Contacts of the helix formed by residues 55 - 70 (chain F) in PDB entry 1ZUM
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 55 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F SER* 6.0 4.7 - - - +
35F LYS* 5.2 9.3 + - - -
53F GLU* 4.7 8.6 - - + +
54F GLY* 1.3 73.7 - - - -
56F LYS* 1.3 84.5 + - - +
57F GLU* 3.3 4.3 - - + +
58F ASP* 2.9 22.9 + - - +
59F VAL* 3.0 18.0 + - - +
227F THR* 3.5 33.6 - - - +
228F ALA* 4.5 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 56 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ASP* 1.3 85.5 + - - +
57F GLU* 1.3 60.5 + - + +
59F VAL* 3.2 3.3 + - - +
60F ASP* 2.9 29.2 + - + +
227F THR 4.8 0.6 + - - +
231F ALA* 3.7 27.8 - - + +
234F SER* 6.1 1.1 - - - -
235F HIS* 5.8 1.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 57 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F VAL* 3.0 39.0 - - + +
55F ASP* 3.1 2.8 + - + +
56F LYS* 1.3 78.3 - - + +
58F ASP* 1.3 65.7 + - - +
60F ASP* 3.8 7.1 - - - +
61F LYS* 3.2 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ILE* 3.5 27.7 - - + +
24F ILE* 3.7 5.9 - - + +
30F ASP 4.1 2.3 - - - +
31F ALA* 3.3 8.7 - - - +
32F VAL* 2.9 37.3 + - - +
33F SER* 5.1 1.2 + - - -
54F GLY* 3.4 5.0 - - - -
55F ASP* 2.9 33.0 + - - +
57F GLU* 1.3 74.4 + - - +
59F VAL* 1.3 65.5 + - - +
61F LYS* 3.2 13.9 + - - +
62F ALA* 3.0 22.5 + - - +
221F VAL* 4.2 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ASP 3.0 15.3 + - - +
56F LYS 3.2 8.0 + - - +
58F ASP* 1.3 77.8 - - - +
60F ASP* 1.3 54.6 + - - +
62F ALA* 3.1 8.0 + - - +
63F VAL* 2.9 46.5 + - + +
190F VAL* 4.8 1.3 - - + -
221F VAL* 4.2 16.4 - - + -
228F ALA* 3.6 27.8 - - + +
231F ALA* 4.0 13.5 - - + +
232F ILE* 3.7 37.0 - - + +
235F HIS* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F LYS* 2.9 18.8 + - + +
57F GLU* 3.8 9.0 - - - +
58F ASP 3.3 0.2 - - - -
59F VAL* 1.3 77.2 - - - +
61F LYS* 1.3 63.4 + - - +
63F VAL* 3.4 1.0 + - - +
64F LYS* 3.0 54.4 + - - +
235F HIS* 3.0 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ILE* 3.9 20.0 - - + +
29F HIS* 3.9 35.5 + - - +
30F ASP 4.7 5.1 + - - -
32F VAL* 4.1 23.5 - - + +
57F GLU 3.2 14.3 + - - +
58F ASP* 3.2 12.8 + - - +
60F ASP* 1.3 82.2 - - + +
62F ALA* 1.3 56.2 + - - +
64F LYS* 3.3 9.8 + - + +
65F ALA* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ILE* 3.7 15.2 - - + +
58F ASP 3.0 13.7 + - - +
59F VAL 3.1 8.3 + - - +
61F LYS* 1.3 75.2 - - - +
63F VAL* 1.3 57.9 + - - +
65F ALA* 3.2 3.3 + - - +
66F ALA* 2.9 28.9 + - - +
190F VAL* 3.9 15.3 - - + -
219F ASN* 3.6 16.9 + - + -
221F VAL* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F VAL* 2.9 29.2 + - + +
