Contacts of the helix formed by residues 66 - 87 (chain A) in PDB entry 4G85
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 SER 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP 4.0 1.0 - - - -
65A TYR* 1.3 75.1 - - - +
67A PRO* 1.4 78.6 - - - +
68A ARG* 3.7 6.3 + - - +
69A GLN* 2.8 37.3 + - - +
70A MET* 2.8 20.1 + - - +
91B VAL 4.1 1.1 - - - -
138B TYR* 3.6 14.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR 4.8 0.4 - - - +
66A SER* 1.4 88.7 - - - +
68A ARG* 1.3 58.3 + - - +
70A MET* 3.1 2.4 + - - +
71A ALA* 2.9 28.2 + - - +
406A THR* 3.8 26.8 - - + +
90B GLU* 3.5 36.6 - - + +
91B VAL* 3.3 19.6 - - - +
92B ILE* 5.5 2.9 - - + -
138B TYR* 3.4 15.0 - - + +
147B ILE* 5.1 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 3.3 6.3 + - - +
67A PRO* 1.3 80.2 - - - +
69A GLN* 1.3 63.2 + - + +
71A ALA* 3.4 6.3 + - - +
72A VAL* 3.1 27.8 + - + +
404A ILE* 4.6 13.7 - - + +
406A THR* 3.6 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP 3.8 6.9 + - - +
65A TYR* 3.6 21.0 - - + -
66A SER* 2.8 42.7 + - - +
68A ARG* 1.3 75.5 - - + +
70A MET* 1.3 58.6 + - - +
72A VAL* 3.5 8.4 + - - +
73A ARG* 3.1 27.9 + - - +
390A PHE* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 3.7 21.8 - - + +
66A SER 2.8 10.8 + - - +
67A PRO 3.4 7.9 - - - +
69A GLN* 1.3 74.7 - - - +
71A ALA* 1.3 55.2 + - - +
73A ARG* 3.4 51.3 + - + +
74A GLU* 2.8 37.0 + - + +
91B VAL* 3.5 55.6 - - + +
92B ILE 4.1 5.6 - - - +
93B ASP* 4.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO 2.9 12.9 + - - +
68A ARG* 3.5 12.3 - - - +
70A MET* 1.3 76.3 - - - +
72A VAL* 1.3 56.6 + - - +
74A GLU* 3.4 12.0 + - - +
75A LYS* 3.0 25.5 + - - +
404A ILE* 3.9 12.6 - - + -
405A ARG 3.7 23.8 - - - +
406A THR* 4.8 3.4 - - - +
91B VAL* 5.3 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG 3.1 17.7 - - - +
69A GLN* 3.7 8.5 - - - +
70A MET 3.3 0.4 - - - -
71A ALA* 1.3 72.0 - - - +
73A ARG* 1.3 66.9 + - - +
75A LYS* 2.9 18.4 + - + +
76A VAL* 3.0 21.3 + - + +
390A PHE* 3.7 26.5 - - + +
393A VAL* 4.0 22.4 - - + -
394A GLU* 4.2 13.7 - - + +
397A LEU* 5.3 4.0 - - + -
404A ILE* 4.3 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TYR* 3.9 18.8 - - + -
69A GLN 3.1 14.1 + - - +
70A MET* 3.4 39.7 - - + +
72A VAL* 1.3 78.2 - - - +
74A GLU* 1.3 59.6 + - + +
76A VAL* 3.0 1.7 + - - +
77A PHE* 2.8 57.7 + - + +
172A TYR* 2.8 38.2 + - - -
390A PHE* 3.3 34.2 - - + -
93B ASP* 3.0 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 2.8 19.1 + - + +
71A ALA* 3.5 14.3 - - - +
73A ARG* 1.3 75.5 - - - +
75A LYS* 1.3 63.5 + - - +
77A PHE* 4.0 5.5 - - - +
78A ASP* 3.1 25.0 + - + +
408A GLU* 4.2 5.7 - - - +
85B LYS* 2.8 33.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA 3.0 12.5 + - - +
72A VAL* 2.9 17.0 + - + +
74A GLU* 1.3 72.3 - - - +
76A VAL* 1.3 63.6 + - + +
78A ASP* 3.7 5.0 + - - +
79A VAL* 3.3 26.6 + - - +
393A VAL* 6.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 3.0 18.5 + - + +
73A ARG 3.5 5.4 - - - +
75A LYS* 1.3 76.2 - - + +
77A PHE* 1.3 66.7 + - - +
79A VAL* 3.0 14.4 + - - +
80A ILE* 3.0 26.7 + - + +
202A LEU* 3.7 22.7 - - + -
386A VAL* 4.2 8.1 - - + -
389A ILE* 3.9 15.5 - - + -
390A PHE* 3.9 27.8 - - + -
393A VAL* 4.1 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 2.8 50.8 + - + +
74A GLU* 4.1 4.3 - - + +
76A VAL* 1.3 72.8 - - - +
78A ASP* 1.3 58.4 + - - +
80A ILE* 3.4 6.9 + - + +
81A ILE* 2.8 52.2 + - + +
152A ILE* 3.7 34.1 - - + -
172A TYR* 3.8 27.8 - + - -
