Contacts of the helix formed by residues 387 - 407 (chain A) in PDB entry 4KYI
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 THR 387 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A SER 4.1 1.2 + - - -
386A PRO* 1.3 75.5 - - - +
388A PRO* 1.3 71.8 - - - +
389A GLU* 2.9 26.0 + - + +
390A GLN* 2.9 40.9 + - + +
391A ARG* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A PRO 3.8 4.0 - - - +
387A THR* 1.3 88.9 - - - +
389A GLU* 1.3 64.1 + - + +
391A ARG* 3.8 18.7 - - + +
392A ALA* 3.4 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A THR* 3.2 22.7 - - + +
388A PRO* 1.3 82.9 - - + +
390A GLN* 1.3 58.6 + - - +
391A ARG 3.2 4.1 + - - -
392A ALA* 3.5 3.7 + - - +
393A ARG* 3.3 18.6 + - - +
139E GLN 4.6 13.6 - - - +
140E PRO* 5.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 3.1 49.6 + - + +
379A VAL* 3.4 17.0 - - - +
383A ASN* 3.0 31.9 + - - +
385A SER 4.7 0.4 + - - -
386A PRO* 3.3 24.2 - - + +
387A THR* 2.9 31.4 + - + +
389A GLU* 1.3 75.3 - - + +
391A ARG* 1.3 60.1 + - - +
393A ARG* 3.8 12.4 - - + +
394A ALA 3.6 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.3 44.2 - - + +
96A GLU* 2.8 39.4 + - - +
98A LEU 5.4 0.6 - - - +
99A ASP* 4.6 14.7 + - - -
379A VAL* 4.8 5.4 - - + -
386A PRO* 4.1 30.5 + - + +
387A THR 2.9 18.4 + - - +
388A PRO* 3.9 14.0 - - + +
389A GLU 3.2 0.2 - - - -
390A GLN* 1.3 76.4 - - - +
392A ALA* 1.3 57.1 + - - +
393A ARG 3.0 4.0 - - - -
394A ALA* 3.1 20.9 + - - +
395A VAL* 3.2 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A PRO 3.4 16.4 + - - +
389A GLU* 4.0 3.8 - - - +
391A ARG* 1.3 77.3 - - - +
393A ARG* 1.3 60.8 + - - +
395A VAL* 3.8 13.0 - - + +
396A LYS* 3.3 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 5.2 7.2 - - - +
389A GLU 3.3 15.2 + - - +
390A GLN* 3.8 14.8 - - + +
391A ARG 3.0 0.2 - - - -
392A ALA* 1.3 76.9 - - - +
394A ALA* 1.3 64.2 + - - +
396A LYS* 3.4 28.9 + - - +
397A ASN* 3.2 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 5.4 3.4 - - + +
49A SER* 4.3 30.2 - - - +
374A ILE* 4.5 4.7 - - - +
375A ASN 4.4 11.0 - - - +
376A THR 4.1 8.3 - - - +
379A VAL* 3.7 28.9 - - + -
390A GLN 3.6 1.6 + - - +
391A ARG* 3.1 9.5 + - - +
393A ARG* 1.3 79.2 - - - +
395A VAL* 1.3 61.3 + - + +
397A ASN* 4.1 2.8 - - - +
398A GLY* 3.6 12.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.8 28.5 - - + +
49A SER 5.5 0.2 - - - -
51A LEU* 4.2 18.6 - - + -
52A GLY* 3.5 30.0 - - - +
55A GLN* 4.7 9.6 - - - +
96A GLU* 5.5 4.5 - - + +
391A ARG 3.2 16.8 + - - +
392A ALA* 3.9 12.6 - - - +
393A ARG 3.1 0.6 - - - -
394A ALA* 1.3 76.7 - - - +
396A LYS* 1.3 60.3 + - - +
397A ASN 3.2 0.2 - - - -
398A GLY 3.2 2.1 + - - -
399A TYR* 2.9 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ALA 3.3 14.7 + - - +
393A ARG* 3.4 27.8 + - - +
395A VAL* 1.3 76.5 - - - +
397A ASN* 1.3 61.4 + - - +
399A TYR* 3.6 10.3 - - + +
400A ASP* 2.3 73.6 + - - +
135E GLU 5.8 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PHE* 4.3 8.2 - - - -
373A TYR 4.3 2.6 - - - +
374A ILE* 3.6 5.5 - - - +
375A ASN* 2.7 55.5 + - + +
393A ARG* 3.2 22.7 + - - +
394A ALA 4.1 5.2 - - - +
396A LYS* 1.3 76.5 - - - +
398A GLY* 1.3 58.3 + - - +
