Contacts of the strand formed by residues 355 - 366 (chain A) in PDB entry 4QDR
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 355 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A ALA 3.6 7.0 - - - -
348A ILE* 4.4 4.9 - - - -
353A GLN 3.7 2.4 + - - -
354A ASN* 1.3 72.7 - - - +
356A TYR* 1.3 60.5 + - - -
357A TYR* 4.3 3.9 - - - -
390A ALA* 3.7 16.6 - - - -
415A HIS* 3.7 23.0 - - - -
416A SER* 4.1 6.1 + - - -
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Residues in contact with TYR 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A TRP* 3.8 19.7 - + - -
319A ARG* 3.6 35.4 + - - -
346A GLY* 3.2 0.5 - - - -
347A ALA 2.9 34.2 + - - +
349A SER* 3.9 13.9 - - - -
352A THR* 4.2 6.2 + - - +
354A ASN* 3.6 42.3 + - + -
355A GLY* 1.3 73.6 - - - -
357A TYR* 1.3 65.5 + - - +
390A ALA* 3.8 2.6 - - - +
415A HIS 3.6 3.1 - - - -
416A SER* 3.5 20.9 - - - -
417A GLY* 3.4 28.0 - - - +
418A ILE 4.9 0.2 - - - -
419A ALA* 3.6 20.6 - - + -
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Residues in contact with TYR 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLY* 3.8 12.3 - - - -
355A GLY 4.3 5.4 - - - -
356A TYR* 1.3 80.4 - - - +
358A VAL* 1.3 64.7 + - - +
359A LYS* 3.8 15.6 + - + +
387A ASN* 3.5 25.8 - - + -
388A ASN* 3.2 30.9 + - - -
389A ASP* 3.3 36.1 - - - +
390A ALA* 3.8 2.5 - - + -
414A TRP* 3.1 5.7 - - - +
415A HIS* 2.8 73.4 + + + -
417A GLY 3.4 4.1 + - - +
419A ALA 4.0 2.9 - - - -
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLY* 5.0 0.2 - - - -
357A TYR* 1.3 74.6 - - - +
359A LYS* 1.3 58.5 + - - +
360A SER 3.3 30.5 - - - +
361A TYR* 4.4 12.3 - - + -
386A ALA* 3.3 3.7 - - + +
387A ASN* 3.0 31.2 + - - +
409A ILE* 5.9 0.2 - - + -
411A PRO* 3.8 18.8 - - + -
413A THR 3.6 6.1 - - - +
414A TRP* 4.0 0.7 - - + -
418A ILE* 3.7 30.7 - - + -
419A ALA 3.7 17.4 + - - +
420A LEU* 3.9 19.3 - - + -
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Residues in contact with LYS 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TYR* 3.8 16.5 + - + -
358A VAL* 1.3 72.6 - - - +
360A SER* 1.3 62.7 + - - +
385A GLN* 3.8 7.4 - - - +
386A ALA* 2.9 22.1 + - - -
387A ASN 3.6 18.3 - - - +
388A ASN* 5.3 7.9 - - - +
413A THR* 2.8 23.4 + - - +
414A TRP* 3.7 27.3 - - - +
415A HIS* 4.0 13.0 + - + +
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL* 3.3 12.7 - - - +
359A LYS* 1.3 80.9 - - - +
361A TYR* 1.3 61.3 + - - +
383A VAL* 3.8 16.4 - - - +
384A PHE 3.1 15.9 - - - -
385A GLN* 4.4 9.4 - - - -
386A ALA* 4.1 2.7 - - - +
412A GLN* 2.9 31.5 + - - +
413A THR* 2.8 28.7 + - - +
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Residues in contact with TYR 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ILE* 3.5 44.0 + - + +
344A THR* 4.0 16.7 + - + +
358A VAL* 4.4 6.5 - - + -
360A SER* 1.3 75.5 - - - +
362A LYS* 1.3 73.7 + - - +
363A LEU 5.4 0.2 - - - -
383A VAL* 3.7 4.5 - - - -
384A PHE* 2.9 65.3 + + + +
386A ALA* 3.7 28.3 - - + -
394A VAL 5.3 0.2 + - - -
396A ASN* 3.0 22.2 + - - +
409A ILE* 3.7 22.0 - - + -
410A ARG 3.3 19.7 - - - +
411A PRO* 3.9 2.9 - - + -
412A GLN* 4.2 5.4 - - - +
420A LEU* 5.7 0.4 - - + -
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Residues in contact with LYS 362 (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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361A TYR* 1.3 84.0 - - - +
363A LEU* 1.3 64.8 + - - +
364A GLU* 6.3 0.7 - - + -
374A VAL* 4.7 9.0 - - + -
381A HIS* 2.9 45.6 + - + +
382A LYS 3.8 17.7 - - - +
383A VAL* 4.4 14.4 - - + -
384A PHE* 4.6 0.2 - - - -
408A ARG 3.7 1.0 - - - +
409A ILE* 3.8 0.5 - - - -
410A ARG* 2.8 44.6 + - + +
412A GLN* 3.8 30.8 + - + +
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Residues in contact with LEU 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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339A LEU* 4.1 17.5 - - + -
342A ILE* 4.0 25.8 - - + -
361A TYR* 5.3 0.2 - - + -
362A LYS* 1.3 76.0 - - - +
364A GLU* 1.3 67.8 + - - +
365A VAL* 4.0 13.0 - - + -
374A VAL* 3.4 9.4 - - - +
375A TYR* 3.0 48.8 + - + +
382A LYS 4.6 1.4 + - - -
384A PHE* 3.8 19.3 - - + -
398A LEU* 4.2 13.0 - - + -
402A LEU* 4.4 5.8 - - + -
407A VAL* 3.7 30.1 - - + -
408A ARG 3.6 5.6 - - - +
409A ILE* 4.2 2.9 - - + -
410A ARG* 5.9 0.2 - - - -
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Residues in contact with GLU 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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362A LYS* 6.3 0.4 - - + -
363A LEU* 1.3 74.1 - - - +
365A VAL* 1.3 66.3 + - - +
372A TRP* 3.3 35.2 - - + +
373A MET 3.2 6.5 - - - +
374A VAL* 3.7 29.5 - - + +
407A VAL* 3.6 0.3 - - - -
408A ARG* 2.8 55.7 + - + +
410A ARG* 2.6 42.5 + - + +
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Residues in contact with VAL 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 4.5 1.8 - - + -
363A LEU* 4.0 23.3 - - + -
364A GLU* 1.3 80.6 - - - +
366A SER* 1.3 62.4 + - - +
371A ASP 3.7 0.2 - - - +
372A TRP* 3.3 6.9 - - - -
373A MET* 2.8 46.2 + - + +
375A TYR 5.7 0.9 - - - +
402A LEU* 3.8 26.0 - - + -
404A THR* 3.1 26.9 - - + +
406A PHE 3.3 11.0 - - - +
407A VAL* 4.3 4.7 - - + -
556A ASP* 4.7 0.5 - - - +
557A THR* 3.7 20.6 + - + +
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Residues in contact with SER 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A VAL* 1.3 76.9 - - - +
367A THR* 1.3 61.1 + - - +
368A ASN* 3.0 4.6 + - - -
369A GLY* 2.6 32.3 + - - -
371A ASP 2.6 26.1 + - - -
372A TRP* 3.5 22.7 - - - -
404A THR* 2.9 10.4 + - - -
405A ARG 3.1 0.2 + - - -
406A PHE* 2.9 28.6 + - - -
556A ASP* 3.4 4.7 - - - -
557A THR* 5.3 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