Contacts of the helix formed by residues 41 - 59 (chain A) in PDB entry 4KEU
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 ASN 41 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 1.3 75.0 - - - +
42A GLU* 1.3 63.7 + - - +
43A ASP* 3.1 23.3 + - - +
44A GLU* 3.1 31.4 + - - +
45A GLU* 3.1 29.6 + - - +
47A ARG* 6.0 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 3.3 23.2 + - - -
33A ARG* 4.1 9.6 + - - +
40A TYR 4.0 1.6 + - - -
41A ASN* 1.3 72.1 + - - +
43A ASP* 1.3 69.8 + - - +
45A GLU* 3.4 11.9 + - - +
46A PHE* 3.0 27.3 + - + +
75A ASP* 5.5 0.5 - - - +
78A PHE* 3.6 18.4 - - - +
81A LYS* 4.1 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN* 3.1 10.5 + - - +
42A GLU* 1.3 84.2 - - - +
44A GLU* 1.3 63.7 + - - +
46A PHE* 3.3 8.5 + - - +
47A ARG* 3.0 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN* 3.1 30.6 + - - +
43A ASP* 1.3 77.5 - - - +
45A GLU* 1.3 66.4 + - + +
47A ARG* 3.2 30.5 + - - +
48A ASN* 2.9 47.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU 5.0 0.9 - - - +
26A ARG* 2.6 44.5 + - - +
33A ARG* 2.7 35.5 + - - -
40A TYR* 3.7 14.9 - - - +
41A ASN 3.1 14.8 + - - +
42A GLU* 3.5 9.4 - - - +
44A GLU* 1.3 76.3 - - + +
46A PHE* 1.3 63.3 + - - +
48A ASN* 3.5 1.7 + - - +
49A ALA* 3.0 25.3 + - - +
78A PHE* 3.7 6.0 - - + -
260A THR* 3.8 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLU* 3.0 21.4 + - - +
43A ASP* 3.5 8.1 - - - +
45A GLU* 1.3 77.2 - - - +
47A ARG* 1.4 62.7 + - + +
49A ALA* 3.4 1.4 + - - +
50A VAL* 2.9 55.8 + - + +
78A PHE* 3.8 16.4 - + + -
81A LYS* 3.6 45.1 - - + -
82A VAL* 3.7 11.9 - - + -
85A ALA* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN* 6.0 0.8 - - - +
43A ASP* 3.0 41.1 + - + +
44A GLU* 3.6 37.1 + - - +
46A PHE* 1.4 80.4 - - + +
48A ASN* 1.3 60.6 + - - +
50A VAL* 3.5 4.3 + - - +
51A ASN* 2.9 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 2.9 39.9 + - - +
45A GLU 3.8 3.4 - - - +
47A ARG* 1.3 79.8 + - - +
49A ALA* 1.3 57.6 + - - +
51A ASN* 3.4 6.4 + - - +
52A GLU* 2.9 35.7 + - + +
259A CYS* 3.5 20.5 + - - +
260A THR* 3.8 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.8 25.4 - - + +
45A GLU 3.0 18.3 + - - +
46A PHE 3.8 2.9 - - - +
48A ASN* 1.3 76.2 - - - +
50A VAL* 1.3 63.3 + - - +
52A GLU* 3.4 1.2 + - - +
53A VAL* 3.0 30.9 + - - +
78A PHE* 4.2 6.1 - - + -
82A VAL* 4.0 20.0 - - + -
259A CYS* 3.7 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 2.9 56.4 + - + +
47A ARG* 3.9 4.5 - - - +
49A ALA* 1.3 75.8 - - - +
51A ASN* 1.3 63.5 + - - +
53A VAL 3.5 0.2 + - - -
54A LYS* 2.9 57.3 + - + +
82A VAL* 4.4 10.1 - - + -
85A ALA* 4.0 14.6 - - + -
86A THR* 3.8 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 2.9 31.4 + - - +
48A ASN* 3.8 7.1 - - - +
50A VAL* 1.3 83.2 - - - +
52A GLU* 1.3 65.9 + - - +