400A ASP* 3.8 4.3 - - - +
401A GLN* 2.8 47.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER 4.6 2.2 - - - -
52A GLY 3.9 6.3 - - - -
53A MET* 3.8 4.6 - - - -
374A ILE* 4.1 30.7 - - - +
394A ALA 3.6 6.7 + - - -
395A VAL 3.2 7.0 + - - -
397A ASN* 1.3 80.5 + - - +
399A TYR* 1.3 55.4 + - - +
401A GLN* 4.5 1.1 - - - +
402A THR* 2.4 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLY* 3.4 21.7 - - - +
55A GLN* 4.5 14.4 - - + +
56A ALA* 3.8 14.3 - - + +
59A GLU* 2.7 41.5 + - - -
395A VAL* 2.9 17.1 + - + +
396A LYS* 3.6 11.7 - - + +
397A ASN 3.2 0.2 - - - -
398A GLY* 1.3 76.9 - - - +
400A ASP* 1.3 77.3 + - - +
402A THR* 3.4 2.6 + - - -
403A MET* 3.0 54.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A LYS* 2.3 60.0 + - - +
397A ASN* 4.1 3.8 - - - +
399A TYR* 1.3 90.2 - - - +
401A GLN* 1.3 60.5 + - - +
403A MET* 3.4 5.4 + - - +
404A GLN* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A PHE* 3.3 32.2 - - - -
320A ARG* 4.3 10.1 - - - +
321A VAL* 5.2 2.0 - - - +
372A ILE* 4.6 5.0 - - + +
373A TYR* 3.0 31.5 - - + +
397A ASN* 2.8 27.3 + - - +
398A GLY* 4.5 2.2 - - - +
400A ASP* 1.3 76.6 - - - +
402A THR* 1.3 60.9 + - - +
404A GLN* 3.4 27.7 + - - +
405A LEU* 3.0 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 3.5 21.6 - - + +
56A ALA* 3.7 23.6 - - + -
57A LEU* 3.8 20.6 - - + -
372A ILE* 3.6 32.7 - - + +
398A GLY* 2.4 26.3 + - - -
399A TYR 3.8 0.2 - - - -
401A GLN* 1.3 77.2 - - - +
403A MET* 1.3 63.0 + - - +
405A LEU* 3.5 3.3 + - - +
406A LEU* 3.1 26.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA* 3.5 32.1 - - - +
59A GLU* 3.6 35.4 - - + +
60A ARG* 3.7 44.6 - - + +
399A TYR* 3.0 32.0 + - + +
400A ASP* 3.6 7.9 - - - +
402A THR* 1.3 77.1 - - - +
404A GLN* 1.3 63.0 + - - +
406A LEU* 3.3 4.5 + - - +
407A ASP* 3.0 33.0 + - - +
172E ASN* 6.2 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASP 2.8 22.4 + - - +
401A GLN* 3.7 30.7 - - - +
403A MET* 1.3 72.0 - - - +
405A LEU* 1.3 62.8 + - - +
407A ASP* 3.5 19.0 + - - +
408A SER* 3.7 8.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
307A LEU* 4.5 3.8 - - + -
369A ASP* 3.2 47.6 - - - +
370A ASN* 3.5 15.7 - - - +
371A MET 3.3 15.5 - - - +
372A ILE* 3.5 31.2 - - + -
401A GLN 3.0 16.7 + - - +
402A THR 3.8 4.3 - - - +
404A GLN* 1.3 74.5 - - - +
406A LEU* 1.3 60.6 + - + +
407A ASP 3.1 1.6 - - - -
408A SER* 2.4 35.2 + - - +
409A HIS* 3.7 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA 4.9 1.3 - - - +
57A LEU* 3.9 24.0 - - + -
60A ARG* 3.7 34.4 + - + +
62A LYS* 4.2 20.9 - - + -
307A LEU* 4.4 17.3 - - + -
372A ILE* 5.4 0.7 - - + -
402A THR* 3.1 26.9 + - + +
403A MET* 3.8 7.2 - - - +
405A LEU* 1.3 82.6 - - + +
407A ASP* 1.3 57.9 + - - +
408A SER 3.0 3.2 + - - -
409A HIS* 3.2 44.3 + - + +
410A LYS* 4.0 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 2.6 33.1 + - - -
403A MET* 3.0 23.3 + - - +
404A GLN* 3.6 11.8 - - - +
405A LEU 3.1 0.6 - - - -
406A LEU* 1.3 74.8 - - - +
408A SER* 1.3 56.5 + - - +
409A HIS 3.4 2.0 - - - -
410A LYS* 3.1 28.6 + - - +
89E LYS* 3.4 33.3 + - - +
----------------------------------------------------------
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