Contacts of the helix formed by residues 114 - 128 (chain B) in PDB entry 2AW9
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 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108B ILE* 3.8 5.8 - - - +
109B ASN* 3.2 14.9 + - - +
112B PHE* 3.4 3.9 + - - +
113B GLY* 1.3 79.3 - - - +
115B PHE* 1.3 59.4 + - - +
116B ASP* 3.5 9.2 + - - +
117B ALA* 3.1 22.7 + - - +
118B PHE* 3.0 26.9 + - - +
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Residues in contact with PHE 115 (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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98B ASN 4.0 7.9 - - - -
99B GLN* 3.6 28.7 - - + +
100B PRO* 3.2 35.0 - - + -
105B LEU* 4.4 14.8 - - + +
108B ILE* 4.0 10.3 - - + +
109B ASN* 3.8 5.1 + - - -
114B SER* 1.3 71.2 - - - +
116B ASP* 1.3 65.7 + - - +
118B PHE* 3.1 17.4 + + - +
119B LYS* 2.8 66.3 + - + +
195B TRP* 4.7 3.6 - + + -
200B TRP* 3.5 32.3 - + - -
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Residues in contact with ASP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B SER* 3.3 8.6 + - - +
115B PHE* 1.3 82.6 - - - +
117B ALA* 1.3 61.4 + - - +
119B LYS* 3.4 27.4 + - - +
120B GLN* 3.2 29.2 + - - +
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Residues in contact with ALA 117 (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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112B PHE* 3.4 25.4 - - - +
113B GLY* 4.7 0.9 - - - -
114B SER* 3.1 20.9 + - - +
116B ASP* 1.3 72.5 - - - +
118B PHE* 1.3 68.4 + - - +
120B GLN* 3.3 15.9 + - - +
121B LYS* 3.1 22.1 + - - +
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Residues in contact with PHE 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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108B ILE* 4.0 12.8 - - + -
112B PHE* 3.9 42.1 - + + +
114B SER 3.0 14.7 + - - +
115B PHE* 3.4 24.2 - + - +
117B ALA* 1.3 76.7 - - - +
119B LYS* 1.3 65.9 + - - +
121B LYS* 3.1 1.6 + - - +
122B PHE* 2.9 33.4 + + + +
137B LEU* 4.0 27.1 - - + -
146B VAL* 4.0 21.5 - - + -
170B LEU* 4.3 4.7 - - + -
195B TRP* 3.6 35.4 - + - -
200B TRP* 3.9 13.7 - + - -
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Residues in contact with LYS 119 (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 PHE* 2.8 50.1 + - + +
116B ASP* 3.5 31.1 + - - +
118B PHE* 1.3 76.1 - - + +
120B GLN* 1.3 52.2 + - - +
122B PHE* 3.6 1.2 - - - +
123B GLU* 2.8 42.3 + - - +
195B TRP* 3.8 53.3 - - + +
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Residues in contact with GLN 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 ASP* 3.2 18.1 + - - +
117B ALA* 3.4 14.5 - - - +
119B LYS* 1.3 79.2 - - - +
121B LYS* 1.3 58.2 + - - +
123B GLU* 3.4 6.2 + - - +
124B ASP* 2.9 39.8 + - - +
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Residues in contact with LYS 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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112B PHE* 3.9 25.0 - - + -
117B ALA 3.1 13.2 + - - +
118B PHE* 3.1 7.4 + - - +
120B GLN* 1.3 78.4 - - - +
122B PHE* 1.3 62.5 + - - +
124B ASP* 3.4 7.4 + - - +
125B ALA* 3.1 23.0 + - - +
145B ASP* 3.3 24.5 + - - -
146B VAL* 3.7 18.2 + - + +
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Residues in contact with PHE 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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118B PHE* 2.9 35.5 + + + +
119B LYS 3.6 3.1 - - - +
121B LYS* 1.3 73.8 - - - +
123B GLU* 1.3 68.6 + - + +
124B ASP 3.1 0.7 + - - -
125B ALA* 3.2 4.0 + - - +
126B ALA* 3.1 22.4 + - + +
135B ALA* 3.8 11.3 - - + +
136B TRP* 3.8 33.2 - - - -
137B LEU 3.8 3.8 - - - -
146B VAL* 3.9 10.8 - - + +
170B LEU* 4.0 22.2 - - + -
172B VAL* 3.4 41.5 - - + -
191B LEU* 5.6 2.7 - - + -
194B PHE* 4.4 9.4 - + - -
195B TRP* 3.3 32.5 - + + -
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Residues in contact with GLU 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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119B LYS* 2.8 27.1 + - - +
120B GLN* 3.9 6.3 - - - +
122B PHE* 1.3 75.0 - - + +
124B ASP* 1.3 52.1 + - - +
126B ALA* 3.3 7.4 + - - +
127B LYS* 2.7 60.4 + - - +
188B PRO* 4.5 5.5 - - - +
191B LEU* 3.8 27.8 - - + +
192B ALA* 3.8 12.4 + - - +
195B TRP* 2.8 37.1 + - + +
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Residues in contact with ASP 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 GLN* 2.9 25.2 + - - +
121B LYS* 3.7 7.8 - - - +
122B PHE 3.1 0.2 + - - -
123B GLU* 1.3 74.5 - - - +
125B ALA* 1.3 64.6 + - - +
127B LYS* 3.5 22.0 + - - +
128B THR* 2.8 40.5 + - + +
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Residues in contact with ALA 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 LYS 3.1 7.1 + - - +
122B PHE 3.7 2.9 - - - +
124B ASP* 1.3 75.2 - - - +
126B ALA* 1.3 61.1 + - - +
128B THR* 3.5 6.3 + - - -
129B ARG* 3.3 23.6 + - - +
135B ALA* 4.3 11.0 - - + -
146B VAL* 3.6 31.6 - - + -
147B VAL* 4.5 12.1 - - - +
148B SER* 4.1 8.5 + - - +
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Residues in contact with ALA 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 PHE* 3.1 12.8 + - + +
123B GLU* 3.4 9.2 - - - +
125B ALA* 1.3 75.9 - - - +
127B LYS* 1.3 61.3 + - - +
129B ARG* 3.5 8.6 + - - +
135B ALA* 3.8 19.9 - - + +
172B VAL* 4.3 3.1 - - + -
174B VAL* 4.1 11.4 - - + +
187B ARG* 2.8 25.6 + - - -
191B LEU* 3.6 28.9 - - + -
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Residues in contact with LYS 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 GLU* 2.7 40.9 + - - +
124B ASP* 3.5 25.9 + - - +
126B ALA* 1.3 74.0 - - - +
128B THR* 1.3 66.0 + - + +
129B ARG 3.2 2.4 + - - +
187B ARG* 3.5 20.3 + - - +
188B PRO* 3.8 31.8 - - + +
191B LEU* 3.7 14.4 - - + -
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Residues in contact with THR 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 ASP* 2.8 34.3 + - + +
125B ALA* 3.5 8.8 + - - -
127B LYS* 1.3 79.8 - - + +
129B ARG* 1.3 62.4 + - - +
130B PHE* 3.2 8.3 + - - +
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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