Contacts of the helix formed by residues 110 - 126 (chain C) in PDB entry 2V1C
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 GLU 110 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C PRO* 3.5 27.4 - - + +
109C SER* 1.3 84.6 - - - +
111C GLN* 1.3 58.8 + - + +
112C ALA 3.3 1.1 - - - -
113C PHE* 3.3 2.6 + - - +
114C ASP* 3.0 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C SER* 2.9 24.9 + - - +
110C GLU* 1.3 79.3 - - + +
112C ALA* 1.3 61.3 + - - +
114C ASP* 3.3 8.3 + - - +
115C LEU* 3.0 25.1 + - - +
143C LEU* 3.9 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 3.9 21.1 - - + -
108C PHE* 3.3 36.6 - - + -
109C SER* 4.0 8.9 + - - +
110C GLU 3.3 0.2 - - - -
111C GLN* 1.3 79.2 - - - +
113C PHE* 1.3 57.4 + - - +
115C LEU* 3.6 1.6 + - - +
116C PHE* 3.0 29.3 + - - +
140C LEU* 4.2 4.3 - - + +
143C LEU* 3.8 18.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLY* 4.2 1.8 - - - -
11C ILE* 4.0 24.7 - - + -
28C LEU* 3.1 36.6 - - + -
29C THR* 3.6 13.9 - - - +
30C PRO* 3.6 41.7 - - + -
55C HIS* 3.7 30.5 - + - -
108C PHE* 4.1 7.9 - + + -
110C GLU* 3.3 9.0 + - - +
111C GLN 3.2 0.6 - - - -
112C ALA* 1.3 79.3 - - - +
114C ASP* 1.3 75.1 + - - +
116C PHE* 3.3 5.2 + + - +
117C ALA* 2.9 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C GLU* 3.0 40.6 + - - +
111C GLN* 3.8 7.5 - - - +
113C PHE* 1.3 88.8 - - - +
115C LEU* 1.3 57.8 + - - +
117C ALA* 3.5 4.5 + - - +
118C ALA* 2.9 30.0 + - - +
121C ARG* 5.0 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLN 3.0 16.8 + - - +
112C ALA 3.8 2.0 - - - +
114C ASP* 1.3 77.2 - - - +
116C PHE* 1.3 56.9 + - - +
118C ALA* 3.2 6.4 + - + +
119C SER* 2.9 25.8 + - - -
136C MET* 3.4 36.6 - - + +
139C LYS* 3.6 29.4 - - + -
140C LEU* 3.5 18.8 - - + +
143C LEU* 3.3 27.6 - - + -
198C VAL* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 3.9 26.5 - - + -
13C ILE* 3.6 31.9 - - + -
28C LEU* 4.1 17.5 - - + -
53C PHE* 5.7 0.7 - + - -
95C MET* 3.7 12.1 - - + -
96C ALA* 3.6 32.1 - - + -
99C ALA* 4.1 17.0 - - + -
108C PHE* 5.9 1.6 - - + -
112C ALA 3.0 19.1 + - - +
113C PHE* 3.7 8.1 - + - +
115C LEU* 1.3 73.8 - - - +
117C ALA* 1.3 67.7 + - - +
119C SER* 2.7 29.4 + - - -
120C LEU* 3.1 26.3 + - + +
140C LEU* 4.5 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 3.9 26.5 - - + -
55C HIS* 5.7 2.5 - - + +
113C PHE* 2.9 30.2 + - + +
114C ASP* 3.8 5.6 - - - +
116C PHE* 1.3 74.0 - - - +
118C ALA* 1.3 63.7 + - - +
120C LEU* 3.1 13.2 + - - +
121C ARG* 3.1 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ASP 2.9 19.0 + - - +
115C LEU* 3.3 9.9 - - + +
116C PHE 3.2 0.2 - - - -
117C ALA* 1.3 76.0 - - - +
