Contacts of the helix formed by residues 148 - 163 (chain A) in PDB entry 2WA0
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 PHE 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 5.0 1.6 - - + -
133A LYS* 3.7 41.3 - - + +
136A MET* 3.6 37.7 - - + -
137A LEU* 3.8 20.2 - - + -
141A ILE* 3.8 16.4 - - + -
144A TYR 3.9 0.4 + - - -
145A LYS 3.1 17.0 + - - +
147A CYS* 1.3 75.2 - - - +
149A PRO* 1.3 80.4 - - + +
150A VAL 3.0 0.3 + - - -
151A ILE 4.5 0.2 - - - +
152A PHE* 2.8 68.8 + + + +
177A TYR* 4.6 7.0 - - - -
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Residues in contact with PRO 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LYS* 6.0 2.0 - - - +
146A ARG 3.6 11.9 - - - +
147A CYS* 3.4 4.5 - - - -
148A PHE* 1.3 103.3 - - + +
150A VAL* 1.3 60.4 + - + +
152A PHE* 4.4 1.6 - - + +
153A GLY* 3.0 25.8 + - - -
300A ILE* 5.1 2.2 - - - +
311A LEU* 5.8 1.8 - - + -
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 5.2 1.8 - - + -
147A CYS* 3.0 10.8 + - + +
149A PRO* 1.3 81.5 - - + +
151A ILE* 1.3 71.7 + - + +
153A GLY* 3.9 0.2 - - - -
154A LYS* 3.1 38.0 + - + +
300A ILE* 3.7 24.7 - - + -
301A ALA 4.0 14.4 - - - +
302A TYR* 4.4 9.6 - - + -
303A PRO* 4.0 27.6 - - + -
311A LEU* 6.6 0.2 - - + -
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A LEU* 3.9 27.1 - - + +
113A LYS* 3.7 38.6 - - + +
114A VAL* 4.0 11.3 - - + +
117A LEU* 4.0 12.6 - - + -
141A ILE* 4.1 28.7 - - + -
144A TYR* 4.3 9.0 - - + -
147A CYS* 2.9 39.2 + - + +
148A PHE 4.1 0.9 - - - +
150A VAL* 1.3 77.7 - - + +
152A PHE* 1.3 64.0 + - - +
154A LYS 4.0 0.2 - - - -
155A ALA* 3.0 26.2 + - - +
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Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 3.6 11.8 - - + +
121A LEU* 4.2 10.5 - - + -
136A MET* 3.8 27.1 - - + -
148A PHE* 2.8 51.1 + + + +
149A PRO* 4.4 2.0 - - + +
151A ILE* 1.3 71.8 - - - +
153A GLY* 1.3 60.8 + - - +
154A LYS 3.2 0.2 + - - -
155A ALA* 3.3 0.9 + - - +
156A SER* 2.8 48.6 + - - -
167A VAL* 3.5 30.3 - - + -
177A TYR* 3.7 36.6 - + - -
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Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO 3.0 22.6 + - - -
150A VAL 3.9 0.7 - - - -
152A PHE* 1.3 79.3 - - - +
154A LYS* 1.3 56.6 + - - +
156A SER* 3.6 6.3 + - - -
157A GLU* 3.1 25.8 + - - +
300A ILE* 4.2 15.7 - - - +
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Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 4.0 16.8 - - + +
150A VAL* 3.1 22.6 + - + +
153A GLY* 1.3 74.4 - - - +
155A ALA* 1.3 61.0 + - - +
157A GLU* 3.6 13.4 + - - +
158A SER* 2.9 30.3 + - - -
300A ILE* 3.0 44.8 + - + +
301A ALA* 4.3 1.3 - - - +
302A TYR* 3.7 62.2 + - + +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 3.9 26.4 - - + +
117A LEU* 4.1 14.6 - - + -
118A ALA* 3.9 16.6 - - - +
121A LEU* 4.5 5.2 - - + -
151A ILE 3.0 19.1 + - - +
152A PHE 3.7 2.7 - - - +
154A LYS* 1.3 76.0 - - - +
156A SER* 1.3 57.6 + - - +
158A SER* 3.2 6.2 + - - -
159A LEU* 2.9 33.8 + - - +
