Contacts of the helix formed by residues 44 - 62 (chain A) in PDB entry 4KZK
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 ASP 44 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 3.0 30.0 + - + +
42A PRO 3.9 4.1 - - - +
43A ASP* 1.3 77.7 + - - +
45A PRO* 1.3 73.5 - - - +
46A TRP* 2.9 21.8 + - - +
47A PHE* 3.0 21.8 + - + +
48A GLN 3.6 5.2 + - - -
235A ASN* 3.8 4.4 + - - -
237A ASP* 3.7 22.8 - - - +
262A ASN* 4.0 2.4 + - - -
600A GAL 2.6 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASP 3.9 7.1 - - - +
44A ASP* 1.3 85.6 - - - +
46A TRP* 1.3 59.2 + - - +
47A PHE 3.2 0.2 - - - -
48A GLN* 3.2 16.4 + - + +
49A ASP* 2.8 32.1 + - - +
237A ASP* 4.3 0.2 - - - +
264A SER* 3.4 12.8 - - - +
265A GLN* 3.7 36.6 - - + +
266A VAL* 3.8 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 2.9 16.1 + - - +
45A PRO* 1.3 79.9 - - - +
47A PHE* 1.3 71.0 + + - +
49A ASP* 3.1 9.7 + - - +
50A GLU* 2.9 42.8 + - + +
119A ASP* 3.3 11.0 + - - -
262A ASN* 3.7 33.2 - - + +
264A SER* 3.8 7.2 + - - -
285A LEU* 3.5 33.0 - - + -
286A ASN 3.8 3.1 - - - -
287A PRO* 3.6 40.6 - - + -
290A HIS* 3.6 33.0 - + + -
600A GAL 3.6 31.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.6 29.6 - - + +
40A LYS* 3.8 25.4 - - + -
41A GLN* 3.4 29.2 - - + +
42A PRO* 4.8 1.6 - - + -
44A ASP* 3.0 28.9 + - - +
46A TRP* 1.3 82.8 - + - +
48A GLN* 1.3 66.8 + - - +
50A GLU* 3.2 21.7 + - - +
51A TRP* 3.0 29.5 + - - +
94A CYS* 3.7 30.7 - - + -
119A ASP* 3.3 23.6 - - - -
600A GAL 4.0 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 2.9 32.6 + - - +
44A ASP 3.6 4.2 + - - +
45A PRO* 3.2 16.5 + - + +
47A PHE* 1.3 80.5 - - - +
49A ASP* 1.3 58.8 + - - +
51A TRP* 3.3 35.9 + - - +
52A ARG* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 2.8 14.9 + - - +
46A TRP* 3.4 9.9 - - - +
48A GLN* 1.3 76.4 - - - +
50A GLU* 1.3 65.8 + - - +
52A ARG* 3.3 23.2 + - - +
53A PHE* 3.1 30.8 + - + -
264A SER* 2.6 31.7 + - - -
265A GLN* 5.0 8.9 - - - +
287A PRO* 3.6 28.0 - - + +
328A ARG* 5.0 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.4 31.0 - - + -
39A VAL* 4.2 0.2 - - - +
46A TRP* 2.9 35.0 + - + +
47A PHE* 3.2 28.0 + - - +
49A ASP* 1.3 77.8 - - - +
51A TRP* 1.3 57.9 + - - +
53A PHE 3.3 0.3 + - - -
54A ALA* 2.8 30.6 + - - +
118A VAL* 3.6 3.5 - - - +
119A ASP* 2.6 31.0 - - - +
287A PRO* 4.2 5.1 - - + +
290A HIS* 3.4 27.1 - - + +
291A GLY* 3.4 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.0 43.6 + + + -
39A VAL* 3.5 32.1 - - + +
42A PRO* 4.4 10.5 - - + -
47A PHE 3.0 15.0 + - - +
48A GLN* 3.6 45.1 - - - +
49A ASP 3.2 0.2 - - - -
50A GLU* 1.3 74.5 - - - +
52A ARG* 1.3 58.6 - - - +
54A ALA* 3.3 3.8 + - - +
55A GLU* 2.9 33.9 + - - +
65A LEU* 4.0 1.8 - - + +
67A LYS* 3.5 41.1 - - + +
68A ILE 3.6 30.3 - - - -
69A ALA* 4.2 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN 3.0 16.7 + - - +
