Contacts of the helix formed by residues 114 - 134 (chain B) in PDB entry 2W9Z
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 ALA 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B PRO* 1.3 75.5 - - - +
115B GLU* 1.3 66.7 + - + +
116B THR 3.5 0.7 - - - -
117B ILE* 3.7 9.0 - - - +
118B LYS* 3.0 41.5 + - - +
208B PHE* 5.7 4.3 - - + -
263B GLU* 4.2 19.7 - - - +
265B GLU* 5.6 3.1 - - - +
294B TYR* 4.8 4.7 + - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PRO* 4.3 2.8 - - + +
114B ALA* 1.3 79.4 - - + +
116B THR* 1.3 58.0 + - - +
117B ILE 3.1 5.2 - - - -
118B LYS* 3.9 26.7 + - - +
119B ASP* 3.2 30.1 + - - +
122B ARG* 4.5 11.8 + - - -
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Residues in contact with THR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 3.7 26.5 - - + +
113B PRO* 4.0 32.0 - - + +
114B ALA 4.1 1.2 - - - +
115B GLU* 1.3 77.6 - - - +
117B ILE* 1.3 60.8 + - + +
119B ASP* 5.1 2.0 - - - -
120B LEU* 2.9 35.5 + - + +
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 5.4 3.6 - - - -
113B PRO 3.2 25.8 + - - +
114B ALA* 3.7 6.7 - - - +
115B GLU 3.1 0.4 - - - -
116B THR* 1.3 82.7 - - + +
118B LYS* 1.3 60.5 + - - +
119B ASP 3.4 0.2 - - - -
120B LEU* 3.8 1.4 - - + +
121B MET* 3.1 29.1 + - - +
204B PHE* 4.3 11.7 - - + -
207B MET* 3.7 39.7 - - + +
208B PHE* 3.5 53.6 - - + -
294B TYR* 4.4 5.4 - - - +
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Residues in contact with LYS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ALA* 3.0 26.7 + - - +
115B GLU* 3.8 22.5 + - - +
117B ILE* 1.3 77.4 - - - +
119B ASP* 1.3 60.0 + - - +
121B MET* 3.6 2.9 + - - +
122B ARG* 3.0 48.5 + - - +
265B GLU* 3.4 23.2 + - - -
294B TYR* 3.4 58.9 + - + +
295B LEU* 3.9 11.4 - - + +
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Residues in contact with ASP 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU 3.2 17.6 + - - +
116B THR* 5.1 1.8 - - - -
118B LYS* 1.3 76.9 - - - +
120B LEU* 1.3 66.9 + - - +
122B ARG* 3.3 22.1 + - - +
123B GLN* 3.1 41.3 + - - +
126B ARG* 4.5 13.2 + - - -
152B GLY 5.3 0.2 - - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B LEU* 4.1 24.0 - - + -
103B TYR* 4.3 28.0 - - + +
104B LEU* 5.1 2.0 - - + -
116B THR* 2.9 26.6 + - + +
117B ILE* 3.5 5.3 + - + +
118B LYS 3.3 0.6 - - - -
119B ASP* 1.3 81.1 - - - +
121B MET* 1.3 62.1 + - - +
123B GLN* 3.6 9.4 + - - +
124B PHE* 3.2 20.4 + - - +
152B GLY* 5.1 9.2 - - - +
154B VAL* 4.0 25.8 - - + +
207B MET* 3.5 24.5 - - + -
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Residues in contact with MET 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ILE 3.1 21.1 + - - +
118B LYS* 3.8 4.5 - - - +
120B LEU* 1.3 75.8 - - - +
122B ARG* 1.3 56.6 + - - +
123B GLN 3.1 0.4 - - - -
124B PHE* 3.2 18.1 - - + +
125B LEU* 2.8 44.9 + - + +
200B VAL* 3.8 22.9 - - + -
203B ILE 5.0 0.2 - - - -
204B PHE* 3.7 47.1 - - + -
207B MET* 3.7 27.1 - - - +
271B LEU* 6.0 0.2 - - + -
275B MET* 4.2 13.9 - - + -
295B LEU* 4.3 13.9 - - + -
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Residues in contact with ARG 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLU* 4.5 9.9 + - - -
118B LYS* 3.0 30.6 + - - +
119B ASP* 3.3 40.4 + - - +
120B LEU 3.3 0.2 - - - -
121B MET* 1.3 77.5 - - - +
123B GLN* 1.3 55.9 + - - +
125B LEU* 4.8 0.9 - - - -
126B ARG* 2.8 57.9 + - - +
290B LEU* 3.5 28.3 - - + +
294B TYR 4.7 0.2 + - - -
295B LEU* 3.1 49.6 + - + +
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ASN* 3.5 19.5 + - - +
119B ASP* 3.1 34.6 + - - +
120B LEU* 3.9 4.8 - - - +
121B MET 3.1 0.4 - - - -
122B ARG* 1.3 75.7 - - - +
124B PHE* 1.3 65.0 + - - +
126B ARG* 2.9 32.0 + - - +
127B GLY 3.0 12.3 + - - -
152B GLY 3.4 14.5 + - - +
153B THR* 2.2 40.0 + - - +
154B VAL* 2.8 29.3 - - + +
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU 3.2 13.9 + - - +
121B MET* 3.2 24.9 - - + +
123B GLN* 1.3 77.4 - - - +
125B LEU* 1.3 62.1 + - - +
