Contacts of the helix formed by residues 107 - 124 (chain A) in PDB entry 2WWR
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 LEU 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A SER* 5.1 0.2 - - - -
83A VAL* 3.8 33.7 - - + +
103A THR* 3.8 21.1 - - - +
105A ASP 3.0 5.5 - - - +
106A VAL* 1.3 77.0 - - - +
108A THR* 1.3 66.5 + - - +
109A ASP 3.6 1.8 - - - -
110A THR* 4.1 2.4 - - - -
111A THR* 2.9 35.3 + - - +
164A ILE* 4.4 11.9 - - + -
296A SER* 4.0 11.2 - - - -
301A THR* 3.8 22.0 - - + -
305A MET* 3.6 34.3 - - + -
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Residues in contact with THR 108 (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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105A ASP* 2.9 33.1 + - - -
106A VAL 3.7 0.4 - - - -
107A LEU* 1.3 80.2 - - - +
109A ASP* 1.3 59.0 + - - +
111A THR* 3.7 1.6 - - - -
112A ALA* 2.8 35.9 + - - +
163A ARG* 3.4 40.7 - - + +
164A ILE* 4.2 14.7 - - - +
167A ALA* 3.7 13.2 - - + -
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Residues in contact with ASP 109 (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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105A ASP 4.2 4.3 - - - +
106A VAL 5.2 2.4 - - - +
107A LEU 3.6 0.2 - - - -
108A THR* 1.3 86.2 + - - +
110A THR* 1.3 53.9 + - - +
112A ALA* 3.2 4.8 + - - +
113A GLU* 2.7 37.6 + - - +
167A ALA* 5.0 0.4 - - - -
171A ARG* 3.3 27.8 + - - +
152B THR* 4.2 28.0 - - + +
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Residues in contact with THR 110 (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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106A VAL 5.0 1.0 + - - -
107A LEU* 3.7 4.7 + - - -
108A THR 3.3 0.4 - - - -
109A ASP* 1.3 78.8 - - - +
111A THR* 1.3 61.1 + - - +
113A GLU* 3.4 8.4 - - - +
114A LEU 3.1 16.5 + - - -
295A GLY 3.1 7.4 - - - +
296A SER* 3.9 11.0 - - - -
298A THR* 3.9 11.8 + - + -
301A THR* 2.5 39.7 + - - +
124B ARG* 3.1 38.8 + - - +
152B THR* 5.0 5.5 + - - -
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Residues in contact with THR 111 (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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107A LEU* 2.9 30.8 + - - +
108A THR 3.8 2.2 - - - -
110A THR* 1.3 71.7 - - - +
112A ALA* 1.3 67.4 + - - +
114A LEU* 3.0 4.1 + - + +
115A ALA* 2.9 21.9 + - - +
164A ILE* 4.2 17.3 - - + -
243A ILE* 3.8 31.6 - - + +
269A ASP* 6.0 0.2 - - - +
295A GLY* 3.4 26.6 + - - +
296A SER* 4.0 5.7 - - - -
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Residues in contact with ALA 112 (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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108A THR 2.8 17.4 + - - +
109A ASP 3.3 8.5 - - - +
111A THR* 1.3 71.0 - - - +
113A GLU* 1.3 62.8 + - - +
115A ALA* 3.1 13.7 + - - +
116A VAL* 3.2 17.5 + - - +
164A ILE* 4.4 3.4 - - - +
167A ALA* 3.5 35.4 - - + -
168A ILE* 3.9 15.2 - - + +
171A ARG* 3.8 15.3 - - - +
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Residues in contact with GLU 113 (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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109A ASP 2.7 20.3 + - - +