49A ASP* 3.3 24.3 + - - +
51A TRP* 1.3 75.0 - - - +
53A PHE* 1.3 96.4 + - + +
55A GLU* 3.4 10.7 + - - +
56A GLN* 3.2 26.3 + - - +
287A PRO* 5.5 0.4 - - - +
328A ARG* 4.8 4.9 - - - +
332A GLY 5.3 1.0 + - - -
333A LEU* 3.3 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASP 3.1 22.9 + - - +
50A GLU 3.9 0.9 - - - +
52A ARG* 1.3 112.3 - - + +
54A ALA* 1.3 57.9 + - - +
56A GLN* 3.1 22.7 + - - +
57A ALA 3.0 22.5 + - - -
287A PRO* 3.8 32.3 - - + +
288A ARG* 3.3 57.4 - - + -
292A TYR* 3.3 24.3 - - + +
332A GLY 4.1 3.8 - - - -
333A LEU* 3.9 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.8 18.4 - - + -
50A GLU 2.8 16.8 + - - +
51A TRP* 3.6 7.0 - - - +
53A PHE* 1.3 76.4 - - - +
55A GLU* 1.3 56.4 + - - +
57A ALA* 3.2 5.6 + - - +
58A ALA* 3.0 25.5 + - - +
63A PHE* 4.1 4.3 - - - -
65A LEU* 3.8 16.3 - - + +
291A GLY 3.4 12.6 + - - +
295A SER* 3.4 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TRP 2.9 19.3 + - - +
52A ARG* 3.4 13.0 - - - +
53A PHE 3.2 0.2 - - - -
54A ALA* 1.3 73.9 - - - +
56A GLN* 1.3 63.8 + - - +
58A ALA* 3.2 8.6 + - - +
59A LYS* 3.0 23.4 + - - +
65A LEU* 3.4 31.2 - - + +
67A LYS* 3.4 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 3.2 12.1 + - - +
53A PHE* 3.1 35.2 + - - +
55A GLU* 1.3 78.9 - - - +
57A ALA* 1.3 58.1 + - - +
59A LYS* 3.4 4.9 + - - +
60A ASP* 2.9 44.2 + - - +
288A ARG* 2.7 27.7 + - - +
292A TYR* 3.6 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE 3.0 8.0 + - - +
54A ALA 3.2 9.8 + - - +
56A GLN* 1.3 77.7 - - - +
58A ALA* 1.3 56.5 + - - +
60A ASP* 4.5 0.2 - - - -
61A LYS* 2.8 30.2 + - - +
63A PHE* 3.4 11.9 - - + -
292A TYR* 3.3 32.5 - - + +
295A SER* 3.7 24.9 - - - -
296A VAL* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA 3.0 13.3 + - - +
55A GLU* 3.2 15.5 + - - +
57A ALA* 1.3 73.8 - - - +
59A LYS* 1.3 59.9 + - - +
62A HIS* 2.9 27.0 + - - -
63A PHE* 3.1 47.7 + - + +
65A LEU* 4.1 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLU 3.0 15.6 + - - +
56A GLN* 3.9 5.2 - - - +
58A ALA* 1.3 77.4 - - - +
60A ASP* 1.3 69.3 + - - +
62A HIS* 3.6 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLN* 2.9 27.3 + - - +
57A ALA 3.8 2.5 - - - +
59A LYS* 1.3 80.7 - - - +
61A LYS* 1.3 62.9 + - + +
62A HIS* 3.3 22.3 + - - -
292A TYR* 2.7 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA 2.8 21.2 + - - +
60A ASP* 1.3 77.1 - - + +
62A HIS* 1.3 77.4 + - - +
63A PHE* 3.5 15.3 - - + -
292A TYR* 5.3 2.5 - - - +
296A VAL* 4.0 34.2 - - + +
299A TYR* 3.3 51.0 + - + -
300A ASP* 3.9 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 4.9 5.4 + - - +
58A ALA 2.9 12.8 + - - -
59A LYS 3.6 9.9 + - - -
60A ASP 3.3 17.9 + - - -
61A LYS* 1.3 84.6 + - - +
63A PHE* 1.3 57.3 + - - +
299A TYR* 4.7 4.4 + - - +
----------------------------------------------------------
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