Contacts of the helix formed by residues 109 - 123 (chain C) in PDB entry 2O2C
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 ASN 109 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C TYR* 3.3 49.3 - - - +
74C HIS* 4.1 11.8 + - + -
81C ARG* 4.5 0.2 - - - +
85C TYR* 2.9 11.5 + - - -
108C ILE* 1.3 73.5 - - - +
110C ASP* 1.3 59.8 + - - +
111C GLU* 3.3 10.0 + - - +
112C ILE* 3.0 30.9 + - - +
113C LYS 3.0 23.7 + - - -
7003C GOL 3.5 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ARG* 2.9 41.3 + - - -
85C TYR* 2.9 22.3 + - - -
109C ASN* 1.3 75.3 - - - +
111C GLU* 1.3 57.6 + - + +
113C LYS* 3.5 7.9 + - - +
114C CYS* 3.0 37.1 + - - +
7003C GOL 3.1 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 3.6 26.0 - - + +
65C GLN* 4.9 1.7 + - - +
66C TYR* 2.8 31.9 + - - -
109C ASN* 3.3 11.8 + - - +
110C ASP* 1.3 74.9 - - + +
112C ILE* 1.3 60.7 + - - +
114C CYS* 3.9 5.2 - - - +
115C ALA* 3.1 28.4 + - - +
118C ARG* 4.5 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 4.0 0.8 - - + +
62C LEU* 4.0 26.9 - - + +
66C TYR* 4.1 21.5 - - + -
74C HIS* 5.9 0.4 - - - +
107C HIS 3.7 13.5 - - - +
108C ILE* 4.0 11.9 - - + -
109C ASN* 3.0 31.0 + - - +
111C GLU* 1.3 71.8 - - - +
113C LYS* 1.3 59.4 + - - +
115C ALA* 3.2 2.9 + - - +
116C LEU* 2.9 35.7 + - + +
379C TRP* 3.7 51.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ARG* 3.2 21.0 + - - +
85C TYR* 3.9 27.2 - - + +
103C TYR* 2.9 32.3 + - + +
108C ILE* 3.8 11.6 - - + +
109C ASN 3.0 16.4 + - - +
110C ASP* 3.7 8.9 + - - +
112C ILE* 1.3 76.4 - - - +
114C CYS* 1.3 63.1 + - - +
116C LEU* 3.3 8.9 + - - +
117C LEU* 3.1 37.3 + - + +
366C GLU* 4.6 21.4 + - - +
367C GLN* 5.5 2.2 - - - +
372C LEU* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ASP* 3.0 23.5 + - - +
111C GLU* 3.9 5.4 - - - +
113C LYS* 1.3 77.4 - - - +
115C ALA* 1.3 57.3 + - - +
117C LEU* 3.3 14.0 + - - +
118C ARG* 3.0 48.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C SER* 3.9 8.4 - - - +
58C GLN* 4.8 4.7 - - + +
59C LEU* 3.7 22.2 - - + +
62C LEU* 3.9 11.4 - - + -
111C GLU 3.1 18.8 + - - +
112C ILE 3.2 4.5 + - - +
114C CYS* 1.3 75.4 - - - +
116C LEU* 1.3 58.6 + - - +
118C ARG* 3.4 27.3 + - - +
119C LEU* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 3.9 24.9 - - + -
108C ILE* 4.3 14.8 - - + -
112C ILE* 2.9 34.1 + - + +
113C LYS* 3.3 8.9 + - - +
115C ALA* 1.3 75.0 - - - +
117C LEU* 1.3 62.0 + - - +
119C LEU* 3.3 9.5 + - + +
120C ALA 3.3 15.8 + - - -
375C LEU* 3.4 59.7 - - + +
376C VAL* 4.8 0.4 - - + +
378C VAL* 4.9 7.0 - - + -
