
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Residues in contact with THR 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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113A PRO* 4.2 4.4 - - - +
115A SER* 4.4 3.1 + - - -
116A ALA 5.0 0.9 + - - -
368A HIS* 6.2 0.9 - - - -
369A GLY 4.6 1.1 + - - -
370A THR* 3.4 20.6 - - - +
371A TRP* 3.1 46.0 + - + +
372A GLN* 5.1 1.6 - - - +
389A TYR* 3.7 23.3 - - + +
390A GLY* 1.3 75.8 - - - +
392A SER* 1.3 65.9 + - - +
415A SER 3.0 11.7 - - - +
416A LYS* 4.4 10.1 - - + -
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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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113A PRO* 3.7 13.9 - - - +
115A SER* 3.2 23.1 - - - -
122A ALA 3.7 14.1 - - - -
123A ILE* 3.8 12.2 - - - +
368A HIS* 4.6 1.7 + - - -
370A THR* 3.8 5.8 - - - +
391A THR* 1.3 79.4 - - - +
393A TYR* 1.3 66.3 + - - +
414A LYS* 3.6 3.5 - - - +
415A SER* 3.0 42.1 + - - +
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Residues in contact with TYR 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER* 3.2 10.3 + - - -
119A GLY* 3.8 10.5 - - - -
120A SER* 3.4 32.0 + - - -
121A ASP* 3.0 22.3 + - - -
123A ILE* 3.9 9.5 - - - +
337A ASN* 4.4 5.4 + - - -
360A ASP* 3.0 46.0 + - + +
365A PHE* 3.9 22.6 - + - -
368A HIS* 3.6 32.3 - + + +
370A THR* 3.7 14.4 - - + -
392A SER* 1.3 80.3 - - - +
394A LYS* 1.3 68.3 + - - +
395A ALA* 4.0 3.1 - - + -
412A PRO* 3.8 12.8 - - + -
413A GLU 3.1 13.9 - - - +
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Residues in contact with LYS 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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74A SER* 3.7 26.4 + - - +
75A HIS* 3.8 24.9 - - + +
87A LEU* 5.2 5.1 - - - +
92A GLY* 3.5 28.1 + - - -
120A SER* 3.6 1.3 - - - +
121A ASP* 3.0 35.6 + - - +
123A ILE* 4.0 5.1 - - + +
393A TYR* 1.3 79.4 - - - +
395A ALA* 1.3 79.0 + - - +
397A ASN* 5.7 4.2 - - - +
412A PRO* 3.2 6.8 - - - +
413A GLU* 3.0 46.2 + - + +
444A ILE* 6.3 0.4 - - + -
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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