Contacts of the helix formed by residues 113 - 128 (chain R) in PDB entry 2A1T
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 113 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R GLU* 2.7 33.9 + - - -
36R ILE* 3.7 15.7 - - - +
111R GLY 2.7 8.7 + - - -
112R ALA* 1.3 73.1 - - - +
114R ALA* 1.3 57.4 + - - +
115R PHE 3.0 11.1 + - - -
116R GLY 3.5 2.3 + - - -
117R LYS* 2.7 38.4 + - - +
167S ASP* 3.3 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113R SER* 1.3 75.0 - - - +
115R PHE* 1.3 61.9 + - - +
117R LYS* 4.3 4.0 - - - +
118R ASN* 3.1 26.2 + - - +
149S PHE* 3.6 25.8 - - + -
164S ARG* 4.9 2.3 + - - +
165S ALA 4.5 0.9 - - - +
166S ILE* 4.1 17.0 - - + -
167S ASP* 3.1 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 115 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R ILE* 3.8 16.2 - - + -
26R ALA 3.3 26.0 - - - -
27R GLU* 3.6 31.4 - - + +
87R LEU* 4.2 32.3 - - + -
92R LEU* 4.0 17.7 - - + -
110R ALA* 4.8 4.7 - - + -
113R SER* 3.0 9.2 + - - +
114R ALA* 1.3 80.4 - - - +
116R GLY* 1.3 79.5 + - - +
118R ASN* 3.3 4.8 + - - +
119R LEU* 3.1 52.9 + - + +
164S ARG* 6.3 0.4 - - - +
167S ASP* 4.5 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110R ALA* 4.2 11.4 - - - -
111R GLY 3.4 21.3 - - - -
113R SER* 3.3 5.9 + - - -
115R PHE* 1.3 92.1 - - - +
117R LYS* 1.3 59.6 + - - +
119R LEU* 3.5 1.3 + - - -
120R LEU* 3.2 36.5 + - - +
167R SER* 5.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112R ALA* 3.6 27.8 - - + +
113R SER 2.7 30.7 + - - +
114R ALA* 4.0 6.1 - - - +
116R GLY* 1.3 72.2 - - - +
118R ASN* 1.3 58.6 + - - +
121R PRO* 2.9 25.2 - - - +
133R SER* 6.2 4.3 - - - -
134R ASP* 4.5 18.5 + - - -
167R SER* 5.0 5.2 - - - +
124S LYS* 5.1 8.6 - - - +
125S GLN* 4.5 15.0 + - - +
130S ASP 6.0 0.2 + - - -
132S ASN* 3.8 29.2 + - + +
136S GLN* 2.9 14.5 + - - -
149S PHE* 4.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 118 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89R PRO* 3.5 23.8 - - - +
114R ALA 3.1 20.4 + - - +
115R PHE* 3.4 6.3 - - - +
117R LYS* 1.3 76.2 - - - +
119R LEU* 1.3 64.6 + - - +
122R ARG 4.6 0.3 + - - -
136S GLN* 3.5 14.8 - - - +
146S GLN* 2.5 44.3 + - - +
148S THR* 2.7 29.4 + - - +
149S PHE* 4.2 3.5 - - + -
164S ARG* 3.4 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R ILE* 3.9 9.9 - - + -
89R PRO* 3.9 19.3 - - + -
92R LEU* 4.0 11.0 - - + -
93R THR* 3.6 20.9 - - - +
96R ILE* 3.8 24.9 - - + -
115R PHE* 3.1 46.6 + - + +
116R GLY* 4.2 2.7 - - - +
118R ASN* 1.3 80.5 - - - +
120R LEU* 1.3 70.1 + - + +
122R ARG* 3.3 13.7 + - - +
123R VAL* 3.4 24.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R ILE* 4.6 11.7 - - + -
108R ILE* 4.4 6.5 - - + +
109R CYS 4.3 13.9 - - - +
110R ALA* 3.7 22.2 - - + +
116R GLY 3.2 16.0 + - - +
119R LEU* 1.3 77.2 - - + +
121R PRO* 1.3 76.8 - - + +
123R VAL* 3.1 15.3 + - + +
124R ALA* 2.9 22.1 + - - +
131R PRO* 5.1 3.4 - - + -
165R VAL* 4.1 24.3 - - + +
166R PHE* 3.6 25.8 - - - +
