Contacts of the helix formed by residues 110 - 128 (chain C) in PDB entry 2C2L
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 110 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C GLN* 2.8 28.9 + - - +
108C MET* 4.0 14.4 + - - +
109C GLU* 1.3 71.6 - - - +
111C TYR* 1.3 65.3 + - - +
112C ASP 2.8 5.3 + - - -
113C GLU* 2.9 31.1 + - - -
114C ALA* 3.1 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C GLN 4.5 0.2 + - - -
106C LEU* 3.7 35.2 + - + -
109C GLU* 3.2 48.5 + - + +
110C SER* 1.3 74.6 - - - +
112C ASP* 1.3 62.7 + - - +
114C ALA* 4.0 5.8 - - - -
115C ILE* 2.9 31.8 + - - +
143C ALA 4.6 0.2 - - - -
146C LYS* 3.8 24.5 + - + +
147C ARG* 3.3 41.3 - - + +
150C SER* 4.0 24.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C SER 2.8 4.8 + - - -
111C TYR* 1.3 74.4 - - - +
113C GLU* 1.3 74.9 + - - +
115C ILE* 3.1 27.1 - - - +
116C ALA* 3.2 8.2 + - - +
147C ARG* 3.3 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C GLN* 2.7 24.7 - - + +
110C SER* 2.9 34.1 + - - +
112C ASP* 1.3 78.9 - - - +
114C ALA* 1.3 66.2 + - - +
116C ALA* 2.8 19.1 + - - +
117C ASN* 2.9 15.2 + - - +
1305C SO4 3.8 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C GLY* 3.4 24.7 - - - +
105C GLN* 2.8 21.9 + - + -
106C LEU* 3.8 22.9 - - + +
110C SER 3.1 9.8 + - - +
111C TYR* 3.8 7.4 - - - +
113C GLU* 1.3 76.4 - - - +
115C ILE* 1.3 64.3 + - + +
117C ASN* 3.2 2.1 + - - -
118C LEU* 3.0 28.8 + - + +
143C ALA* 5.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C TYR* 2.9 17.4 + - - +
112C ASP* 3.1 24.7 - - - +
114C ALA* 1.3 75.3 - - + +
116C ALA* 1.3 58.0 + - + +
118C LEU* 3.8 9.9 - - - -
119C GLN* 2.8 35.9 + - + +
140C LEU* 3.6 10.0 - - + +
143C ALA* 3.9 33.9 - - + +
144C LYS* 4.4 17.7 - - + +
147C ARG* 4.2 21.3 - - - +
304C TYR* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASP 3.5 9.6 - - - +
113C GLU* 2.8 18.2 + - - +
115C ILE* 1.3 80.7 - - + +
117C ASN* 1.3 58.6 + - - +
119C GLN* 3.1 9.5 - - - +
120C ARG* 2.8 44.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C HIS* 3.6 35.2 + - + +
101C LEU* 4.0 9.0 - - - +
102C GLY* 3.9 6.1 - - - -
105C GLN* 3.0 37.2 + - - +
113C GLU 2.9 13.9 + - - +
114C ALA 3.9 3.4 - - - +
116C ALA* 1.3 73.4 - - - +
118C LEU* 1.3 57.6 + - - +
120C ARG* 3.1 24.6 + - - +
121C ALA* 2.7 35.5 + - - +
1305C SO4 3.2 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C PHE* 3.6 48.2 - - + +
102C GLY* 4.4 2.5 - - - -
103C GLN* 4.0 17.5 - - - +
106C LEU* 5.2 1.8 - - + -
114C ALA 3.0 21.7 + - - +
115C ILE* 3.7 1.3 - - - +
117C ASN* 1.3 73.6 - - - +
119C GLN* 1.3 66.6 + - - +
121C ALA* 3.1 5.6 + - - +
122C TYR* 2.8 25.2 + - - +
136C ILE* 4.2 6.0 - - + +
139C ALA* 3.6 25.1 - - + +
140C LEU* 3.4 29.4 - - + +
143C ALA* 3.7 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ILE* 2.8 25.3 + - + +
