Contacts of the helix formed by residues 122 - 138 (chain A) in PDB entry 2HXO
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 THR 122 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY 5.1 1.6 + - - -
68A ASP* 2.6 32.7 + - - +
114A GLN* 4.2 1.6 + - - -
120A TRP 4.1 7.6 - - - +
121A GLY* 1.3 75.5 - - - -
123A VAL* 1.3 65.3 + - - +
124A ALA 3.5 0.4 - - - -
125A PRO* 3.4 10.6 - - - +
126A ARG* 3.2 40.1 + - - +
198B TYR* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY 5.6 0.2 - - - +
67A THR* 4.5 6.1 - - + -
68A ASP* 3.8 19.5 - - + +
71A VAL* 3.8 41.3 - - + -
111A LEU* 4.2 14.4 - - + -
114A GLN* 3.0 40.8 + - + +
115A LEU* 5.0 1.6 - - + -
122A THR* 1.3 79.3 + - - +
124A ALA* 1.3 73.3 + - + +
126A ARG* 3.2 5.5 + - + +
127A ILE* 3.1 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLN* 5.1 6.1 - - + +
115A LEU* 3.5 29.2 - - + -
118A THR 5.9 1.1 - - - +
121A GLY* 4.6 3.5 + - - +
123A VAL* 1.3 82.8 - - + +
125A PRO* 1.3 66.0 - - + +
127A ILE* 3.1 8.4 + - - +
128A PHE* 2.9 38.9 + - + -
153A MSE 5.0 0.7 - - - -
190B TRP* 4.4 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLY 3.2 24.2 - - - +
122A THR* 3.4 13.5 - - - +
124A ALA* 1.3 96.9 - - + +
126A ARG* 1.3 56.8 + - + +
128A PHE* 3.7 3.8 - - + -
129A GLU* 2.8 29.6 + - - +
190B TRP* 3.8 33.0 - - + +
193B LEU* 4.0 27.4 - - + -
198B TYR* 4.2 7.0 - - + +
201B THR* 3.4 7.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 2.7 45.9 + - - -
71A VAL* 6.4 0.4 - - + -
72A THR* 4.7 10.7 + - - +
122A THR* 3.2 31.9 + - - +
123A VAL* 3.2 5.3 + - + +
124A ALA 3.2 1.0 - - - -
125A PRO* 1.3 75.5 - - + +
127A ILE* 1.3 67.4 + - + +
129A GLU* 3.4 7.1 + - - +
130A SER* 2.8 28.5 + - - -
198B TYR* 3.4 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A VAL* 3.4 32.5 - - + -
75A VAL* 4.7 8.1 - - + -
93A VAL* 4.7 5.8 - - + -
97A LEU* 4.2 26.0 - - + -
111A LEU* 5.9 2.7 - - + -
123A VAL* 3.1 22.9 + - + +
124A ALA* 3.6 2.2 - - - +
126A ARG* 1.3 79.3 - - + +
128A PHE* 1.3 64.7 + - - +
130A SER* 3.1 7.1 + - - +
131A LEU* 3.0 38.4 + - + +
153A MSE 3.3 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 5.7 3.4 - - + -
124A ALA* 2.9 21.7 + - + +
125A PRO* 3.8 8.1 - - + +
127A ILE* 1.3 79.9 - - - +
129A GLU* 1.3 57.1 + - - +
131A LEU* 4.1 4.2 - - + +
132A GLY 2.8 24.8 + - - -
146A PHE* 3.6 24.7 - + - -
149A SER* 3.9 16.6 - - - -
150A SER* 3.5 46.0 - - - -
153A MSE 3.3 40.2 - - + -
190B TRP* 4.0 21.3 - + + -
200B PHE* 3.4 17.2 - + + -
201B THR* 4.5 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO 2.8 18.3 + - - +
126A ARG* 3.7 6.7 - - - +
127A ILE 3.2 0.2 - - - -
128A PHE* 1.3 76.1 - - - +
130A SER* 1.3 64.0 + - - +
133A ARG* 3.0 64.3 + - - +
197B ALA 4.3 0.7 - - - +
198B TYR* 3.4 26.8 - - + +
199B PRO* 3.1 18.0 - - - +
200B PHE* 3.1 16.6 + - - +
