Contacts of the helix formed by residues 115 - 128 (chain C) in PDB entry 2GTP
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 115 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C THR* 4.2 15.9 - - + -
112C GLU* 2.9 18.1 + - + +
114C ASP* 1.3 81.9 - - + +
116C LEU* 1.3 63.1 + - - +
117C PRO* 3.4 3.4 - - - -
118C CYS* 3.5 11.5 + - + +
119C LYS* 3.2 25.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
108C TYR* 3.6 45.3 - - + +
111C THR* 3.7 24.2 - - + +
112C GLU 3.6 9.0 - - - +
113C SER* 3.6 20.4 - - - +
114C ASP 3.4 0.2 - - - -
115C LEU* 1.3 78.0 - - - +
117C PRO* 1.3 61.0 - - + +
119C LYS* 4.4 0.7 - - - -
120C ALA* 2.7 37.4 + - - +
153C PRO* 4.1 12.8 - - - +
154C THR 4.2 4.9 - - - -
155C PRO* 4.0 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C SER 4.1 3.4 - - - +
114C ASP 3.4 14.8 - - - +
115C LEU 3.4 3.8 - - - -
116C LEU* 1.3 93.9 - - + +
118C CYS* 1.3 59.4 - - - +
120C ALA* 3.7 2.1 + - - +
121C GLU* 3.1 26.2 + - - +
150C ILE 4.8 3.8 - - - +
151C LYS 5.7 1.3 - - - +
153C PRO* 3.6 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 3.5 13.7 + - + +
116C LEU 3.2 0.4 - - - -
117C PRO* 1.3 79.5 - - - +
119C LYS* 1.3 62.6 + - - +
120C ALA 3.2 0.2 - - - -
121C GLU* 3.4 5.4 + - - +
122C GLU* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ASP* 3.8 16.8 - - - +
108C TYR* 3.6 27.1 - - + -
111C THR* 3.1 37.2 - - + +
115C LEU* 3.2 19.3 + - - +
116C LEU* 3.8 2.7 - - - +
118C CYS* 1.3 77.9 - - - +
120C ALA* 1.3 57.2 + - - +
122C GLU* 3.4 18.1 + - - +
123C ILE* 3.0 45.4 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
108C TYR* 3.5 16.9 - - + +
116C LEU 2.7 21.5 + - - +
117C PRO 3.8 3.8 - - - +
119C LYS* 1.3 71.1 - - - +
121C GLU* 1.3 59.9 + - - +
123C ILE 3.5 0.3 + - - -
124C TYR* 3.0 30.1 + - - +
150C ILE* 3.7 17.8 - - + +
153C PRO* 3.8 23.1 - - + -
157C CYS* 4.7 0.2 - - - -
158C PHE* 3.5 12.5 - - + -
----------------------------------------------------------
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 PRO 3.1 16.2 + - - +
118C CYS* 3.4 5.2 + - - +
120C ALA* 1.3 79.1 - - - +
122C GLU* 1.3 57.9 + - - +
124C TYR* 3.4 3.5 + - + +
125C LYS* 2.8 69.2 + - + +
150C ILE* 4.0 19.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
118C CYS* 2.9 19.9 + - - +
119C LYS* 3.6 19.8 - - - +
121C GLU* 1.3 77.3 - - - +
123C ILE* 1.3 60.4 + - - +
125C LYS* 3.5 4.5 + - - +
126C ALA* 3.0 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C PHE* 3.9 15.5 - - + -
104C ALA* 3.5 37.5 - - + +
105C CYS* 5.2 0.4 - - - -
107C ASP* 5.7 0.7 - - - +
108C TYR* 3.7 19.5 - - + -
119C LYS* 3.0 26.5 + - + +
122C GLU* 1.3 79.3 - - + +
124C TYR* 1.3 60.8 + - - +
126C ALA* 4.5 0.7 - - - -
127C PHE* 2.9 50.5 + - + +
128C VAL* 3.7 0.4 + - + -
158C PHE* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ALA 3.0 19.0 + - - +
121C GLU* 3.7 8.1 - - + +
123C ILE* 1.3 77.8 - - - +
125C LYS* 1.3 66.3 + - + +
128C VAL* 2.9 41.1 + - + -
129C HIS* 2.8 65.6 + + + -
143C ARG* 4.0 13.6 + - - +
146C THR* 4.1 6.3 - - + -
147C ALA* 3.5 39.2 - - + +
150C ILE* 3.7 26.7 - - + -
158C PHE* 4.3 1.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C GLU* 2.8 54.5 + - + +
122C GLU* 4.0 4.5 - - - +
124C TYR* 1.3 82.9 - - + +
126C ALA* 1.3 57.7 + - - +
129C HIS* 4.3 26.8 - - + +
132C ALA* 3.1 25.3 - - - +
133C ALA 4.7 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C GLU* 3.0 21.3 + - + +
123C ILE* 3.3 0.8 + - - -
125C LYS* 1.3 76.5 - - - +
127C PHE* 1.3 78.8 + - + +
132C ALA* 3.3 10.9 - - - +
133C ALA* 4.0 2.8 + - - +
134C LYS* 3.3 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLU 4.1 3.4 - - - -
100C GLU* 3.9 28.5 - - + -
101C PHE* 3.6 48.0 - + + -
104C ALA* 3.7 19.3 - - + -
123C ILE* 2.9 26.7 + - + +
125C LYS 3.4 0.2 - - - -
126C ALA* 1.3 92.4 - - + +
128C VAL* 1.3 59.0 + - - +
132C ALA* 3.8 4.7 - - - -
134C LYS* 3.4 36.3 - - + +
135C GLN* 3.2 5.7 - - - -
136C ILE* 2.9 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C PHE* 4.1 24.9 - - + -
123C ILE 4.0 4.3 - - - +
124C TYR* 2.9 48.3 + - + -
127C PHE* 1.3 74.8 - - - +
129C HIS* 1.3 69.5 - - - +
135C GLN* 4.4 4.5 + - - +
136C ILE* 4.5 5.7 - - + +
138C ILE* 3.7 27.4 - - + +
143C ARG* 3.2 22.2 - - + -
146C THR* 4.2 13.2 - - + +
158C PHE* 4.5 9.2 - - + -
161C ALA* 5.5 0.9 - - + -
----------------------------------------------------------
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