116C ALA* 3.1 10.3 - - - +
118C LEU* 1.3 76.9 - - - +
120C ARG* 1.3 56.5 + - - +
122C TYR* 3.1 29.5 + - - +
123C SER* 3.2 8.5 + - - -
140C LEU* 3.8 25.6 - - + +
144C LYS* 5.0 10.1 - - - +
239C GLU* 5.8 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C HIS* 4.1 21.3 + - + +
116C ALA* 2.8 23.7 + - - +
117C ASN* 3.1 40.0 + - - +
119C GLN* 1.3 70.5 - - - +
121C ALA* 1.3 62.1 + - - +
122C TYR 2.9 5.2 - - - -
123C SER* 2.6 25.2 + - - +
124C LEU* 3.1 25.2 + - + +
1305C SO4 4.5 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 3.2 29.7 - - - +
98C HIS* 3.4 24.2 - - + +
99C PHE* 3.5 24.9 - - + +
117C ASN 2.7 23.1 + - - +
118C LEU* 3.1 5.6 + - - +
120C ARG* 1.3 73.4 - - - +
122C TYR* 1.3 58.8 + - - +
124C LEU* 4.0 5.3 - - - +
125C ALA* 3.3 7.3 + - - +
136C ILE* 4.0 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU 2.8 10.8 + - - +
119C GLN* 3.1 21.1 - - - +
121C ALA* 1.3 78.7 - - - +
123C SER* 1.3 63.0 + - - +
125C ALA* 3.5 2.9 + - + +
126C LYS* 3.0 47.0 + - + +
136C ILE* 3.4 33.0 - - + -
137C PRO* 4.4 23.5 - - + +
140C LEU* 5.1 9.2 - - + -
236C ILE* 5.3 6.1 - - - +
237C SER* 5.8 1.9 - - - -
257C ASP* 4.9 8.7 + - - -
260C GLU* 5.0 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLN 3.2 6.5 + - - -
120C ARG* 2.6 31.2 + - - +
122C TYR* 1.3 80.8 - - - +
124C LEU* 1.3 59.0 + - - +
126C LYS* 3.1 14.2 + - - +
127C GLU* 2.7 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLY 4.7 1.3 - - - +
93C GLN* 3.8 28.0 - - + +
94C SER 4.3 3.6 - - - +
95C VAL* 4.5 4.3 - - + -
98C HIS* 3.7 35.0 - - + +
120C ARG* 3.1 22.2 + - + +
121C ALA* 4.0 5.8 - - - +
123C SER* 1.3 84.5 + - - +
125C ALA* 1.3 55.6 + - - +
127C GLU* 2.9 25.5 + - - +
128C GLN* 2.7 51.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 3.4 20.1 - - + +
121C ALA 3.3 16.9 + - - +
122C TYR* 3.6 5.8 - - + +
124C LEU* 1.3 79.4 - - - +
126C LYS* 1.3 61.2 + - - +
128C GLN 3.6 0.2 + - - -
129C ARG 3.3 1.2 + - - -
130C LEU* 2.9 40.9 + - + +
132C PHE* 4.3 12.6 - - + -
136C ILE* 4.1 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C TYR* 3.0 37.4 + - + +
123C SER* 3.1 14.5 + - - +
125C ALA* 1.3 75.7 - - - +
127C GLU* 1.3 66.1 + - - +
129C ARG* 3.0 13.5 + - - -
130C LEU 5.0 2.5 - - - -
260C GLU* 4.1 28.0 + - - +
264C ARG* 3.4 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C GLN* 4.4 11.0 - - - +
123C SER 2.7 16.3 + - - +
124C LEU* 2.9 23.5 + - - +
126C LYS* 1.3 76.9 - - - +
128C GLN* 1.3 82.8 + - - +
129C ARG* 3.1 8.7 + - - +
264C ARG* 4.6 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C GLN* 3.0 38.3 + - - +
95C VAL* 3.1 26.3 - - - +
124C LEU* 2.7 27.3 + - - +
127C GLU* 1.3 86.2 + - - +
129C ARG* 1.3 69.5 + - - +
130C LEU* 3.2 25.2 + - + +
----------------------------------------------------------
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