201B THR* 2.6 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 4.7 9.6 - - - +
93A VAL* 4.0 27.3 - - - +
126A ARG 2.8 19.3 + - - -
127A ILE* 3.4 11.5 - - - +
129A GLU* 1.3 78.9 - - - +
131A LEU* 1.3 61.9 + - - +
133A ARG* 4.3 3.1 - - - +
134A GLN* 3.5 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 4.2 25.3 - - + +
93A VAL* 3.9 27.8 - - + -
127A ILE* 3.0 37.8 + - + +
128A PHE* 4.1 4.7 - - + +
130A SER* 1.3 73.5 - - - +
132A GLY* 1.3 66.3 + - - +
134A GLN* 3.1 17.7 + - - +
135A VAL* 3.1 14.5 + - - +
149A SER* 3.9 27.8 - - - +
152A LEU* 4.2 13.0 - - + -
153A MSE 4.1 19.5 - - + +
156A ILE* 4.6 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A PHE 2.8 14.8 + - - -
131A LEU* 1.3 73.9 - - - +
133A ARG* 1.3 56.5 + - - +
135A VAL* 2.9 4.5 + - - +
136A GLN* 2.9 31.7 + - - +
149A SER* 3.5 6.6 + - - -
200B PHE* 3.3 40.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 3.0 45.0 + - - +
130A SER* 4.3 5.6 - - - +
131A LEU 3.4 0.2 - - - -
132A GLY* 1.3 74.2 - - - +
134A GLN* 1.3 66.4 + - - +
136A GLN* 3.5 15.3 + - - +
137A ALA* 3.0 26.7 + - - +
196B ASP 4.9 2.0 + - - -
197B ALA* 2.9 29.1 + - - +
199B PRO* 3.6 15.9 - - + +
200B PHE* 4.1 6.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A SER 4.7 0.3 - - - -
86A PRO* 3.1 30.8 - - + +
89A ALA* 3.5 28.5 - - + +
90A VAL* 3.5 22.9 - - + +
93A VAL* 6.0 0.9 - - + -
130A SER 3.5 18.3 + - - +
131A LEU 3.1 7.3 + - - +
133A ARG* 1.3 84.7 - - - +
135A VAL* 1.3 61.4 + - - +
137A ALA* 3.2 6.8 + - - +
138A MSE 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 5.8 0.4 - - + -
131A LEU 3.1 12.8 + - - +
132A GLY* 2.9 10.2 + - - +
134A GLN* 1.3 77.2 - - + +
136A GLN* 1.3 62.4 + - - +
138A MSE 3.1 18.1 + - - +
140A VAL* 3.3 46.4 + - + +
145A TRP* 4.2 17.0 - - + -
148A ALA* 3.9 21.3 - - + -
149A SER* 3.8 13.7 - - - +
152A LEU* 4.1 19.5 - - + -
228A ILE* 4.8 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLY 2.9 15.6 + - - +
133A ARG* 3.7 20.2 - - - +
135A VAL* 1.3 77.3 - - - +
137A ALA* 1.3 63.0 + - - +
139A GLY* 2.9 15.2 + - - -
140A VAL 4.2 1.5 + - - +
145A TRP* 3.2 60.0 - - + +
199B PRO* 5.3 3.2 + - - +
200B PHE* 3.7 29.2 + - + +
203B ALA* 5.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.6 23.6 - - + +
133A ARG 3.0 17.6 + - - +
134A GLN* 3.2 11.0 + - - +
136A GLN* 1.3 76.3 - - - +
138A MSE 1.3 57.9 + - - +
139A GLY* 3.1 3.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PRO* 3.7 18.4 - - + +
87A GLN* 3.6 24.0 - - + +
90A VAL* 5.2 1.3 - - - -
134A GLN 2.9 22.3 + - - +
135A VAL* 3.4 13.2 - - - +
136A GLN 3.0 0.6 - - - -
137A ALA* 1.3 77.0 - - - +
139A GLY* 1.3 62.8 + - - +
140A VAL* 4.3 6.6 - - + +
225A LEU* 3.5 27.6 - - + +
228A ILE* 3.7 22.0 - - + -
229A THR* 3.0 42.8 - - + +
232A HIS* 3.8 13.3 - - - +
----------------------------------------------------------
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