60F ASP 3.8 4.7 - - - +
62F ALA* 1.3 75.7 - - - +
64F LYS* 1.3 57.9 + - + +
66F ALA* 3.4 2.1 + - - +
67F ARG* 2.9 27.7 + - - +
161F VAL* 4.5 4.8 - - + +
190F VAL* 3.9 17.3 - - + -
235F HIS* 3.6 41.7 - - + +
237F ASP* 4.0 25.4 - - + +
238F VAL* 3.9 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F ASP* 3.0 49.3 + - - +
61F LYS* 3.7 9.2 - - + +
63F VAL* 1.3 79.3 - - + +
65F ALA* 1.3 61.5 + - - +
67F ARG* 3.4 5.9 + - - +
68F ALA* 3.0 24.9 + - - +
235F HIS* 6.3 0.6 - - + -
237F ASP* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F ILE* 3.6 22.2 - - + -
25F ASN* 3.4 38.0 - - - +
61F LYS 3.0 6.8 + - - +
62F ALA 3.6 5.4 - - - +
64F LYS* 1.3 77.0 - - - +
66F ALA* 1.3 57.2 + - - +
68F ALA* 3.4 7.4 + - - +
69F ALA* 3.0 28.1 + - - +
215F PRO 4.8 0.2 - - - +
216F GLY* 3.9 5.2 - - - -
219F ASN* 3.9 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ALA 2.9 16.6 + - - +
63F VAL 3.7 4.0 - - - +
65F ALA* 1.3 75.6 - - - +
67F ARG* 1.3 66.6 + - - +
69F ALA* 3.2 2.6 + - - +
70F PHE 3.0 17.5 + - - -
161F VAL* 3.8 16.2 - - + -
188F VAL* 3.4 30.5 - - + +
189F VAL 4.6 1.6 - - - +
190F VAL* 4.1 4.5 - - + -
216F GLY 3.3 12.7 + - - +
219F ASN* 3.6 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F VAL 2.9 21.4 + - - +
64F LYS* 3.8 7.2 - - - +
66F ALA* 1.3 72.4 - - - +
68F ALA* 1.3 62.0 + - - +
70F PHE* 3.2 36.0 + - - +
71F GLN* 2.9 43.7 + - - +
161F VAL* 3.4 16.7 - - + +
237F ASP* 2.7 54.8 + - - +
239F ASP* 2.7 34.4 + - - -
3103F GAI 5.8 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F LYS 3.0 17.9 + - - +
65F ALA* 3.6 7.0 - - - +
67F ARG* 1.3 78.5 - - - +
69F ALA* 1.3 60.7 + - - +
70F PHE 3.2 0.9 + - - -
71F GLN* 3.2 26.0 + - - +
74F SER* 4.2 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F ALA 3.0 15.4 + - - +
66F ALA 3.6 4.5 - - - +
68F ALA* 1.3 75.1 - - - +
70F PHE* 1.3 54.9 + - - +
71F GLN 3.4 0.2 - - - -
74F SER* 2.7 27.4 + - - -
75F PRO* 6.3 0.2 - - - -
76F TRP* 3.8 13.4 - - + +
77F ARG* 4.2 0.2 - - - +
188F VAL* 4.1 8.5 - - + -
214F PRO* 5.8 1.1 - - + -
215F PRO 3.5 23.8 - - - +
216F GLY 3.7 14.6 - - - +
217F VAL* 3.9 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F ALA 3.0 15.8 + - - +
67F ARG* 3.5 30.1 - - - +
68F ALA 3.1 0.6 - - - -
69F ALA* 1.3 77.9 - - - +
71F GLN* 1.3 59.2 + - - +
76F TRP* 5.0 0.2 - + - -
77F ARG* 2.7 70.3 + - - +
158F PRO* 3.7 15.0 - - + -
160F GLY* 3.5 28.5 - - - -
161F VAL* 5.0 0.4 - - + -
186F GLY 3.7 22.2 - - - -
187F ASN* 4.5 0.4 - - - -
188F VAL* 4.0 17.9 - - + -
3103F GAI 3.5 32.1 - - - -
----------------------------------------------------------
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