127B GLY 3.6 0.5 + - - -
128B LEU* 3.2 21.7 + - + +
141B LEU* 3.5 30.1 - - + -
146B ILE* 3.9 19.7 - - + -
154B VAL* 4.1 5.1 - - + +
156B LEU* 3.6 30.8 - - + +
200B VAL* 3.0 60.6 - - + -
203B ILE* 4.2 16.6 - - + -
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B MET* 2.8 25.1 + - + +
124B PHE* 1.3 71.0 - - - +
126B ARG* 1.3 55.0 + - - +
128B LEU* 3.0 3.8 + - + +
129B ASP* 2.7 37.1 + - - +
197B MET* 3.9 24.7 - - + -
200B VAL* 3.8 30.7 - - + -
275B MET* 4.5 6.7 - - + -
286B ALA* 3.9 10.4 - - + +
289B ALA* 3.8 10.8 - - + -
290B LEU* 3.3 48.9 - - + +
295B LEU* 4.1 15.3 - - + -
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B HIS* 3.9 10.6 + - + +
70B ASN* 3.2 21.6 - - - +
119B ASP* 4.5 9.7 + - - -
122B ARG* 2.8 50.4 + - - +
123B GLN* 2.9 22.6 + - - +
125B LEU* 1.3 76.8 - - - +
127B GLY* 1.3 58.7 + - - +
128B LEU 2.9 0.3 + - - -
129B ASP* 3.0 5.5 + - - +
130B PHE* 2.8 28.2 + - - +
290B LEU* 3.2 21.1 - - + +
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B HIS* 3.7 9.6 - - - -
70B ASN* 3.6 29.6 - - - +
71B VAL* 3.7 2.6 - - - +
123B GLN 3.0 13.1 + - - -
126B ARG* 1.3 73.1 - - - +
128B LEU* 1.3 56.3 + - - +
130B PHE* 3.5 2.3 - - - +
131B LEU* 3.3 34.0 + - - +
156B LEU* 3.6 9.9 - - - -
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PHE* 3.2 18.4 + - + +
125B LEU* 3.0 8.3 + - + +
126B ARG 2.9 0.6 - - - -
127B GLY* 1.3 77.5 - - - +
129B ASP* 1.3 59.3 + - - +
130B PHE 3.2 1.6 - - - -
131B LEU* 4.5 11.0 - - + +
132B HIS* 3.0 80.3 + - + +
138B HIS* 5.1 4.0 - - + +
141B LEU* 4.2 20.4 - - + -
156B LEU* 4.2 12.6 - - + -
196B ASP* 3.9 15.0 - - + +
197B MET* 3.9 23.1 - - - -
200B VAL* 4.4 7.9 - - + -
286B ALA* 4.0 2.0 - - + -
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B LEU 2.7 20.0 + - - +
126B ARG* 3.5 7.9 - - - +
128B LEU* 1.3 72.6 - - - +
130B PHE* 1.3 62.6 + - - +
132B HIS* 4.0 5.7 - - - +
133B ALA* 3.2 24.8 + - - +
286B ALA* 3.9 13.5 - - + +
287B PHE* 3.2 45.6 + - - +
290B LEU* 4.7 5.0 - - + +
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Residues in contact with PHE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 6.3 3.8 - - - -
63B LEU* 3.6 32.1 - - + -
66B PHE* 3.2 52.9 - + + -
68B HIS* 3.7 44.6 - + + +
71B VAL* 4.5 5.8 - - + -
126B ARG 2.8 11.7 + - - +
127B GLY 3.5 9.2 - - - +
128B LEU 3.2 0.2 - - - -
129B ASP* 1.3 75.4 - - - +
131B LEU* 1.3 85.4 + - + +
133B ALA* 3.2 10.2 + - + +
134B ASN* 3.1 31.0 - - - +
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU* 4.4 8.1 - - + -
71B VAL* 3.4 24.9 - - + -
127B GLY 3.3 19.7 + - - +
128B LEU* 4.1 16.4 - - + +
129B ASP 3.6 0.2 - - - -
130B PHE* 1.3 94.7 - - + +
132B HIS* 1.3 63.5 + - + +
134B ASN* 3.0 11.2 + - - +
136B ILE* 2.7 49.7 + - + +
137B VAL* 5.7 0.2 - - - -
138B HIS* 5.3 4.3 - - + +
156B LEU* 4.6 4.7 - - + -
159B PHE* 3.4 42.6 - - + -
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 3.0 50.0 + - + +
129B ASP* 4.2 7.4 - - - +
131B LEU* 1.3 77.0 - - + +
133B ALA* 1.3 57.4 + - - +
134B ASN 3.1 0.2 - - - -
135B CYS* 3.1 19.5 + - - +
136B ILE 3.2 19.7 - - - +
137B VAL* 4.6 0.2 - - - -
193B THR* 2.8 45.6 + - + +
196B ASP* 2.8 26.4 + - + +
197B MET* 4.7 6.4 - - + +
286B ALA* 4.5 7.9 + - + +
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 5.4 15.0 - - + +
129B ASP* 3.2 21.7 + - - +
130B PHE* 3.2 8.6 + - + +
132B HIS* 1.3 77.1 - - - +
134B ASN* 1.3 63.6 + - - +
135B CYS* 3.3 5.0 + - - -
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Residues in contact with ASN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 6.1 0.2 - - - +
62B ARG* 5.6 4.2 - - - +
63B LEU* 3.3 33.6 - - + +
66B PHE* 3.3 27.5 - - - -
130B PHE* 3.1 23.9 + - - +
131B LEU* 3.0 10.3 + - - +
133B ALA* 1.3 83.0 - - - +
135B CYS* 1.3 72.7 + - - +
136B ILE* 3.1 14.5 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
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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