174A CYS* 5.2 1.1 - - + -
386A VAL* 3.2 31.9 - - + -
390A PHE* 3.8 13.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 3.1 19.7 + - + +
75A LYS* 3.9 5.6 - - - +
77A PHE* 1.3 73.4 - - - +
79A VAL* 1.3 68.9 + - + +
81A ILE* 4.6 4.0 - - - +
82A ARG* 2.9 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS 3.3 15.7 + - - +
76A VAL 3.0 7.1 + - - +
78A ASP* 1.3 78.2 - - + +
80A ILE* 1.3 64.7 + - - +
82A ARG* 3.9 6.0 - - - +
83A CYS* 3.4 17.5 + - - +
86A ARG* 5.4 0.5 + - - -
198A ILE* 4.3 5.1 - - - +
201A SER* 3.0 43.7 - - - +
202A LEU* 3.7 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.0 32.7 + - + +
77A PHE* 3.5 12.1 - - + +
79A VAL* 1.3 75.2 - - - +
81A ILE* 1.3 59.2 + - - +
83A CYS* 2.9 22.2 + - - +
84A PHE* 3.1 42.0 + - + -
152A ILE* 4.2 5.4 - - + -
174A CYS* 3.8 17.7 - - - -
198A ILE* 3.8 30.3 - - + -
202A LEU* 4.8 2.7 - - + -
384A ILE* 3.9 25.4 - - + -
386A VAL* 5.0 5.4 - - + -
389A ILE* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 2.8 39.1 + - + +
78A ASP* 4.3 2.9 - - - +
80A ILE* 1.3 68.5 - - - +
82A ARG* 1.3 65.9 + - - +
83A CYS 2.7 6.6 + - - -
84A PHE* 2.9 8.3 + - + +
85A LYS* 2.8 41.7 + - + +
150A TYR* 3.4 29.4 - - + +
152A ILE* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP* 2.9 48.0 + - - +
79A VAL* 3.9 6.1 - - - +
81A ILE* 1.3 75.2 - - - +
83A CYS* 1.3 55.5 + - - +
85A LYS* 3.8 10.0 + - - +
86A ARG* 3.4 39.0 + - - +
437B LYS* 5.9 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL 3.4 10.7 + - - +
80A ILE 2.9 12.4 + - - +
81A ILE 2.7 5.3 + - - -
82A ARG* 1.3 74.5 - - - +
84A PHE* 1.3 63.3 + - - -
85A LYS 3.1 1.3 - - - -
86A ARG* 3.2 24.8 + - - +
87A HIS* 3.2 15.8 - - - -
194A ILE* 3.8 18.8 - - - -
197A GLU* 3.7 29.8 - - + +
198A ILE* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.1 36.3 + - + -
81A ILE* 2.9 8.6 + - - +
83A CYS* 1.3 75.4 - - - +
85A LYS* 1.3 59.1 + - - +
87A HIS* 2.9 22.7 + - - +
88A GLY 3.2 8.3 + - - -
89A ALA* 3.5 12.0 + - + +
150A TYR* 3.2 55.9 - + + -
152A ILE* 4.6 1.1 - - + -
174A CYS* 4.4 11.4 - - - -
175A ASP 4.7 1.8 - - - -
176A PHE* 3.6 31.9 - + + -
194A ILE* 3.8 16.8 - - + -
198A ILE* 3.6 23.3 - - + -
382A LEU* 4.4 7.4 - - + -
384A ILE* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 2.8 30.7 + - + +
82A ARG* 3.9 8.7 - - - +
84A PHE* 1.3 79.0 - - - +
86A ARG* 1.3 59.9 + - - +
88A GLY* 3.3 12.9 + - - +
89A ALA 4.9 7.6 - - - +
91A VAL* 6.2 1.1 - - - -
150A TYR* 3.8 25.8 - - + +
408B GLU* 3.0 52.7 + - + +
409B THR 4.7 1.0 + - - -
437B LYS* 4.0 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL 5.4 0.4 + - - -
82A ARG* 3.4 35.6 + - - +
83A CYS* 3.2 34.0 + - - +
84A PHE 3.1 0.4 - - - -
85A LYS* 1.3 78.3 - - - +
87A HIS* 1.3 59.0 + - + +
88A GLY 3.4 0.6 + - - -
197A GLU* 3.1 26.9 + - - +
201A SER* 5.9 1.4 + - - -
432B TRP* 3.4 34.7 + - + +
435B GLY* 3.7 19.5 + - - -
436B ILE 3.2 24.2 - - - +
437B LYS* 3.4 13.5 - - + +
438B ALA 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A CYS* 3.2 22.0 - - - +
84A PHE* 2.9 9.7 + - - +
86A ARG* 1.3 83.5 - - + +
88A GLY* 1.3 56.9 + - - +
89A ALA 3.5 0.9 - - - -
148A LYS* 2.9 27.3 + - - +
176A PHE* 4.9 4.9 - - + -
190A GLU* 2.4 35.4 + - - +
193A LYS* 4.3 3.6 - - + -
194A ILE* 3.5 32.1 - - + +
197A GLU* 2.9 36.4 + - - -
432B TRP* 3.5 31.3 - + - +
438B ALA 4.0 8.5 - - - +
439B GLU* 4.0 4.3 - - - +
----------------------------------------------------------
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