Contacts of the strand formed by residues 404 - 423 (chain A) in PDB entry 4NYK
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 ILE 404 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A LEU* 3.9 26.7 - - + -
222A MET* 4.7 13.9 - - + -
223A LEU 3.4 6.5 - - - +
224A ASP* 4.1 12.8 - - + -
269A GLY* 2.5 39.0 + - - -
380A ILE* 3.8 30.3 - - + +
389A LEU* 5.0 3.8 - - + -
393A TYR* 5.8 2.0 - - + -
399A TYR* 4.5 3.1 - - + -
400A ILE* 3.2 52.9 + - + +
403A ASN* 1.3 86.7 - - + +
405A LEU* 1.3 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A ILE 4.8 0.4 - - - +
222A MET* 3.2 4.7 - - - +
223A LEU* 2.8 51.3 + - + +
225A ILE* 3.7 27.8 - - + -
245A GLY* 5.1 0.2 - - - -
246A ILE* 4.0 33.2 - - + +
266A VAL* 4.0 30.1 - - + +
267A ALA 4.1 6.5 - - - +
268A PRO* 4.2 8.5 - - + -
270A PHE 3.6 8.3 - - - -
380A ILE* 4.6 0.4 - - - -
403A ASN 4.4 0.9 - - - +
404A ILE* 1.3 82.5 - - - +
406A VAL* 1.3 70.0 + - - +
407A LEU* 4.4 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLU* 3.6 30.1 - - + +
221A ILE 3.4 6.1 - - - +
222A MET* 3.6 26.0 - - + -
266A VAL* 5.0 1.0 - - - +
270A PHE 3.2 7.4 + - - +
271A GLN* 3.3 27.4 - - + +
272A THR* 2.9 27.5 + - - -
380A ILE* 3.5 28.3 - - + -
405A LEU* 1.3 80.7 - - - +
407A LEU* 1.3 63.8 + - - +
408A ASP* 3.7 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 5.5 1.3 - - + -
93A PHE* 5.9 1.6 - - + -
219A LEU* 3.7 1.8 - - + +
220A GLU* 3.2 4.9 - - - -
221A ILE* 2.8 56.5 + - + +
223A LEU* 6.1 0.2 - - + -
246A ILE* 4.6 8.1 - - + -
248A VAL* 4.1 25.1 - - + -
264A PHE* 4.9 1.8 - - + -
266A VAL* 3.9 26.9 - - + -
272A THR* 3.7 9.6 - - - +
274A VAL* 4.1 20.0 - - + -
405A LEU* 4.4 8.5 - - + -
406A VAL* 1.3 74.6 - - - +
408A ASP* 1.3 66.0 + - - +
409A ILE* 4.1 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A THR* 4.3 14.9 - - + +
219A LEU 3.4 5.0 - - - +
220A GLU* 2.7 34.5 - - - +
271A GLN* 2.7 32.9 + - - +
272A THR 2.9 11.5 + - - +
273A PHE* 4.1 17.0 - - + -
274A VAL* 2.7 34.8 + - - +
406A VAL* 3.7 2.1 - - - +
407A LEU* 1.3 77.5 - - - +
409A ILE* 1.3 59.8 + - - +
410A PHE* 4.0 10.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
88A PHE* 3.9 15.7 - - + -
89A PRO* 5.8 2.0 - - + -
91A VAL* 3.7 36.6 - - + -
218A GLY* 3.5 2.3 - - - -
219A LEU* 2.9 50.6 + - + +
248A VAL* 4.6 4.5 - - + -
250A ILE* 3.6 31.2 - - + -
264A PHE* 5.0 2.7 - - + -
274A VAL* 3.6 7.6 - - + +
276A CYS* 4.3 7.9 - - - -
407A LEU* 4.1 27.6 - - + +
408A ASP* 1.3 77.0 - - - +
410A PHE* 1.3 64.0 + - - +
411A PHE* 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 4.9 0.7 - - - -
214A GLY* 3.3 33.2 - - - +
215A THR* 3.5 34.1 - - + +
217A ASN 5.0 0.4 - - - -
218A GLY* 4.4 7.9 - - - -
273A PHE* 4.0 25.4 - + + -
274A VAL 3.1 13.6 + - - +
275A SER* 3.6 28.5 - - - -
276A CYS* 2.7 35.7 + - - +
408A ASP* 4.0 9.9 - - + -
409A ILE* 1.3 80.1 - - - +
411A PHE* 1.3 77.8 + - - +
412A GLU* 5.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 4.1 13.7 - - + -
88A PHE* 4.0 27.6 - + - -
89A PRO* 3.9 23.3 - - + -
210A THR* 4.6 12.3 - - + +
212A LYS 4.8 6.4 + - - +
213A GLY* 3.2 2.3 - - - -
214A GLY 2.9 26.4 + - - +
217A ASN 5.6 1.2 + - - -
275A SER* 4.5 0.7 - - - -
276A CYS* 3.3 27.8 - - + -
277A GLN 3.6 7.2 - - - -
278A GLU* 3.6 27.4 - - + -
371A TYR* 4.2 10.8 - + - -
409A ILE* 5.8 1.1 - - + -
410A PHE* 1.3 91.2 - - - +
412A GLU* 1.3 60.3 + - - +
415A ASN* 3.6 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 412 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A GLY* 3.3 11.4 - - - -
214A GLY 4.7 0.9 - - - +
275A SER* 3.9 20.4 + - - +
276A CYS 3.2 15.8 + - - +
277A GLN* 3.6 25.0 + - - +
374A GLU* 4.3 16.5 - - - +
410A PHE* 5.3 1.8 - - - -