167R SER* 3.8 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 121 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117R LYS* 2.9 26.2 - - - +
118R ASN 3.9 2.9 - - - +
119R LEU 3.5 2.9 - - - -
120R LEU* 1.3 94.7 - - + +
122R ARG* 1.3 61.1 + - - +
124R ALA* 3.4 1.9 - - - +
125R ALA* 3.0 17.7 + - - +
131R PRO* 4.1 12.5 - - + -
133R SER* 5.7 0.9 - - - +
132S ASN 3.6 9.6 - - - +
133S GLN* 3.8 15.9 - - + -
136S GLN* 3.6 25.8 - - + +
137S MET* 3.2 26.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89R PRO* 3.4 26.1 + - + -
90R GLU* 3.6 25.2 - - - +
93R THR* 3.5 15.4 - - + +
118R ASN 4.6 1.8 - - - +
119R LEU 3.3 11.1 + - - +
120R LEU 3.1 1.0 - - - -
121R PRO* 1.3 75.7 - - - +
123R VAL* 1.3 56.8 + - - +
125R ALA* 3.1 7.1 + - - +
126R LYS* 2.8 38.6 + - + +
196R ILE* 4.4 4.4 - - - +
136S GLN* 4.1 6.7 - - - +
139S ALA* 3.7 14.1 + - - +
140S GLY* 3.9 16.1 - - - -
143S ASP* 4.1 12.3 + - - +
144S TRP 2.8 32.7 + - - -
146S GLN* 2.8 54.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R THR* 3.9 14.1 + - + +
96R ILE* 3.7 36.3 - - + -
97R LEU* 4.4 9.2 - - + -
108R ILE* 4.6 7.2 - - + -
119R LEU* 3.4 35.2 - - + +
120R LEU* 3.4 13.9 - - + +
122R ARG* 1.3 71.9 - - - +
124R ALA* 1.3 67.5 + - - +
126R LYS* 3.0 4.7 + - - +
127R LEU* 2.7 35.5 + - + +
165R VAL* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120R LEU 2.9 7.7 + - - +
121R PRO 3.4 6.1 - - - +
123R VAL* 1.3 75.1 - - - +
125R ALA* 1.3 50.4 + - - +
127R LEU 2.9 3.2 + - - +
128R GLU 2.4 35.0 + - - -
129R VAL* 3.1 38.5 + - + +
131R PRO* 3.3 35.7 - - + -
165R VAL* 4.5 5.9 - - + +
137S MET* 4.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R PRO 3.0 11.5 + - - +
122R ARG* 3.1 8.9 + - - +
124R ALA* 1.3 77.9 - - - +
126R LYS* 1.3 66.2 + - - +
128R GLU* 3.4 11.2 + - - +
137S MET* 3.5 30.0 - - + +
140S GLY* 4.6 5.2 - - - -
141S PHE* 3.1 46.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 126 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R THR* 3.9 14.8 - - + -
97R LEU* 3.5 39.6 - - + +
122R ARG* 2.8 17.6 + - + +
123R VAL 3.4 7.2 - - - +
125R ALA* 1.3 83.4 - - - +
127R LEU* 1.3 63.0 + - - +
128R GLU* 3.5 6.2 + - - +
140S GLY* 2.4 42.0 + - - +
141S PHE* 4.2 4.5 - - - +
143S ASP* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96R ILE* 6.2 0.2 - - + -
97R LEU* 4.2 22.7 - - + -
100R GLN* 4.2 21.1 - - + +
108R ILE* 3.7 19.1 - - + -
123R VAL* 2.7 24.0 + - + +
124R ALA 3.7 4.7 - - - +
126R LYS* 1.3 71.2 - - - +
128R GLU* 1.3 72.6 + - - +
129R VAL* 3.9 14.1 - - + +
163R VAL* 3.6 40.8 - - + +
165R VAL* 4.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124R ALA 2.4 19.0 + - - -
125R ALA* 3.4 15.7 + - - +
126R LYS 3.3 6.9 - - - +
127R LEU* 1.3 76.0 - - - +
129R VAL* 1.3 59.4 + - - +
161R GLU* 4.0 6.6 - - - +
102S LEU* 4.7 12.6 - - - +
106S ARG* 2.8 33.1 + - - +
141S PHE* 5.2 1.3 - - + -
----------------------------------------------------------
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