Contacts of the helix formed by residues 71 - 85 (chain F) in PDB entry 3ZPL
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 71 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28E ASP* 5.1 2.2 - - - +
65F ALA* 4.3 1.8 - - - -
70F ILE* 1.3 79.9 - - - +
72F ARG* 1.3 59.3 + - - +
73F SER* 3.6 9.7 + - - -
74F ARG* 3.2 23.1 + - - +
75F LEU* 2.9 27.2 + - - +
160F PRO* 3.4 32.3 - - + +
163F ARG* 4.1 25.1 - - + +
14G T 4.4 13.4 + - + +
15G C 5.9 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F MET* 5.8 4.5 - - + +
62F THR* 3.0 37.4 + - - +
65F ALA* 4.5 8.1 - - + -
70F ILE 4.1 0.8 + - - -
71F THR* 1.3 74.1 - - - +
73F SER* 1.3 53.0 + - - +
75F LEU* 3.3 9.4 + - - +
76F SER* 2.8 37.2 + - - -
160F PRO 4.3 1.8 + - - -
161F TRP* 3.0 30.3 + - - +
162F LEU* 4.2 12.2 - - - +
163F ARG* 3.9 20.3 + - - +
3H A 5.3 1.6 - - - +
4H G 3.3 50.7 + - - -
5H A 4.1 20.7 + - + -
6H T 3.7 13.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F THR* 3.1 10.2 - - - -
72F ARG* 1.3 76.6 - - - +
74F ARG* 1.3 65.4 + - - +
76F SER* 3.2 4.6 + - - -
77F HIS* 3.1 27.1 + - - -
14G T 4.3 4.5 - - - -
15G C 2.7 28.2 + - - -
16G A 3.0 9.0 + - - -
6H T 3.8 12.2 + - - +
7H T 2.5 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E THR* 5.0 8.9 - - - +
43F VAL* 3.5 25.4 - - - +
44F TYR* 5.9 0.4 - - - -
70F ILE* 3.8 39.2 - - + +
71F THR* 3.2 17.7 + - - +
73F SER* 1.3 78.0 - - - +
75F LEU* 1.3 58.5 + - - +
77F HIS* 3.4 4.6 + - - +
78F ALA* 2.9 28.9 + - + +
13G C 2.7 60.5 + - + +
14G T 3.5 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F LEU* 3.8 25.6 - - + -
61F MET* 2.9 50.0 - - + +
64F LEU* 3.8 16.4 - - + -
65F ALA* 3.4 18.6 - - + +
70F ILE* 4.1 11.1 - - + +
71F THR 2.9 14.3 + - - +
72F ARG* 3.5 10.5 - - - +
74F ARG* 1.3 74.9 - - - +
76F SER* 1.3 59.3 + - - +
78F ALA* 3.2 2.7 + - - +
79F VAL* 2.8 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F MET* 4.7 2.0 - - - -
72F ARG 2.8 23.2 + - - -
73F SER 3.2 5.1 + - - -
75F LEU* 1.3 72.7 - - - +
77F HIS* 1.3 65.0 + - - +
79F VAL 3.7 0.7 - - - -
80F ALA* 2.9 23.5 + - - +
90F ARG* 3.8 8.8 + - - +
5H A 4.1 0.2 - - - +
6H T 2.8 51.6 + - - +
7H T 3.6 20.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 77 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F TYR* 4.8 3.1 - - - +
73F SER 3.1 19.0 + - - -
74F ARG* 3.7 7.0 - - - +
76F SER* 1.3 78.6 - - - +
78F ALA* 1.3 64.0 + - - +
80F ALA* 3.2 10.7 + - - +
81F ARG* 3.2 20.8 + - - +
12G T 6.2 1.3 - - + -
13G C 4.4 16.8 + + + +
14G T 3.3 26.5 + - + -
7H T 3.7 18.0 + + + +
8H G 2.7 46.5 + + - -
9H A 3.8 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F TYR* 3.4 37.2 + - + +
47F LEU* 4.0 21.1 - - + -
70F ILE* 5.8 0.7 - - + -
74F ARG* 2.9 19.0 + - + +
75F LEU* 3.6 5.6 - - - +
77F HIS* 1.3 76.8 - - - +
79F VAL* 1.3 56.9 + - - +
81F ARG* 3.2 4.9 + - - +
82F LEU* 2.9 32.9 + - - +
13G C 4.8 1.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F LEU* 5.0 1.1 - - + -
61F MET* 3.9 16.8 - - + -
64F LEU* 4.8 3.4 - - + -
75F LEU* 2.8 39.6 + - + +
76F SER 3.9 2.7 - - - +
78F ALA* 1.3 73.7 - - + +
80F ALA* 1.3 58.8 + - - +
81F ARG 3.1 1.6 - - - -
82F LEU* 4.2 13.9 - - + +
83F GLU* 2.8 28.8 + - + +
88F VAL* 3.7 24.9 - - + -
90F ARG* 3.7 29.4 - - + +
102F ALA* 4.8 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F SER 2.9 13.7 + - - +
77F HIS* 3.5 13.5 - - - +
79F VAL* 1.3 75.8 - - - +
81F ARG* 1.3 57.5 + - - +
83F GLU* 3.7 6.3 - - - +
84F LYS* 3.0 27.4 + - - +
90F ARG* 4.4 15.5 - - - +
7H T 5.0 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F GLN* 4.1 4.8 + - - -
39F GLY 3.1 27.9 + - - -
40F MET* 3.8 13.9 - - - +
41F PRO* 4.1 1.4 - - - +
44F TYR* 3.6 22.9 - - + +
77F HIS 3.2 8.4 + - - +
78F ALA 3.2 9.3 + - - +
79F VAL 3.1 0.4 - - - -
80F ALA* 1.3 79.3 - - - +
82F LEU* 1.3 64.0 + - - +
84F LYS* 3.4 7.9 + - + +
85F ASN* 3.1 47.7 + - - +
87F TRP* 3.8 15.2 - - - -
11G A 4.7 1.4 + - - -
12G T 2.7 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F MET* 4.4 6.1 - - - -
44F TYR* 3.9 31.0 - - + -
47F LEU* 4.2 23.8 - - + -
48F LEU* 4.0 21.8 - - + -
78F ALA 2.9 26.0 + - - +
79F VAL* 4.1 7.2 - - + +
80F ALA 3.4 0.2 - - - -
81F ARG* 1.3 78.4 - - - +
83F GLU* 1.3 59.3 + - - +
85F ASN* 3.1 6.7 + - - +
86F GLY 3.0 8.5 + - - -
87F TRP* 3.0 50.3 + - + -
88F VAL* 4.0 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F VAL* 2.8 18.2 + - + +
80F ALA* 3.7 4.9 - - - +
82F LEU* 1.3 75.8 - - - +
84F LYS* 1.3 66.4 + - - +
86F GLY* 3.0 13.9 + - - -
88F VAL* 3.3 22.7 - - - +
89F ARG* 3.9 3.5 - - + +
90F ARG* 3.0 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ALA 3.0 15.7 + - - +
81F ARG* 3.4 12.6 - - + +
82F LEU 3.3 0.2 - - - -
83F GLU* 1.3 77.9 - - - +
85F ASN* 1.3 61.1 + - + +
86F GLY* 3.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F ARG* 3.1 36.0 + - - +
82F LEU* 3.1 25.5 + - - +
84F LYS* 1.3 77.0 - - - +
86F GLY* 1.3 59.6 + - - +
87F TRP* 3.2 50.3 + - + -
----------------------------------------------------------
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