Contacts of the helix formed by residues 111 - 133 (chain A) in PDB entry 4WNO
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 111 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR 4.3 0.6 + - - -
110A LEU* 1.3 77.1 - - - +
112A GLU* 1.3 64.7 + - - +
113A ASP* 3.5 9.1 + - - +
114A THR* 3.1 28.5 + - - -
115A ILE* 2.9 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A SER* 1.3 74.5 - - - +
113A ASP* 1.3 59.5 + - - +
115A ILE* 3.3 7.2 + - - -
116A ARG* 2.9 33.3 + - - +
215A LEU* 4.6 10.0 - - + +
246A GLU 4.5 1.7 - - - +
247A THR* 3.5 11.8 - - - +
248A SER* 2.6 52.3 + - - -
251A LEU* 3.5 25.4 - - + +
277A PHE* 3.6 14.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A SER* 3.2 7.9 + - - +
112A GLU* 1.3 80.1 - - - +
114A THR* 1.3 57.9 + - - +
116A ARG* 2.9 28.3 + - - +
117A LEU* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TYR* 4.5 7.7 + - + +
110A LEU* 4.1 17.3 - - + -
111A SER* 3.1 26.7 + - - -
113A ASP* 1.3 74.3 - - - +
115A ILE* 1.3 67.3 + - - +
117A LEU* 3.2 10.4 + - + +
118A PHE* 3.0 54.8 + - + -
157A ASN* 5.2 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 3.6 26.2 - - + +
111A SER 2.9 14.5 + - - +
112A GLU* 3.6 10.5 - - - +
114A THR* 1.3 75.8 - - - +
116A ARG* 1.3 57.1 + - - +
118A PHE* 3.3 5.9 + - - +
119A LEU* 2.8 34.7 + - + +
211A VAL* 4.0 29.8 - - + +
214A CYS* 3.9 18.8 - - + -
215A LEU* 3.9 39.3 - - + +
251A LEU* 4.6 4.9 - - + -
277A PHE* 4.1 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 2.9 13.9 + - - +
113A ASP* 2.9 36.2 + - - +
114A THR 3.2 0.2 - - - -
115A ILE* 1.3 77.4 - - - +
117A LEU* 1.3 56.1 + - - +
119A LEU* 3.7 1.4 - - - +
120A GLN* 2.8 61.7 + - + +
277A PHE* 2.8 62.7 + - + +
278A LEU* 4.2 0.6 - - - +
279A ASP 3.9 10.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ASP 3.0 14.7 + - - +
114A THR* 3.2 13.4 + - + +
116A ARG* 1.3 78.4 - - - +
118A PHE* 1.3 78.4 + - + +
120A GLN* 3.6 14.7 + - - +
121A GLN* 3.3 41.7 + - + +
156A PRO 4.7 2.0 - - - +
157A ASN* 3.6 37.9 - - + +
159A ILE 4.2 5.6 - - - +
160A ARG* 4.7 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.8 30.3 - - + -
103A TYR* 3.8 34.1 - + - -
110A LEU* 4.0 8.7 - - + -
114A THR* 3.0 29.3 + - + +
115A ILE* 3.9 4.5 - - - +
117A LEU* 1.3 90.4 - - + +
119A LEU* 1.3 62.0 + - - +
121A GLN* 3.2 7.6 + - - +
122A ILE* 3.0 37.5 + - + +
146A LEU* 4.7 1.6 - - + -
156A PRO 5.2 0.7 - - - -
159A ILE* 3.8 41.3 - - + -
161A VAL* 3.6 26.3 - - + +
214A CYS* 5.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 2.8 20.7 + - + +
116A ARG* 3.9 0.7 - - - +
118A PHE* 1.3 76.6 - - - +
120A GLN* 1.3 58.9 + - - +
122A ILE* 4.3 15.0 - - + -
123A ALA* 2.8 32.1 + - - +
207A ILE* 3.8 28.9 - - + -
211A VAL* 3.8 22.9 - - + -
254A LEU* 3.7 30.5 - - + -
258A LEU* 5.7 0.4 - - + -
272A PHE* 4.0 15.3 - - + -
277A PHE* 4.3 8.7 - - + -
278A LEU* 3.5 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 2.8 34.6 + - - +
117A LEU* 3.8 19.3 - - - +
118A PHE 3.3 0.2 - - - -
119A LEU* 1.3 77.4 - - - +
121A GLN* 1.3 58.7 + - + +
123A ALA* 3.4 6.6 + - - +
124A GLY* 3.1 22.7 + - - -
278A LEU* 2.9 43.1 + - + +
279A ASP 3.7 1.6 - - - -
280A ALA* 3.3 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 3.0 50.1 + - - +
117A LEU* 3.3 30.0 + - + +
118A PHE* 3.2 11.0 + - - +
119A LEU 3.2 0.4 - - - -
120A GLN* 1.3 76.1 - - + +
122A ILE* 1.3 64.0 + - - +
124A GLY* 3.1 9.5 + - - +
125A ALA 3.2 10.0 + - - -
159A ILE 3.3 21.0 + - - -
160A ARG* 3.2 34.9 - - - +
161A VAL* 3.0 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ASN* 5.3 0.9 - - - -
100A LEU* 5.1 2.5 - - + -
