Contacts of the helix formed by residues 73 - 82 (chain F) in PDB entry 2ZJQ
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 PRO 73 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F GLN* 3.7 22.0 - - - +
52F ILE* 3.1 22.7 - - + +
54F PRO* 3.7 15.0 - - + -
71F THR 3.7 0.6 - - - +
72F PRO* 1.3 85.7 - - + +
74F MET* 1.3 66.0 + - - +
75F SER* 4.1 10.3 - - - +
76F TYR* 3.1 30.0 + - + +
77F LEU* 3.1 14.8 + - - +
79F ARG* 5.6 1.8 - - - +
111F LYS* 4.4 3.6 - - - +
1071X U 5.3 5.4 - - - +
1074X G 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 74 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F PRO* 1.3 72.5 - - - +
75F SER* 1.3 60.9 + - - +
76F TYR 3.2 0.6 + - - -
77F LEU* 3.8 10.6 - - + +
78F ILE* 3.2 31.9 + - + +
107F ILE* 4.0 15.5 - - + -
111F LYS* 3.5 26.0 - - + +
115F LEU* 5.7 6.5 - - + -
126F THR* 5.1 1.6 - - + +
127F VAL* 3.5 53.6 - - + +
130F THR* 4.2 26.5 - - + +
1070X G 3.5 24.7 - - - +
1071X U 4.5 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F PRO* 3.1 7.9 - - - +
74F MET* 1.3 79.9 - - - +
76F TYR* 1.3 56.7 + - - +
78F ILE* 4.4 0.4 - - - -
79F ARG* 3.0 35.2 + - - +
130F THR* 4.9 8.0 - - - +
134F MET* 3.3 18.5 - - - +
1073X G 4.0 1.9 + - - -
1074X G 2.9 49.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F ASP 3.5 15.6 + - - -
51F ALA* 3.5 18.4 - - + -
52F ILE* 3.5 45.1 - - + -
72F PRO* 4.9 5.2 - - + -
73F PRO* 3.1 21.5 + - + +
75F SER* 1.3 78.6 - - - +
77F LEU* 1.3 67.7 + - + +
78F ILE 3.1 2.0 - - - -
79F ARG* 3.1 46.9 + - + +
80F LYS* 3.1 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LYS* 6.0 4.0 - - - +
72F PRO* 3.9 26.0 - - + +
73F PRO 3.1 13.8 + - - +
74F MET* 3.6 10.1 + - - +
76F TYR* 1.3 80.5 - - + +
78F ILE* 1.3 56.8 + - - +
80F LYS* 3.4 12.9 + - + +
81F ALA* 3.2 27.7 + - - +
107F ILE* 3.7 36.1 - - + -
111F LYS* 3.6 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F MET* 3.2 20.2 + - + +
76F TYR 3.1 0.8 - - - -
77F LEU* 1.3 74.3 - - + +
79F ARG* 1.3 57.2 + - - +
80F LYS 3.0 5.4 - - - -
81F ALA* 4.6 3.6 - - - +
82F ALA* 3.0 31.2 + - + +
84F ILE* 3.6 9.1 - - + +
99F LEU* 4.2 20.6 - - + -
107F ILE* 5.6 6.7 - - + -
127F VAL* 5.8 2.0 - - + +
130F THR* 5.1 4.3 - - + -
131F ALA* 3.8 33.2 - - + +
134F MET* 3.5 37.0 - - + -
136F VAL* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F ILE* 4.2 13.1 - - - +
73F PRO* 5.6 1.0 - - - +
75F SER* 3.0 25.5 + - - +
76F TYR* 3.1 47.7 + - + +
78F ILE* 1.3 76.7 - - - +
80F LYS* 1.3 56.0 + - - +
83F GLY* 3.5 4.9 - - - -
84F ILE* 3.1 63.6 + - + +
85F GLY 5.2 4.7 + - - -
86F LYS* 5.2 3.0 - - - +
87F GLY* 5.1 6.0 - - - +
134F MET* 4.5 6.1 - - + -
1074X G 5.2 1.8 + - - -
1075X C 3.8 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F LYS* 3.0 34.1 - - - +
49F GLY 5.1 2.6 + - - -
50F ASP* 4.8 6.6 + - - +
51F ALA* 4.4 7.8 - - + +
76F TYR* 3.1 35.5 + - + +
77F LEU* 3.7 13.9 - - + +
78F ILE 3.0 0.2 - - - -
79F ARG* 1.3 80.4 - - - +
81F ALA* 1.3 62.8 + - - +
82F ALA 3.6 0.2 - - - -
83F GLY* 3.9 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F LEU 3.2 15.8 + - - +
78F ILE* 4.4 2.9 - - - +
80F LYS* 1.3 80.0 - - - +
82F ALA* 1.3 60.7 + - - +
83F GLY 3.3 0.2 - - - -
99F LEU* 5.1 8.1 - - + -
103F GLN* 4.0 30.5 - - + -
106F GLU* 5.5 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ILE* 3.0 21.7 + - + +
81F ALA* 1.3 77.1 - - - +
83F GLY* 1.3 63.0 + - - +
84F ILE* 4.0 14.9 - - + +
97F GLY* 5.3 2.7 - - - -
98F LYS 4.5 24.0 - - - +
99F LEU* 5.0 7.9 - - + -
136F VAL* 4.9 4.0 - - + -
----------------------------------------------------------
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