Contacts of the helix formed by residues 76 - 99 (chain C) in PDB entry 5L5E
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 LEU 76 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 3.9 24.9 - - + -
16B GLY 5.1 4.3 - - - +
17B ARG* 6.3 0.4 - - - -
18B LEU* 4.0 15.3 - - + +
153B SER* 6.4 2.0 - - - -
24C ALA* 4.4 14.6 + - + +
27C ARG* 6.6 0.2 - - - -
73C PHE* 4.0 1.0 - - - -
75C GLY* 1.3 70.2 - - - -
77C ASN* 1.3 65.3 + - - +
78C ALA* 4.7 1.8 - - + +
79C ASP* 3.5 33.9 - - + +
80C SER* 3.3 17.8 + - - -
125C ARG* 4.0 9.9 - - - +
128C GLY* 2.9 18.3 + - - +
129C VAL* 3.4 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ASN* 3.1 36.1 + - - +
157B THR* 5.6 2.6 - - - +
47C ARG* 5.5 8.9 + - - +
59C PRO* 6.1 1.2 - - - +
61C LYS* 4.2 14.3 - - - +
73C PHE* 3.5 23.2 - - + -
75C GLY 3.4 14.1 + - - -
76C LEU* 1.3 70.6 - - - +
78C ALA* 1.3 63.2 + - - +
80C SER* 2.6 21.7 + - - -
81C ARG* 3.4 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLN* 3.4 16.5 - - + +
153B SER* 3.3 26.7 - - - +
154B GLY 3.5 19.3 - - - +
155B ASN* 3.9 4.0 - - + +
76C LEU* 3.4 2.4 - - + +
77C ASN* 1.3 78.9 - - - +
79C ASP* 1.3 64.6 + - - +
81C ARG* 3.4 24.2 + - - +
82C ILE* 3.4 18.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLN* 3.0 25.9 - - - +
122B THR* 4.7 0.2 + - - -
123B GLN* 4.6 0.7 - - - -
76C LEU* 3.5 17.2 + - + +
77C ASN 3.3 0.2 - - - -
78C ALA* 1.3 77.6 - - - +
80C SER* 1.3 63.1 + - - +
82C ILE* 3.2 15.4 + - - +
83C LEU* 3.5 8.1 + - - +
125C ARG* 2.8 38.9 + - - -
127C PHE* 3.7 21.3 - - + -
128C GLY 3.1 15.1 + - - -
129C VAL* 3.5 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 5.6 1.3 - - - +
73C PHE* 3.1 52.0 - - - -
76C LEU 3.3 4.2 + - - -
77C ASN 2.6 20.5 + - - -
79C ASP* 1.3 77.6 - - - +
81C ARG* 1.3 58.8 + - - +
83C LEU* 3.3 7.0 + - - +
84C ILE* 2.9 39.1 + - - +
129C VAL* 4.2 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ARG* 3.8 18.4 - - - +
115B SER* 3.2 21.8 + - - -
116B ASP* 2.8 37.8 + - - +
119B GLN* 4.6 1.0 - - - +
154B GLY 2.8 29.7 + - - -
155B ASN* 4.2 5.3 - - - +
156B TYR* 3.5 36.5 - - - +
59C PRO* 6.2 1.6 - - - -
77C ASN* 3.8 8.5 + - - +
78C ALA* 3.4 24.1 + - - +
79C ASP 3.2 0.6 - - - -
80C SER* 1.3 84.0 + - - +
82C ILE* 1.3 57.5 + - - +
84C ILE* 3.4 10.1 + - + +
85C GLU* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASP* 3.9 25.6 - - + +
119B GLN* 3.2 32.5 - - + +
123B GLN* 4.9 2.5 - - - +
78C ALA 3.4 15.0 - - - +
79C ASP* 3.2 9.3 + - - +
81C ARG* 1.3 77.7 - - - +
83C LEU* 1.3 61.4 + - - +
85C GLU* 3.6 5.1 + - - +
86C LYS* 3.2 42.5 + - - +
118C TYR* 5.0 3.1 - - - +
127C PHE* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 5.6 3.6 - - + -
79C ASP 3.5 3.1 + - - +
80C SER* 3.3 7.7 + - - +
82C ILE* 1.3 76.9 - - - +
84C ILE* 1.3 60.5 + - + +
86C LYS* 3.5 5.2 + - + +
87C ALA* 2.9 31.1 + - - +
111C VAL* 4.3 17.8 - - + +
114C VAL* 3.7 32.5 - - + -
115C GLN* 4.1 31.9 - - + +
127C PHE* 3.9 33.7 - - + -
129C VAL* 4.2 22.0 - - + -
131C THR* 4.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C SER* 3.4 24.5 - - - +
65C ILE* 4.1 13.2 - - + +
71C LEU* 3.9 27.8 - - + -
73C PHE* 4.8 7.4 - - + -
80C SER* 2.9 34.1 + - - +
81C ARG* 3.7 10.1 - - + +
83C LEU* 1.3 76.1 - - + +
85C GLU* 1.3 57.0 + - - +
87C ALA* 3.3 2.5 + - - +
88C ARG* 2.9 68.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ARG 2.9 18.8 + - - +
82C ILE* 3.9 5.8 - - - +
84C ILE* 1.3 78.1 - - - +
86C LYS* 1.3 64.5 + - + +
88C ARG* 3.3 16.9 + - - +
89C VAL* 3.0 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ILE* 3.2 35.5 + - + +
83C LEU* 3.8 5.2 - - + +
85C GLU* 1.3 82.2 - - + +