119C SER* 1.3 58.8 + - - +
120C LEU 3.2 0.2 + - - -
121C ARG* 3.2 27.6 + - - +
122C GLY* 2.8 27.4 + - - -
136C MET* 3.5 16.4 - - + +
202C PHE* 6.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C MET* 3.0 27.2 - - - +
115C LEU 2.9 10.9 + - - -
116C PHE* 2.7 22.6 + - - -
118C ALA* 1.3 76.4 - - - +
120C LEU* 1.3 58.5 + - - +
122C GLY* 3.6 0.9 + - - -
123C VAL* 3.0 34.6 + - - +
132C VAL* 3.7 4.2 - - - +
136C MET* 3.3 39.6 - - - +
140C LEU* 6.1 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 3.9 34.1 - - + -
53C PHE* 4.2 22.7 - - + +
80C LEU* 3.9 14.5 - - + +
83C LEU* 4.1 3.2 - - + +
91C PHE 5.0 0.2 - - - +
92C ALA* 3.5 35.2 - - + +
95C MET* 4.2 4.9 - - + -
116C PHE* 3.1 31.1 + - + +
117C ALA 3.1 9.3 + - - +
119C SER* 1.3 86.7 + - - +
121C ARG* 1.3 60.6 + - - +
123C VAL* 3.5 6.3 + - + +
124C ALA* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 4.3 11.8 - - + +
114C ASP 5.0 1.6 + - - -
117C ALA* 3.1 31.5 + - - +
118C ALA* 3.6 28.5 - - - +
120C LEU* 1.3 72.2 - - - +
122C GLY* 1.3 66.6 + - - +
124C ALA* 3.0 1.8 + - - -
125C HIS* 2.8 49.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ALA 2.8 16.0 + - - -
119C SER 3.7 2.7 - - - -
121C ARG* 1.3 77.2 - - - +
123C VAL* 1.3 61.9 + - - +
124C ALA 3.1 0.2 + - - -
125C HIS* 5.8 0.2 - - - -
126C GLN* 3.0 37.1 + - - +
132C VAL* 3.8 19.6 - - - +
202C PHE* 5.5 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 3.4 24.5 - - + -
88C ARG* 3.2 44.6 + - - +
91C PHE* 3.7 41.1 - - + +
92C ALA* 4.0 5.6 - - + +
95C MET* 5.2 2.0 - - + -
119C SER* 3.0 20.7 + - - +
120C LEU* 3.9 5.6 - - - +
121C ARG 3.4 0.2 - - - -
122C GLY* 1.3 72.1 - - - +
124C ALA* 1.3 56.7 + - - +
129C PRO* 4.1 16.7 - - + +
132C VAL* 4.1 11.4 - - + -
133C ALA* 4.6 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 4.0 9.0 - - + -
82C THR* 2.6 39.6 + - + +
83C LEU* 3.9 14.4 - - + -
85C GLU* 5.2 0.2 - - - +
88C ARG* 3.2 14.4 + - - -
120C LEU 3.0 17.6 + - - +
121C ARG 3.0 5.3 + - - +
123C VAL* 1.3 79.5 - - - +
125C HIS* 1.3 75.3 + - + +
126C GLN 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU* 3.3 29.3 - - + +
82C THR* 4.6 11.7 - - + +
88C ARG* 3.9 3.6 + - - -
121C ARG* 2.8 48.3 + - + +
124C ALA* 1.3 78.6 - - + +
126C GLN* 1.3 68.3 + - + +
127C PRO* 4.1 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ARG* 1.8 30.9 + - - +
122C GLY* 3.0 26.3 + - - +
125C HIS* 1.3 82.7 + - - +
127C PRO* 1.3 72.2 - - + +
128C ASP* 3.1 5.6 + - + +
129C PRO* 3.7 5.5 - - - +
132C VAL* 4.1 16.8 - - + +
202C PHE* 3.8 28.7 - - + -
----------------------------------------------------------
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