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 5.0 0.6 - - - +
152A PHE* 2.8 51.0 + - - -
153A GLY* 3.6 7.2 - - - -
155A ALA* 1.3 71.0 - - - +
157A GLU* 1.3 56.9 + - - +
159A LEU* 3.0 6.0 + - - +
160A LYS* 2.9 30.6 + - - +
165A ILE 4.5 0.7 - - - +
167A VAL* 4.0 24.4 + - - +
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLY 3.1 13.6 + - - +
154A LYS* 3.6 12.5 + - - +
156A SER* 1.3 77.4 - - - +
158A SER* 1.3 59.4 + - - +
160A LYS* 3.3 7.8 + - - +
161A MET* 3.0 41.7 + - + +
297A ARG* 3.3 46.3 + - - +
298A VAL 4.8 0.3 - - - +
299A ARG* 4.9 4.7 - - - +
300A ILE* 3.1 27.3 + - + +
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 5.0 6.2 - - - +
118A ALA* 5.0 9.9 - - - -
154A LYS 2.9 18.3 + - - -
155A ALA* 3.2 7.8 + - - -
157A GLU* 1.3 73.7 - - - +
159A LEU* 1.3 61.3 + - - +
161A MET* 5.0 1.3 - - - -
162A ILE* 2.9 55.7 + - - +
163A PHE* 3.6 5.1 + - - -
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ALA* 3.6 35.0 - - + +
121A LEU* 3.6 26.2 - - + -
122A LEU* 4.1 12.6 - - + -
155A ALA 2.9 16.2 + - - +
156A SER* 3.3 10.5 - - - +
158A SER* 1.3 75.1 - - - +
160A LYS* 1.3 58.2 + - - +
163A PHE* 2.9 24.2 + - + -
164A GLY 2.9 24.8 + - - -
165A ILE* 3.0 37.6 + - + +
167A VAL* 3.8 20.4 - - + -
179A LEU* 4.0 4.3 - - + -
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A SER 2.9 12.2 + - - +
157A GLU* 3.5 11.4 - - - +
159A LEU* 1.3 76.1 - - - +
161A MET* 1.3 62.2 + - + +
164A GLY* 3.2 23.4 + - - -
165A ILE 3.2 12.5 + - - +
166A ASP* 3.5 23.8 + - - +
182A CYS* 3.9 14.8 - - - -
201A GLY* 4.9 0.5 - - - -
204A ILE* 5.8 0.3 - - - +
290A HIS* 4.1 28.1 + - + -
293A ARG* 4.2 25.8 - - - +
294A VAL* 4.3 20.1 - - + +
297A ARG* 6.6 0.2 - - - -
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Residues in contact with MET 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLU* 3.0 27.7 + - + +
158A SER* 5.0 0.7 - - - -
160A LYS* 1.3 84.8 - - + +
162A ILE* 1.3 67.8 + - + +
201A GLY* 4.4 5.0 - - - +
205A ILE* 4.2 19.2 - - - +
290A HIS* 6.2 0.7 - - - -
294A VAL* 4.0 28.0 - - + -
297A ARG* 3.6 41.1 - - - +
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Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A SER* 2.9 36.0 + - - +
161A MET* 1.3 84.0 - - + +
163A PHE* 1.3 86.4 + - + +
164A GLY 3.5 0.2 - - - -
198A PRO 4.8 0.2 - - - +
201A GLY* 3.6 12.1 + - - -
205A ILE* 5.9 0.8 - - - +
239A VAL* 5.1 3.4 - - + -
240A TYR* 3.2 37.6 + - + +
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Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ALA* 5.4 7.0 - - + -
119A HIS* 5.9 2.7 - + - -
122A LEU* 3.9 27.1 - - + -
158A SER* 3.8 13.7 - - - -
159A LEU* 2.9 24.3 + - + +
162A ILE* 1.3 95.8 - - + +
164A GLY* 1.3 63.1 + - - +
165A ILE* 3.3 12.9 + - + -
197A PHE* 3.7 19.3 - + + -
198A PRO* 3.5 44.4 - - + +
200A THR* 3.5 2.3 - - - -
201A GLY 3.3 13.9 + - - +
239A VAL* 3.4 31.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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