110A THR* 3.4 9.7 - - - +
112A ALA* 1.3 72.7 - - - +
114A LEU* 1.3 56.9 + - - +
116A VAL* 3.7 3.5 + - - +
117A SER* 2.8 29.3 + - - +
171A ARG* 3.9 13.4 - - - +
120B LEU* 4.1 13.2 - - + +
124B ARG* 2.8 27.3 + - + +
149B TYR 5.3 0.2 - - - -
150B GLY* 3.2 17.3 - - - -
151B LEU* 2.7 41.3 + - - +
152B THR* 4.1 8.9 + - - -
175B PHE* 4.0 18.7 - - + +
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Residues in contact with LEU 114 (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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110A THR 3.1 12.1 + - - +
111A THR* 3.0 8.9 + - + +
113A GLU* 1.3 75.0 - - - +
115A ALA* 1.3 64.6 + - - +
116A VAL 3.2 0.2 - - - -
117A SER* 3.0 9.0 + - - -
118A LEU* 2.8 32.3 + - + +
243A ILE* 5.2 1.8 - - + -
269A ASP* 3.5 35.4 - - + +
291A LEU* 4.2 12.3 - - + -
294A ILE* 3.6 31.9 - - + +
295A GLY* 3.7 12.6 - - - +
124B ARG* 3.4 31.4 - - + +
126B LEU* 4.5 9.6 - - + -
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Residues in contact with ALA 115 (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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111A THR 2.9 11.3 + - - +
112A ALA 3.1 9.4 + - - +
114A LEU* 1.3 77.3 - - - +
116A VAL* 1.3 55.5 + - - +
118A LEU* 3.4 4.1 + - - +
119A LEU* 2.9 29.2 + - - +
168A ILE* 3.6 30.7 - - + -
213A VAL* 4.7 7.2 - - + +
241A ILE* 4.3 4.6 - - + +
243A ILE* 3.9 29.1 - - + +
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Residues in contact with VAL 116 (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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112A ALA 3.2 14.0 + - - +
113A GLU 3.9 6.7 - - - +
115A ALA* 1.3 71.2 - - - +
117A SER* 1.3 56.8 + - - +
119A LEU* 3.6 6.4 - - + +
120A LEU* 2.8 54.5 + - + +
168A ILE* 4.3 13.9 - - + -
171A ARG* 4.0 25.8 - - + -
172A LEU* 3.8 28.3 - - + -
175A PHE* 4.7 2.9 - - + -
120B LEU* 4.3 0.4 - - + -
175B PHE* 4.0 20.4 - - + -
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Residues in contact with SER 117 (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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113A GLU 2.8 21.1 + - - -
114A LEU* 3.0 13.8 + - - -
116A VAL* 1.3 75.1 - - - +
118A LEU* 1.3 57.8 + - - +
120A LEU* 4.1 1.8 - - - +
121A THR* 3.1 32.2 + - - -
117B SER 5.6 0.7 - - - +
120B LEU* 3.3 37.5 - - - +
121B THR* 4.7 1.0 + - - -
124B ARG* 4.1 7.8 - - - +
126B LEU* 3.6 23.5 - - - +
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Residues in contact with LEU 118 (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 LEU* 2.8 18.9 + - + +
115A ALA* 3.6 5.4 - - - +
117A SER* 1.3 70.9 - - - +
119A LEU* 1.3 61.7 + - - +
121A THR* 3.2 6.2 - - + +
122A THR* 2.6 43.5 + - - +
241A ILE* 4.4 11.0 - - + -
242A ASN 4.7 0.7 - - - +
243A ILE* 4.7 3.1 - - + -
267A GLY* 3.8 15.5 - - - +
268A LEU 3.6 34.1 - - - +
269A ASP* 3.7 11.0 - - + +
289A VAL* 3.7 24.5 - - + -
291A LEU* 3.8 25.6 - - + -
126B LEU* 4.3 2.8 - - - +
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Residues in contact with LEU 119 (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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115A ALA 2.9 17.6 + - - +
