Contacts of the helix formed by residues 130 - 153 (chain A) in PDB entry 1WXI
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 130 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU 4.1 1.0 + - - -
129A LEU* 1.3 76.9 - - - +
131A ASP* 1.3 65.0 + - - +
132A PHE* 3.7 8.0 + - - +
133A VAL* 3.3 30.0 + - - +
134A ARG* 2.9 22.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A SER* 1.3 73.4 - - - +
132A PHE* 1.3 62.6 + - - +
134A ARG* 3.3 22.2 + - - +
135A GLY* 3.0 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A SER* 3.2 7.5 + - - +
131A ASP* 1.3 78.1 - - - +
133A VAL* 1.3 70.2 + - + +
135A GLY* 3.1 11.1 + - - -
136A ASN* 3.3 37.6 + - - +
300A AMP 4.0 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 3.7 27.4 - - + -
130A SER* 3.3 27.6 + - - +
132A PHE* 1.3 81.8 - - + +
134A ARG* 1.3 65.9 + - - +
136A ASN* 3.1 13.5 + - + +
137A GLU* 3.0 21.0 + - + +
140A ARG* 5.4 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 4.5 9.6 + - - -
115A VAL* 4.7 0.4 - - + -
119A GLU* 3.0 41.3 + - - +
123A ARG* 5.2 6.3 - - - +
128A GLU* 5.3 2.4 + - - -
129A LEU* 3.6 25.4 + - + +
130A SER 2.9 19.0 + - - +
131A ASP* 3.3 29.6 + - - +
133A VAL* 1.3 77.9 - - - +
135A GLY* 1.3 63.1 + - - +
137A GLU* 3.2 11.6 + - - +
138A LYS* 3.0 46.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASP 3.0 12.8 + - - -
132A PHE 3.1 5.8 + - - -
133A VAL 3.1 0.6 - - - -
134A ARG* 1.3 79.2 - - - +
136A ASN* 1.3 60.9 + - - +
138A LYS* 3.3 15.9 + - - +
139A ALA* 3.1 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PHE* 3.3 38.2 + - - +
133A VAL* 3.1 12.7 + - + +
135A GLY* 1.3 73.5 - - - +
137A GLU* 1.3 61.3 + - - +
139A ALA* 3.1 2.8 + - - +
140A ARG* 2.9 52.2 + - - +
172A THR* 2.9 26.4 + - + +
300A AMP 3.6 31.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.3 19.9 - - + +
118A SER* 3.4 28.3 - - - -
119A GLU* 2.6 38.6 + - - +
122A LEU* 4.6 4.2 - - - +
129A LEU* 3.5 16.6 - - + +
133A VAL* 3.0 13.3 + - + +
134A ARG* 3.3 9.2 - - - +
136A ASN* 1.3 77.8 - - - +
138A LYS* 1.3 57.2 + - - +
140A ARG* 3.2 12.3 + - - +
141A GLU* 2.9 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 3.6 52.1 - - + +
111A ILE* 3.8 8.1 - - + +
115A VAL* 4.3 20.2 - - + -
134A ARG* 3.0 36.8 + - - +
135A GLY* 3.5 12.7 - - - +
137A GLU* 1.3 77.2 - - - +
139A ALA* 1.3 62.0 + - - +
141A GLU* 3.2 3.1 + - - +
142A ARG* 3.1 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLY 3.1 7.6 + - - +
136A ASN 3.1 9.2 + - - +
138A LYS* 1.3 80.7 - - - +
140A ARG* 1.3 55.6 + - - +
142A ARG* 3.4 14.8 + - - +
143A MET 3.2 20.1 + - - -
172A THR* 3.6 28.5 - - - +
175A GLY* 3.7 11.5 - - - -
176A ASP* 4.2 14.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 6.1 1.6 - - - +
136A ASN* 2.9 41.2 + - - +
137A GLU* 3.7 8.7 - - - +
138A LYS 3.2 0.2 - - - -
139A ALA* 1.3 77.0 - - - +
141A GLU* 1.3 59.0 + - - +
143A MET* 3.3 9.0 + - + +
144A LYS* 3.0 35.4 + - + +
172A THR* 3.6 6.8 - - + +
173A LYS* 2.9 31.2 + - - +
174A TYR* 3.7 19.7 + - - +
175A GLY* 4.0 9.4 - - - -
300A AMP 2.7 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.8 26.8 - - + +
114A ALA* 3.4 31.9 - - + +
115A VAL* 4.1 13.5 - - + -
118A SER* 5.1 4.9 + - - -
137A GLU* 2.9 16.9 + - + +
138A LYS 3.2 4.7 + - - +
140A ARG* 1.3 76.8 - - - +
142A ARG* 1.3 57.8 + - - +
144A LYS* 3.2 36.1 + - - +
145A ALA* 3.0 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 2.9 49.9 + - + -
85A TYR* 4.0 17.2 - - - +
88A GLN* 5.4 0.4 - - - +
111A ILE* 3.8 19.2 - - + +
