Contacts of the strand formed by residues 394 - 415 (chain A) in PDB entry 4QDQ
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 VAL 394 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ILE 3.7 0.9 - - - +
343A ALA* 3.3 2.9 - - - -
344A THR* 3.0 34.1 + - - +
361A TYR* 5.3 0.2 + - - -
385A GLN 4.0 20.4 - - - +
386A ALA* 4.2 12.6 - - - +
387A ASN* 3.8 30.1 - - - +
388A ASN* 4.5 11.9 - - - +
392A GLU* 4.5 5.4 - - + +
393A VAL* 1.3 78.8 - - - +
395A LEU* 1.3 68.6 + - - +
396A ASN* 4.5 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ALA* 3.8 16.6 - - + -
342A ILE 3.4 11.4 - - - +
343A ALA* 4.0 6.5 - - + +
393A VAL* 4.2 4.8 + - + -
394A VAL* 1.3 75.6 - - - +
396A ASN* 1.3 71.3 + - - +
397A LYS* 3.7 29.2 + - + +
425A PHE* 3.7 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ALA* 3.3 4.4 - - - -
342A ILE* 2.7 40.9 + - + +
361A TYR* 3.1 27.2 + - - +
384A PHE* 3.7 28.2 - - + +
385A GLN* 2.9 30.5 + - - +
386A ALA* 4.7 0.4 - - - +
394A VAL* 4.5 9.2 + - - +
395A LEU* 1.3 79.9 - - - +
397A LYS* 1.3 62.9 - - - +
398A LEU* 3.7 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASN* 5.8 7.1 - - - +
340A THR 3.6 8.1 - - - +
341A ALA* 4.2 8.7 - - + -
384A PHE* 5.2 3.2 - - - -
395A LEU* 3.7 26.3 - - + +
396A ASN* 1.3 73.1 - - - +
398A LEU* 1.3 67.9 + - - +
399A HIS* 3.4 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 3.5 40.6 - - + +
340A THR* 2.8 25.0 + - - +
341A ALA* 4.4 2.2 - - - +
342A ILE* 4.6 8.1 - - + -
363A LEU* 4.1 7.4 - - + -
375A TYR* 3.7 17.3 - - + +
384A PHE* 3.5 35.9 - - + -
396A ASN 3.7 2.6 + - - +
397A LYS* 1.3 75.0 - - - +
399A HIS* 1.3 62.8 + - - +
400A ALA* 3.0 14.5 + - - +
401A PRO* 4.3 5.7 - - - +
402A LEU* 4.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A TYR* 3.6 19.4 + + - -
376A ARG 3.4 25.8 + - - -
377A HIS* 3.2 48.1 + + + -
378A GLY 5.1 1.4 + - - -
382A LYS* 4.7 5.0 - - + +
397A LYS 3.4 4.8 + - - -
398A LEU* 1.3 71.9 - - - +
400A ALA* 1.3 69.6 + - + +
401A PRO* 4.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A TYR* 2.9 33.1 + - + +
398A LEU* 3.0 7.0 - - - +
399A HIS* 1.3 91.6 - - + +
401A PRO* 1.4 73.8 - - + +
402A LEU* 4.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A MET* 3.6 23.5 - - + +
339A LEU 3.6 7.6 - - - +
340A THR* 3.8 20.9 - - + -
398A LEU* 4.3 9.4 - - + +
399A HIS 4.2 4.7 - - - +
400A ALA* 1.4 89.9 - - - +
402A LEU* 1.3 61.4 + - - +
403A LEU 4.5 0.2 + - - -
559A ASP* 5.8 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A THR 3.3 3.3 - - - +
338A MET* 3.5 5.9 - - - +
339A LEU* 2.8 47.7 + - + +
363A LEU* 4.0 11.7 - - + -
365A VAL* 3.8 38.4 - - + -
373A MET* 4.1 8.1 - - + -
375A TYR* 3.6 37.5 - - + -
398A LEU* 4.0 6.7 - - + -
400A ALA* 4.4 0.7 - - + +
401A PRO* 1.3 80.0 - - - +
403A LEU* 1.3 62.1 + - - +
404A THR* 3.7 1.4 + - + -
557A THR* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LEU* 4.0 20.2 - - + -
337A THR 3.5 26.5 - - - +
338A MET* 3.7 19.1 - - - +
367A THR* 4.7 0.3 - - - +
402A LEU* 1.3 70.4 - - - +
404A THR* 1.3 63.8 + - - +
429A VAL* 3.8 25.1 - - + -
502A ILE* 3.9 32.1 - - + -
557A THR* 3.9 9.0 - - - +
558A PRO* 3.4 37.8 + - + +
559A ASP* 5.3 0.7 - - - -
560A ILE* 4.2 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 4.5 3.5 - - + +
335A PHE 3.8 0.3 - - - +
336A LEU* 3.5 12.9 - - - +
337A THR* 2.8 41.9 + - - +
339A LEU* 4.4 10.3 - - + -
365A VAL* 3.2 18.5 - - + +
366A SER 3.0 30.3 + - - -
367A THR* 4.9 1.3 - - - -
402A LEU* 4.4 7.9 - - + +
403A LEU* 1.3 76.4 - - - +
405A ARG* 1.3 64.9 + - - +
406A PHE 3.2 3.1 + - - -
407A VAL* 4.0 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ASP* 2.7 37.8 + - - +
333A LEU* 2.9 38.4 + - - +
334A ARG* 3.0 37.2 + - - +
335A PHE* 4.1 11.2 - - - +
336A LEU* 4.6 3.8 - - + +