54A LYS* 3.5 12.5 + - - +
55A ARG* 3.1 26.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 2.9 22.3 + - + +
49A ALA 3.7 0.4 - - - +
51A ASN* 1.3 76.0 - - - +
53A VAL* 1.3 63.8 + - - +
55A ARG* 2.3 38.4 + - - +
56A ALA 3.1 17.5 + - - -
257A TYR* 3.4 30.0 + - + +
259A CYS* 3.6 22.4 - - + -
279A SER* 4.0 3.3 - - - -
280A ILE* 3.2 47.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.6 27.6 - - + -
49A ALA 3.0 21.5 + - - +
50A VAL 3.9 3.4 - - - +
52A GLU* 1.3 75.7 - - + +
54A LYS* 1.3 63.5 + - - +
56A ALA* 3.2 7.5 + - - +
57A MET* 2.9 32.3 + - + +
64A ILE* 4.2 13.5 - - + -
82A VAL* 4.0 7.9 - - + -
86A THR* 3.6 29.6 - - + +
88A ILE* 3.7 25.6 - - + -
259A CYS* 5.3 0.2 - - - -
280A ILE* 5.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 2.9 37.4 + - + +
51A ASN* 3.8 12.5 - - - +
52A GLU 3.3 0.2 - - - -
53A VAL* 1.3 76.7 - - - +
55A ARG* 1.3 61.7 + - - +
57A MET* 3.3 11.3 + - - +
58A GLN* 3.0 32.1 + - - +
85A ALA 3.8 21.2 + - - -
86A THR* 4.1 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASN* 3.1 14.2 + - - +
52A GLU* 2.3 56.4 + - - +
54A LYS* 1.3 75.8 - - - +
56A ALA* 1.4 62.1 + - - +
58A GLN* 3.2 29.5 + - - +
59A PHE* 3.4 29.6 + - + -
279A SER* 3.8 12.0 + - - -
280A ILE* 4.0 0.8 - - - +
281A THR* 3.0 39.2 + - + +
285A GLU* 4.9 3.1 + - - -
292B LYS* 4.2 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 4.5 4.0 - - + -
52A GLU 3.1 13.6 + - - +
53A VAL* 3.2 11.2 + - - +
55A ARG* 1.4 74.6 - - - +
57A MET* 1.3 61.9 + - - +
59A PHE* 3.1 10.7 + - - +
60A GLY 3.4 0.2 + - - -
61A VAL* 3.1 45.4 + - + +
64A ILE* 4.7 2.9 - - + -
280A ILE* 4.0 21.8 - - + +
281A THR* 3.7 11.8 - - + +
284A PHE* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 2.9 28.2 + - - +
54A LYS* 3.7 8.7 - - - +
55A ARG 3.2 0.2 - - - -
56A ALA* 1.3 73.2 - - - +
58A GLN* 1.3 64.7 + - - +
60A GLY* 3.1 13.2 + - - -
61A VAL 3.7 15.4 + - - +
62A LYS* 5.5 2.2 - - - +
86A THR* 3.6 27.8 - - - +
87A GLY 4.0 5.4 - - - +
88A ILE* 3.7 48.7 - - + +
58B GLN 5.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS* 3.0 21.4 + - + +
55A ARG* 3.2 30.6 + - - +
57A MET* 1.3 78.1 - - + +
59A PHE* 1.3 60.2 + - + +
60A GLY 3.3 1.1 - - - -
58B GLN 3.4 14.6 - - - +
59B PHE* 3.6 18.5 - - - +
60B GLY* 5.1 0.5 - - - -
292B LYS* 4.7 8.7 - - - +
298B GLU* 5.0 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ARG* 3.4 31.5 + - + -
56A ALA 3.1 9.6 + - - +
58A GLN* 1.3 79.7 - - + +
60A GLY* 1.3 58.2 + - - +
61A VAL 3.6 0.9 - - - -
281A THR* 3.8 31.2 - - + -
284A PHE* 3.6 47.9 - + + -
285A GLU* 4.5 9.4 - - + -
58B GLN* 3.1 23.1 + - - -
59B PHE* 3.5 30.5 - + + -
284B PHE* 3.4 43.3 - + + -
285B GLU* 5.1 0.4 - - - -
289B PRO* 5.1 1.8 - - + -
----------------------------------------------------------
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