138A LYS* 3.1 40.5 + - - +
139A ALA* 3.6 14.3 - - - +
141A GLU* 1.3 75.3 - - - +
143A MET* 1.3 65.2 + - - +
145A ALA* 3.5 4.4 + - - +
146A GLN* 3.1 35.7 + - - +
400A AMP 3.5 53.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ALA 3.2 9.2 + - - +
140A ARG* 3.5 17.5 - - + +
142A ARG* 1.3 77.0 - - - +
144A LYS* 1.3 75.8 + - + +
146A GLN* 3.2 10.6 + - - +
147A TYR* 3.0 46.2 + - + -
157A VAL* 6.4 0.4 - - - -
174A TYR* 3.4 24.5 - - + +
175A GLY 3.5 19.7 - - - +
178A GLY* 3.6 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 3.0 22.5 + - + +
141A GLU* 3.2 38.4 + - - +
143A MET* 1.3 92.0 - - + +
145A ALA* 1.3 63.3 + - - +
147A TYR* 3.3 4.4 + - - +
148A SER* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 3.8 27.1 - - + -
109A VAL* 4.6 14.8 - - + -
111A ILE* 5.1 2.2 - - + -
141A GLU* 3.0 20.7 + - - +
142A ARG* 3.8 1.8 - - - +
143A MET 3.3 0.2 - - - -
144A LYS* 1.3 75.4 - - - +
146A GLN* 1.3 63.6 - - - +
148A SER* 3.3 6.5 + - - -
149A ILE* 3.1 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.0 18.1 - - + +
45A LEU* 3.9 4.3 - - - -
46A GLY* 3.2 27.8 + - - +
81A VAL* 4.9 5.8 - - + -
83A LEU* 3.9 20.1 - - + +
142A ARG* 3.1 28.3 + - - +
143A MET* 3.7 8.4 - - - +
145A ALA* 1.3 77.7 - - - +
147A TYR* 1.3 56.2 + - - +
149A ILE* 3.3 6.7 + - - +
150A ALA* 2.9 28.2 + - - +
157A VAL* 3.7 29.0 - - + +
158A VAL 4.6 2.9 - - - +
176A ASP* 6.3 1.4 - - - +
400A AMP 5.2 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A MET* 3.0 43.7 + - + +
144A LYS* 3.9 4.3 - - - +
145A ALA 3.3 0.2 - - - -
146A GLN* 1.3 73.9 - - - +
148A SER* 1.3 60.3 + - - +
150A ALA* 3.8 4.6 - - + +
151A GLY* 2.9 25.3 + - - -
157A VAL* 3.8 21.8 - - + -
178A GLY 3.3 22.2 + - - -
179A THR* 3.1 22.0 + - - -
180A ASP* 2.7 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS* 3.0 19.1 + - - +
145A ALA* 3.7 7.0 - - - -
146A GLN 3.3 0.2 - - - -
147A TYR* 1.3 77.8 - - - +
149A ILE* 1.3 63.6 + - - +
151A GLY* 3.3 2.1 + - - -
152A MET* 3.2 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.2 19.5 - - + -
79A ILE* 4.6 6.1 - - + -
81A VAL* 3.9 33.0 - - + -
107A LEU* 4.2 28.3 - - + -
109A VAL* 4.5 14.1 - - + -
145A ALA* 3.1 19.2 + - + +
146A GLN* 3.6 7.9 - - - +
148A SER* 1.3 76.1 - - - +
150A ALA* 1.3 63.2 + - - +
152A MET* 3.2 4.9 + - - -
153A THR* 2.8 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 4.1 10.0 - - + +
146A GLN 2.9 16.9 + - - +
147A TYR* 3.8 7.9 - - + +
149A ILE* 1.3 77.1 - - - +
151A GLY* 1.3 62.7 + - - +
153A THR* 3.7 6.3 - - - -
154A SER* 3.1 6.6 + - - -
155A GLY 2.9 47.6 + - - +
156A VAL* 4.5 0.2 - - - -
157A VAL* 4.0 18.4 - - + -
180A ASP* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A TYR 2.9 17.8 + - - -
148A SER* 3.3 3.3 + - - -
149A ILE 3.2 0.6 - - - -
150A ALA* 1.3 77.9 - - - +
152A MET* 1.3 64.9 + - - +
154A SER* 4.3 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A SER* 3.2 16.1 + - - +
149A ILE* 3.2 7.1 + - - +
151A GLY* 1.3 81.9 - - - +
153A THR* 1.3 64.3 + - + +
154A SER* 3.6 1.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LYS* 4.2 3.5 - - - +
42A SER* 3.0 30.2 + - - -
44A VAL* 4.3 2.3 - - - +
77A GLN* 5.4 1.1 - - - +
79A ILE* 5.2 5.7 - - + +
105A ARG* 4.6 19.5 - - - +
107A LEU* 6.1 1.8 - - + -
149A ILE* 2.8 33.5 + - + +
150A ALA* 3.3 9.1 + - - -
152A MET* 1.3 86.1 - - + +
154A SER* 1.3 70.2 + - - +
155A GLY 4.0 2.1 + - - -
----------------------------------------------------------
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