87C ALA* 1.3 57.5 + - - +
89C VAL* 3.3 7.5 + - - +
90C GLU* 2.9 29.5 + - - +
110C TYR* 3.6 20.5 + - + +
114C VAL* 3.9 30.3 - - + -
117C ARG* 4.7 11.3 - - - +
118C TYR* 4.1 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 3.6 26.0 - - + +
71C LEU* 5.1 1.1 - - + -
83C LEU 2.9 17.3 + - - +
84C ILE* 3.5 5.2 - - - +
86C LYS* 1.3 76.0 - - - +
88C ARG* 1.3 57.8 + - - +
90C GLU* 3.3 2.4 + - - +
91C ALA* 2.9 30.0 + - - +
107C LEU* 3.8 8.8 - - + +
110C TYR* 4.1 10.2 - - - -
111C VAL* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ARG* 6.1 3.6 - - - +
63C SER* 3.7 19.2 + - - +
64C LYS* 2.8 28.5 + - - +
65C ILE* 3.6 30.3 - - + +
84C ILE* 2.9 40.5 + - - +
85C GLU* 3.6 15.7 + - - +
87C ALA* 1.3 76.4 - - - +
89C VAL* 1.3 61.5 + - + +
91C ALA* 3.5 3.0 + - - +
92C GLN* 3.3 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLU* 3.0 38.3 + - + +
86C LYS* 3.6 10.5 - - - +
88C ARG* 1.3 75.4 - - + +
90C GLU* 1.3 60.8 + - - +
92C GLN* 3.4 6.5 + - - +
93C SER* 2.9 30.3 + - - -
110C TYR* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LYS 2.9 17.2 + - - +
87C ALA 3.7 4.0 - - - +
89C VAL* 1.3 78.3 - - - +
91C ALA* 1.3 57.5 + - - +
93C SER* 4.0 12.7 + - - -
94C HIS* 2.8 34.7 + - - +
102C VAL* 5.3 0.2 - - + -
106C TYR* 2.9 37.9 + - + -
107C LEU* 5.2 4.5 - - + -
110C TYR* 3.6 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 4.0 20.6 - - + +
66C ASP* 4.0 18.5 - - - +
87C ALA 2.9 18.1 + - - +
88C ARG 3.6 6.3 - - - +
90C GLU* 1.3 76.7 - - - +
92C GLN* 1.3 60.8 - - - +
94C HIS* 3.5 2.9 + - - +
95C ARG* 3.3 29.4 + - - +
102C VAL* 4.1 22.6 + - + +
107C LEU* 4.9 0.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE 5.2 2.3 - - - +
66C ASP* 3.9 19.9 - - - +
88C ARG 3.3 13.5 + - - +
89C VAL* 3.8 7.6 - - - +
90C GLU 3.3 0.4 - - - -
91C ALA* 1.3 74.8 - - - +
93C SER* 1.3 60.4 + - - +
95C ARG* 3.5 21.8 + - - +
96C LEU* 3.0 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C VAL* 2.9 21.2 + - - -
90C GLU* 3.2 20.0 + - - -
92C GLN* 1.3 77.6 - - - +
94C HIS* 1.3 52.3 + - - +
96C LEU* 3.7 7.7 - - - +
97C THR* 2.8 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C GLU* 2.8 21.2 + - - +
91C ALA 3.7 1.8 - - - +
92C GLN 3.3 0.2 - - - -
93C SER* 1.3 74.6 - - - +
95C ARG* 1.3 60.1 + - - +
97C THR* 3.9 4.5 - - - -
98C LEU* 2.8 63.5 + - + +
99C GLU 3.7 0.2 + - - -
100C ASP* 2.7 31.5 + - + -
101C PRO 3.8 16.0 - - - -
102C VAL* 3.5 20.1 - - + +
103C THR 5.4 0.7 - - - -
106C TYR* 3.8 37.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ASP* 3.1 36.5 + - - -
67C SER* 4.5 7.5 + - - -
68C HIS* 4.4 3.4 + - - -
91C ALA 3.3 12.2 + - - +
92C GLN* 3.7 28.4 - - - +
94C HIS* 1.3 78.9 - - - +
96C LEU* 1.3 57.0 + - - +
99C GLU* 3.2 27.3 + - - +
100C ASP 3.5 9.6 + - - +
101C PRO* 3.4 46.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLN 3.0 18.5 + - - +
93C SER* 3.7 8.7 - - - +
94C HIS 3.1 0.4 - - - -
95C ARG* 1.3 80.1 - - - +
97C THR* 1.3 64.3 + - + +
99C GLU* 4.6 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C SER* 2.8 29.4 + - - +
94C HIS* 3.7 3.8 + - - -
96C LEU* 1.3 85.2 - - + +
98C LEU* 1.3 79.3 + - - +
99C GLU* 3.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C HIS* 2.8 47.1 + - + +
97C THR* 1.3 96.3 - - - +
99C GLU* 1.3 69.3 + - - +
100C ASP* 3.2 7.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C HIS 3.7 0.2 + - - -
95C ARG* 3.2 22.6 + - - +
96C LEU 5.1 5.2 - - - +
97C THR 5.6 0.9 - - - -
98C LEU* 1.3 77.7 - - - +
100C ASP* 1.3 67.2 + - - +
101C PRO* 4.7 1.1 - - - +
----------------------------------------------------------
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