Contacts of the helix formed by residues 115 - 129 (chain B) in PDB entry 1WB8
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 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109B ILE* 3.8 5.5 - - - +
110B ASN* 3.4 15.0 + - - +
113B TYR* 3.2 3.6 + - - +
114B GLY* 1.3 79.4 - - - +
116B PHE* 1.3 66.8 + - - +
117B ASP* 3.5 14.1 + - - +
118B ARG* 3.1 23.9 + - - +
119B PHE* 3.1 22.0 + - - +
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Residues in contact with PHE 116 (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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99B GLY 3.8 24.0 - - - -
100B LYS* 3.7 36.5 - - + +
101B PRO* 3.6 21.8 - - + -
109B ILE* 3.9 11.9 - - + -
110B ASN* 3.8 6.6 + - - +
115B SER* 1.3 73.9 - - - +
117B ASP* 1.3 65.9 + - - +
119B PHE* 3.2 16.1 + + - +
120B LYS* 2.8 54.9 + - + +
192B TRP* 4.4 9.2 - + - -
197B TRP* 3.5 32.5 - + - -
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Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS* 4.9 10.8 + - - -
115B SER* 3.2 11.3 + - - +
116B PHE* 1.3 88.6 + - - +
118B ARG* 1.3 60.2 - - - +
120B LYS* 3.5 10.5 + - - +
121B GLN* 3.2 26.9 + - - +
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR* 3.4 26.7 - - + +
115B SER* 3.1 16.1 + - - +
117B ASP* 1.3 73.2 - - - +
119B PHE* 1.3 67.7 + - - +
121B GLN* 3.1 41.8 + - - +
122B VAL* 3.0 43.7 + - + +
125B GLU* 5.4 6.5 + - - -
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 3.7 23.8 - - + -
113B TYR* 3.9 38.7 - + + +
115B SER 3.1 14.5 + - - +
116B PHE* 3.4 21.3 - + - +
118B ARG* 1.3 76.7 - - - +
120B LYS* 1.3 60.5 - - - +
122B VAL* 3.3 1.7 + - - +
123B PHE* 2.9 52.8 + + + +
138B LEU* 3.9 39.3 - - + -
149B ILE* 4.2 5.8 - - + -
167B LEU* 4.0 12.6 - - + -
192B TRP* 4.0 21.1 - + - -
197B TRP* 4.4 6.5 - + - -
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Residues in contact with LYS 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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116B PHE* 2.8 40.2 + - + +
117B ASP* 3.6 10.8 - - - +
119B PHE* 1.3 83.1 - - - +
121B GLN* 1.3 59.0 + - + +
124B THR* 2.7 36.1 + - - +
189B ASN* 4.9 9.5 + - - -
192B TRP* 3.5 60.3 - - + +
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP 3.2 12.0 + - - +
118B ARG* 3.1 44.8 + - - +
120B LYS* 1.3 78.2 - - + +
122B VAL* 1.3 57.9 + - - +
124B THR* 3.4 4.8 + - - -
125B GLU* 2.9 31.8 + - - +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR* 4.6 13.9 - - + -
118B ARG* 3.0 46.3 + - + +
119B PHE* 3.8 5.8 - - - +
121B GLN* 1.3 73.1 - - - +
123B PHE* 1.3 61.8 + - - +
125B GLU* 3.7 11.4 - - - +
126B THR* 2.8 38.8 + - - +
149B ILE* 3.8 19.5 - - + -
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Residues in contact with PHE 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 2.9 35.4 + + + +
120B LYS 4.0 3.4 - - - +
122B VAL* 1.3 74.6 - - - +
124B THR* 1.3 61.3 + - - +
126B THR* 3.4 3.4 + - - -
127B ALA* 2.8 32.6 + - + +
136B ALA* 3.9 36.6 - - + -
137B VAL* 3.7 26.9 - - - -
138B LEU* 4.1 8.5 - - + -
149B ILE* 4.0 24.2 - - + +
167B LEU* 4.9 5.2 - - + -
169B LEU* 4.6 7.9 - - + -
188B VAL* 5.9 0.7 - - + -
191B TRP* 3.9 26.5 - + - -
192B TRP* 3.6 26.9 - + + -
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Residues in contact with THR 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 LYS* 2.7 25.7 + - - +
121B GLN* 3.7 4.9 - - - -
123B PHE* 1.3 76.4 - - - +
125B GLU* 1.3 65.9 + - - +
127B ALA* 3.3 6.1 + - - +
128B ASN* 3.0 45.7 + - - +
185B ALA 5.9 0.7 - - - +
188B VAL* 4.2 15.0 - - + -
189B ASN* 5.8 4.0 - - + +
192B TRP* 3.2 23.1 + - - +
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Residues in contact with GLU 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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118B ARG* 5.4 8.5 + - - -
121B GLN 2.9 18.4 + - - +
122B VAL* 3.7 10.4 - - - +
123B PHE 3.3 0.2 - - - -
124B THR* 1.3 79.0 - - - +
126B THR* 1.3 62.5 + - - +
128B ASN* 3.4 6.9 + - - +
129B SER* 3.2 21.9 + - - -
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Residues in contact with THR 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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122B VAL* 2.8 28.6 + - - +
123B PHE 3.7 3.6 - - - -
124B THR 3.3 0.2 - - - -
125B GLU* 1.3 77.3 - - - +
127B ALA* 1.3 61.0 + - - +
129B SER* 2.6 27.0 + - - +
130B LEU 3.7 0.9 + - - -
136B ALA* 6.1 0.9 - - + -
149B ILE* 3.6 31.1 - - + +
150B MET* 5.2 0.4 - - - -
151B THR* 3.6 26.8 - - + +
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Residues in contact with ALA 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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123B PHE* 2.8 20.9 + - + +
124B THR 3.7 4.5 - - - +
126B THR* 1.3 76.5 - - - +
128B ASN* 1.3 60.7 + - - +
129B SER 3.4 0.7 + - - -
130B LEU* 3.6 8.1 + - - +
136B ALA* 3.8 16.4 - - + +
151B THR* 4.6 1.8 - - - -
169B LEU* 4.4 11.7 - - + -
171B GLU* 2.6 45.2 - - - +
184B ARG* 3.7 0.7 + - - -
188B VAL* 4.4 10.3 - - + -
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Residues in contact with ASN 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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213A PMS 5.3 2.1 - - - -
124B THR* 3.0 39.6 + - - +
125B GLU* 3.9 6.8 - - - +
127B ALA* 1.3 76.8 - - - +
129B SER* 1.3 58.7 + - - +
130B LEU 3.3 0.4 - - - +
184B ARG* 3.4 20.7 + - - +
185B ALA* 3.5 37.7 + - - +
188B VAL* 3.7 14.4 - - - +
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Residues in contact with SER 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 GLU* 3.2 11.0 + - - -
126B THR* 2.6 26.7 + - - +
128B ASN* 1.3 78.1 - - - +
130B LEU* 1.3 64.6 + - - +
131B PRO* 3.1 11.7 - - - +
151B THR* 4.9 1.6 - - - +
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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