366A SER 3.0 9.6 + - - +
367A THR* 3.8 19.6 + - - +
368A ASN* 5.8 1.2 + - - +
404A THR* 1.3 80.8 + - - +
406A PHE* 1.3 81.1 + - + +
443B GLY 2.8 27.3 + - - -
444B LEU* 2.8 26.3 + - - +
446B ALA* 4.4 8.1 - - - +
449B GLN* 5.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLN* 3.4 26.9 - - + +
331A VAL 3.4 2.2 - - - -
332A ASP* 3.4 33.9 - - + -
365A VAL* 3.3 5.5 - - - +
366A SER* 2.8 31.6 + - - +
368A ASN* 3.6 19.1 - - - -
369A GLY* 3.4 20.9 - - - -
372A TRP* 3.5 20.9 - - + -
404A THR* 3.2 6.8 + - - -
405A ARG* 1.3 114.7 - - + +
407A VAL* 1.3 60.8 + - - +
446B ALA* 4.0 17.0 - - + -
449B GLN* 5.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LEU 3.7 0.3 - - - +
330A GLN* 3.2 5.0 - - - +
331A VAL* 2.8 39.0 + - + +
333A LEU* 4.2 17.0 - - + -
339A LEU* 4.0 14.6 - - + -
363A LEU* 3.7 22.7 - - + -
364A GLU 3.7 2.9 - - - -
365A VAL* 4.4 2.0 - - + -
404A THR* 4.0 20.4 - - + -
406A PHE* 1.3 78.5 - - - +
408A ARG* 1.3 63.7 + - - +
409A ILE* 4.3 9.8 - - + +
422A LEU* 5.9 0.4 - - + -
424A LEU* 4.1 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A TYR* 3.5 47.5 + - + -
329A LEU 3.2 3.8 - - - +
330A GLN* 2.8 29.3 + - + +
362A LYS 3.8 0.3 - - - +
363A LEU* 3.5 9.5 - - - +
364A GLU* 2.8 69.9 + - + +
369A GLY 4.8 1.8 + - - -
372A TRP* 3.3 50.6 - - + +
407A VAL* 1.3 75.2 - - - +
409A ILE* 1.3 62.4 + - - +
410A ARG* 3.6 11.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A TYR* 3.2 5.4 - - - -
329A LEU* 2.9 32.1 + - + +
342A ILE* 3.9 40.4 - - + -
344A THR* 5.2 1.3 - - + -
361A TYR* 3.6 35.2 - - + -
362A LYS 3.7 1.8 - - - -
363A LEU* 4.1 12.6 - - + -
407A VAL* 4.3 7.9 - - + +
408A ARG* 1.3 73.0 - - - +
410A ARG* 1.3 63.0 + - - +
411A PRO* 3.4 6.3 - - + +
420A LEU* 3.8 26.5 - - + -
422A LEU* 4.0 26.2 - - + -
424A LEU* 4.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ASN 4.8 5.8 + - - +
326A LYS* 3.5 29.7 + - - +
327A GLU 3.6 7.5 + - - +
328A TYR* 3.9 23.7 - - + -
361A TYR* 3.9 2.5 - - - -
362A LYS* 2.9 38.0 + - + +
364A GLU* 2.6 49.2 + - + -
374A VAL* 5.6 4.5 - - - -
408A ARG* 3.6 23.2 - - + +
409A ILE* 1.3 78.4 - - - +
411A PRO* 1.4 61.5 - - - +
412A GLN* 2.7 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A TRP* 4.3 9.0 - - + -
324A SER 4.0 1.3 - - - +
325A ASN* 3.3 24.4 - - - -
327A GLU 3.6 14.6 - - - +
328A TYR* 4.5 1.6 - - - -
358A VAL* 3.7 28.3 - - + -
360A SER 3.5 7.4 - - - +
361A TYR* 4.0 2.2 - - + -
409A ILE* 3.4 13.2 - - + +
410A ARG* 1.4 86.0 - - - +
412A GLN* 1.3 59.9 + - - +
414A TRP* 4.4 2.0 - - + -
418A ILE* 3.9 39.5 - - + -
420A LEU* 4.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ASN* 3.6 33.1 + - - +
360A SER* 2.7 22.6 + - - +
361A TYR* 4.0 3.8 - - - -
362A LYS* 3.8 48.6 + - + +
383A VAL* 5.0 6.5 - - + -
410A ARG* 2.7 34.7 + - - +
411A PRO* 1.3 79.0 + - - +
413A THR* 1.3 66.7 + - + +
414A TRP* 3.2 17.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A VAL* 3.5 7.1 - - - +
359A LYS* 2.7 38.2 + - - +
360A SER* 2.5 35.9 + - - +
412A GLN* 1.3 85.3 - - + +
414A TRP* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ASP* 3.8 29.9 - - + +
324A SER* 3.5 36.8 - - - -
325A ASN* 3.7 3.8 - - + -
357A TYR 3.3 14.8 - - - +
358A VAL* 4.2 2.5 - - - -
359A LYS* 3.8 14.1 - - - +
411A PRO* 4.1 2.9 - - + -
412A GLN 3.2 26.0 - - - -
413A THR* 1.3 96.9 - - - +
415A HIS* 1.3 59.9 + - - +
416A SER 4.0 4.4 + - - -
417A GLY* 3.5 32.1 - - - +
418A ILE* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLY 4.1 6.7 - - - -
356A TYR* 3.7 0.9 - - - -
357A TYR* 2.9 67.1 + + + +
359A LYS* 3.9 6.5 - - + +
414A TRP* 1.3 70.8 - - - +
416A SER* 1.3 68.0 + - - +
417A GLY 2.6 24.0 + - - +
702A GOL 2.8 30.9 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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