116A VAL* 3.6 6.3 - - + +
118A LEU* 1.3 77.3 - - - +
120A LEU* 1.3 58.9 + - + +
122A THR* 3.6 1.2 - - - -
123A CYS* 3.0 33.1 + - - -
151A LEU* 4.4 16.8 - - + -
156A VAL* 5.6 0.2 - - + -
168A ILE* 6.1 0.2 - - + -
172A LEU* 4.0 36.3 - - + -
211A PHE* 3.5 38.6 - - + -
213A VAL* 4.7 10.8 - - + -
239A VAL* 4.3 4.5 - - + -
241A ILE* 3.6 32.7 - - + +
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Residues in contact with LEU 120 (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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116A VAL* 2.8 40.9 + - + +
117A SER* 4.1 3.4 - - - +
119A LEU* 1.3 75.2 - - + +
121A THR* 1.3 62.6 + - - +
123A CYS* 3.7 10.3 - - - -
124A ARG* 3.2 30.9 + - + +
151A LEU* 3.8 28.5 - - + -
175A PHE* 3.9 24.9 - - + -
113B GLU* 4.2 12.3 - - + +
116B VAL* 4.3 0.9 - - + -
117B SER* 3.1 34.9 + - - +
120B LEU* 4.1 15.9 - - + -
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Residues in contact with THR 121 (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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117A SER 3.1 17.5 + - - +
118A LEU* 3.2 19.5 - - + +
120A LEU* 1.3 76.8 - - - +
122A THR* 1.3 65.7 + - - +
125A ARG 3.5 0.5 + - - -
126A LEU* 3.0 51.2 + - - +
127A PRO* 3.4 12.5 - - + +
130A ILE* 5.9 0.2 - - - +
289A VAL* 4.5 9.9 - - + -
117B SER* 5.4 0.4 - - - +
121B THR* 2.8 25.6 + - - +
126B LEU* 3.5 18.2 - - + +
130B ILE* 5.7 0.8 - - + +
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Residues in contact with THR 122 (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 LEU* 2.6 37.4 + - - +
119A LEU 3.6 3.8 - - - -
121A THR* 1.3 77.1 - - - +
123A CYS* 1.3 64.0 + - - +
125A ARG* 3.2 17.0 + - - +
127A PRO* 5.3 0.2 - - - -
239A VAL* 3.8 21.1 - - + -
241A ILE* 4.4 4.5 - - - -
265A ALA* 3.9 16.7 - - + +
266A ALA 3.7 24.5 - - - +
267A GLY* 3.9 3.7 - - - +
287A ASN 5.0 1.1 - - - +
289A VAL* 3.7 18.5 - - + +
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Residues in contact with CYS 123 (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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119A LEU* 3.0 27.3 + - - +
120A LEU* 3.5 22.9 - - - -
122A THR* 1.3 77.3 - - - +
124A ARG* 1.3 67.8 + - - +
125A ARG* 3.3 4.4 + - - +
148A GLY* 3.1 7.3 - - - -
149A TYR* 3.0 47.0 + - - +
150A GLY* 5.5 1.1 - - - -
151A LEU* 5.5 2.0 - - - -
211A PHE* 3.7 22.7 - - + -
239A VAL* 4.1 15.3 - - + -
265A ALA* 5.8 0.9 - - - -
113B GLU* 5.7 0.9 - - - -
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Residues in contact with ARG 124 (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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120A LEU* 3.2 19.1 + - + +
123A CYS* 1.3 86.3 - - - +
125A ARG* 1.3 69.8 + - - +
126A LEU* 3.3 21.7 + - + +
146A LEU 4.6 4.7 - - - +
148A GLY* 4.4 3.6 - - - -
149A TYR 4.2 8.3 - - - -
110B THR* 3.0 19.6 + - - +
113B GLU* 2.7 38.3 + - - +
114B LEU* 3.5 18.9 - - + +
117B SER* 3.9 11.2 - - - +
294B ILE* 3.0 38.8 + - - +
295B GLY 3.1 13.7 + - - -
297B ALA* 3.5 18.8 + - - +
298B THR* 3.7 20.0 - - - +
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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