379C TRP* 4.2 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LYS* 3.1 35.5 + - + +
114C CYS* 3.6 14.4 - - - +
115C ALA 3.3 0.2 - - - -
116C LEU* 1.3 75.0 - - - +
118C ARG* 1.3 63.4 + - - +
120C ALA* 3.3 7.0 + - + +
121C GLU* 3.2 20.6 + - - +
365C PRO* 3.6 38.6 - - + +
366C GLU* 4.1 24.9 - - + +
371C LEU* 4.0 4.9 - - + -
372C LEU* 4.4 9.0 - - + -
375C LEU* 3.9 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C SER* 4.0 9.2 - - - -
58C GLN* 2.9 32.8 + - - +
62C LEU* 5.3 2.2 - - - +
111C GLU 4.5 3.0 + - - -
114C CYS* 3.0 37.0 + - - +
115C ALA* 3.5 30.3 - - - +
116C LEU 3.3 0.4 - - - -
117C LEU* 1.3 73.6 - - + +
119C LEU* 1.3 60.1 + - - +
121C GLU* 3.2 8.4 + - - +
122C GLU* 2.9 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 4.0 12.6 - - + -
53C CYS* 4.5 6.3 - - + -
55C SER* 3.3 21.5 + - - +
56C TRP* 3.8 46.2 - - + +
59C LEU* 3.9 14.8 - - + -
115C ALA 3.1 12.9 + - - +
116C LEU* 3.4 13.2 - - + +
117C LEU 3.2 0.2 - - - -
118C ARG* 1.3 75.2 - - - +
120C ALA* 1.3 57.2 + - - +
122C GLU* 3.3 1.6 + - - +
123C ARG* 3.0 43.8 + - + +
375C LEU* 5.2 0.4 - - + -
378C VAL* 4.4 10.1 - - + -
556C ILE* 4.1 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU 3.3 9.3 + - - +
117C LEU* 3.3 10.7 + - - +
119C LEU* 1.3 81.0 - - - +
121C GLU* 1.3 58.0 + - - +
123C ARG* 3.7 0.8 + - - -
124C GLY 3.4 3.1 + - - -
125C ILE* 3.1 44.1 + - + +
126C ARG 4.9 0.3 + - - -
365C PRO* 6.5 0.4 - - + -
371C LEU* 3.9 31.2 - - + -
375C LEU* 4.4 9.4 - - + +
556C ILE* 5.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C LEU 3.2 12.4 + - - +
118C ARG* 3.5 11.9 - - - +
119C LEU 3.2 0.2 - - - -
120C ALA* 1.3 76.5 - - - +
122C GLU* 1.3 63.1 + - + +
124C GLY* 3.2 14.0 + - - -
126C ARG* 4.3 24.2 + - - +
127C GLN* 4.6 11.0 + - - +
365C PRO* 5.7 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C CYS* 3.5 18.5 - - - +
54C ALA* 3.1 29.4 + - - +
55C SER* 3.0 35.9 + - - +
58C GLN* 4.9 1.4 + - - -
118C ARG* 2.9 19.7 + - + +
119C LEU 3.8 4.3 - - - +
121C GLU* 1.3 77.4 - - + +
123C ARG* 1.3 62.9 + - - +
124C GLY 3.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASP* 4.9 1.4 + - - -
49C THR* 3.3 40.4 + - - -
50C LEU* 3.9 14.5 - - + +
53C CYS* 3.8 19.5 - - - -
119C LEU* 3.0 35.7 + - + +
120C ALA* 4.4 2.9 - - - +
121C GLU 3.3 0.2 - - - -
122C GLU* 1.3 75.5 - - - +
124C GLY* 1.3 62.8 + - - +
125C ILE* 3.6 14.9 - - + +
128C PHE* 5.7 0.7 - - - +
555C ALA* 3.9 8.9 + - - +
556C ILE* 2.9 37.7 + - + +
557C TRP 3.8 3.0 + - - -
558C GLY* 3.5 25.3 - - - +
----------------------------------------------------------
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