411A PHE* 1.3 78.4 - - - +
413A ALA* 1.3 67.4 + - - +
414A LEU* 3.7 20.5 - - - +
415A ASN* 3.4 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 413 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA* 3.5 21.8 - - + +
212A LYS 5.6 0.3 - - - -
213A GLY* 4.0 14.1 + - - +
412A GLU* 1.3 76.9 - - - +
414A LEU* 1.3 65.6 + - + +
415A ASN* 3.1 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 414 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 4.2 22.2 - - + +
81A VAL* 3.6 16.6 - - - +
82A ALA* 3.8 21.3 - - + +
277A GLN* 2.5 39.7 + - - +
412A GLU* 3.7 15.8 - - - +
413A ALA* 1.3 76.2 - - + +
415A ASN* 1.3 57.5 + - - +
416A TYR 3.4 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 415 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL 3.3 0.4 + - - -
82A ALA* 3.7 0.9 - - - -
83A ALA* 2.8 37.5 + - - +
86A LEU* 3.9 21.2 - - + +
210A THR* 4.8 3.0 + - - +
211A MET 4.1 19.0 + - - -
212A LYS 4.3 9.9 + - - -
277A GLN* 3.6 4.7 - - - +
278A GLU* 2.7 34.1 + - - +
411A PHE* 3.6 24.9 - - + +
412A GLU 3.4 17.5 - - - +
413A ALA 3.1 6.3 + - - -
414A LEU* 1.3 71.7 - - - +
416A TYR* 1.3 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 3.6 1.7 - - - +
81A VAL* 2.8 50.6 + - + +
83A ALA* 3.7 23.8 - - + -
86A LEU* 3.5 21.8 - - + -
277A GLN* 4.8 1.3 - - - -
278A GLU* 3.4 27.4 - - + -
280A ARG* 3.6 38.1 + - + +
414A LEU 3.4 2.1 - - - -
415A ASN* 1.3 83.9 + - - +
417A GLU* 1.3 64.7 + - - +
418A THR* 3.3 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LEU* 3.2 31.9 - - - +
79A ASP 3.3 7.2 - - - +
80A GLU* 3.5 25.0 - - + +
277A GLN* 3.4 21.8 - - - +
278A GLU 2.6 14.0 + - - +
279A GLN* 3.2 22.3 + - + -
280A ARG* 2.7 34.1 + - - +
416A TYR* 1.3 79.1 - - - +
418A THR* 1.3 60.7 + - - +
419A ILE* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 3.3 9.6 - - - +
78A LEU* 3.2 6.8 - - - +
79A ASP* 3.0 43.0 + - - +
81A VAL* 5.9 0.2 - - - +
280A ARG* 3.4 6.1 - - + +
282A ILE* 4.1 25.6 - - + -
416A TYR* 3.3 29.0 + - - +
417A GLU* 1.3 72.5 - - - +
419A ILE* 1.3 65.4 + - - +
420A GLU* 3.8 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A THR* 3.7 22.4 - - + -
77A LYS 3.7 2.5 - - - -
78A LEU* 3.7 22.7 - - + +
279A GLN* 4.4 14.4 - - + +
280A ARG 2.8 12.4 + - - +
281A LEU* 3.6 35.2 - - + +
282A ILE 3.1 21.8 + - - +
283A TYR* 5.7 1.0 - - - -
417A GLU* 4.0 22.9 - - + +
418A THR* 1.3 79.0 - - - +
420A GLU* 1.3 57.0 + - - +
421A GLN* 4.0 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 2.8 58.7 + - + +
282A ILE* 3.5 41.6 - - + +
418A THR* 3.8 7.8 - - + +
419A ILE* 1.3 72.5 - - - +
421A GLN* 1.3 75.5 + - - +
422A LYS* 3.1 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A HIS* 2.9 34.9 + - + +
75A VAL 3.3 1.9 + - - -
76A THR* 3.1 37.6 + - - +
282A ILE* 3.0 17.5 + - - +
283A TYR* 4.3 21.8 - - + -
284A LEU* 3.7 37.8 - - + +
419A ILE* 4.2 10.4 - - - +
420A GLU* 1.3 83.5 - - - +
422A LYS* 1.3 62.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A HIS* 3.2 2.1 - - - -
75A VAL* 2.7 50.2 + - + +
76A THR 5.0 0.7 - - - -
77A LYS* 3.8 33.3 - - + +
284A LEU* 4.1 6.1 - - - -
420A GLU* 3.1 45.4 + - - +
421A GLN* 1.3 77.2 - - - +
423A LYS* 1.3 65.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 423 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PRO 4.1 4.9 - - - -
74A HIS* 4.5 1.1 - - - +
75A VAL* 4.9 1.9 - - - +
284A LEU* 4.2 20.6 - - + -
285A PRO* 5.9 1.3 - - - -
288A TRP* 3.5 60.7 - - + +
422A LYS* 1.3 76.6 - - - +
424A ALA* 1.3 62.0 + - - +
425A TYR 3.6 3.1 - - - +
426A GLU* 3.4 37.4 + - - +
----------------------------------------------------------
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