118A PHE* 3.0 28.5 + - + +
119A LEU* 3.8 20.2 - - + +
121A GLN* 1.3 74.4 - - - +
123A ALA* 1.3 57.6 + - - +
125A ALA* 3.2 8.0 + - - +
126A MET* 2.9 40.8 + - + +
139A LEU* 6.2 0.7 - - + -
144A ILE* 4.3 32.8 - - + -
161A VAL* 4.2 11.4 - - + -
163A ILE* 4.6 11.7 - - + -
207A ILE* 4.2 21.1 - - + -
210A ILE* 4.9 16.6 - - + -
272A PHE* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU 2.8 18.9 + - - +
120A GLN* 3.5 5.8 - - - +
122A ILE* 1.3 78.0 - - - +
124A GLY* 1.3 56.8 + - - +
126A MET* 3.2 1.0 + - - -
127A ARG* 2.9 31.6 + - - +
272A PHE* 3.8 21.5 - - + -
273A PHE* 3.6 17.2 - - + +
278A LEU* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A HIS* 3.4 21.2 + - - -
74A ASN* 5.1 0.4 - - - -
120A GLN 3.1 14.0 + - - -
121A GLN* 3.1 5.1 + - - -
123A ALA* 1.3 76.4 - - - +
125A ALA* 1.3 61.7 + - - +
127A ARG* 3.2 22.9 + - - +
128A LEU 3.4 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A HIS* 3.6 13.0 - - - +
74A ASN* 3.6 31.9 - - + +
75A ILE* 3.8 12.8 - - + -
121A GLN 3.2 7.0 + - - +
122A ILE 3.6 7.2 - - - +
124A GLY* 1.3 76.0 - - - +
126A MET* 1.3 62.5 + - - +
128A LEU* 3.1 5.2 + - - +
129A LEU* 3.0 27.5 + - - +
163A ILE* 3.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 2.9 24.7 + - + +
123A ALA* 3.2 6.9 + - - +
125A ALA* 1.3 72.8 - - - +
127A ARG* 1.3 60.4 + - - +
129A LEU* 3.7 25.7 - - + +
130A HIS* 2.8 32.4 + - - +
134A ILE 5.6 0.7 - - - +
139A LEU* 4.2 7.6 - - - -
163A ILE* 4.1 15.7 - - - -
203A ASP* 3.9 33.7 - - + +
207A ILE* 3.6 27.4 - - + -
269A PHE* 4.0 22.2 - - + -
272A PHE* 4.6 2.7 - - + -
273A PHE* 3.9 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ALA* 2.9 19.3 + - - +
124A GLY* 3.4 14.8 - - - +
126A MET* 1.3 75.8 - - - +
128A LEU* 1.3 58.1 + - - +
130A HIS* 3.5 1.9 + - - +
131A SER* 2.9 30.4 + - - -
273A PHE* 3.4 61.5 + - + +
274A HIS* 4.7 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.9 23.6 - - + -
71A LYS 3.7 27.1 - - - +
72A HIS* 3.8 24.5 - - + -
75A ILE* 4.1 3.8 - - + -
124A GLY 3.4 6.7 + - - +
125A ALA 3.1 9.2 + - - +
127A ARG* 1.3 78.6 - - - +
129A LEU* 1.3 66.9 + - - +
131A SER* 2.9 24.4 + - - +
132A LYS* 3.0 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.4 6.3 - - + -
75A ILE* 3.7 24.7 - - + -
125A ALA* 3.0 27.2 + - + +
126A MET* 3.4 30.5 + - + +
128A LEU* 1.3 74.7 - - - +
130A HIS* 1.3 63.7 + - - +
132A LYS* 3.1 3.8 + - - +
133A GLY 3.0 18.7 + - - -
134A ILE* 3.0 41.6 + - + +
136A HIS* 3.9 30.3 - - + +
163A ILE* 5.2 1.8 - - + -
166A PHE* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A MET 2.8 22.1 + - - +
127A ARG 3.8 3.4 - - - +
129A LEU* 1.3 72.8 - - - +
131A SER* 1.3 64.2 + - - +
133A GLY* 3.2 12.8 + - - +
134A ILE 4.7 3.4 - - - +
269A PHE* 3.4 58.2 - + + +
273A PHE* 4.3 10.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ARG* 2.9 18.9 + - - -
128A LEU* 2.9 30.7 + - - +
130A HIS* 1.3 78.4 - - - +
132A LYS* 1.3 63.3 + - - +
133A GLY 3.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 2.8 33.2 + - + +
70A LEU* 4.3 7.9 - - + +
71A LYS 5.7 0.4 - - - +
128A LEU* 3.0 42.6 + - + +
129A LEU 3.8 3.8 - - - +
131A SER* 1.3 80.7 - - - +
133A GLY* 1.3 61.0 + - - +
134A ILE* 3.9 17.9 - - + -
171A TYR* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU 3.0 3.6 + - - -
130A HIS* 3.2 11.7 + - - -
131A SER 3.3 1.0 - - - -
132A LYS* 1.3 80.1 - - - +
134A ILE* 1.3 59.7 + - - +
135A ILE* 5.5 1.3 - - - -
171A TYR* 3.3 6.6 - - - +
172A LEU* 2.8 40.4 + - - +
----------------------------------------------------------
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