Contacts of the helix formed by residues 116 - 131 (chain B) in PDB entry 3CWR
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 ASP 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B MSE 3.4 12.9 + - - +
113B LEU 3.5 2.8 + - - +
114B ALA 3.5 0.8 + - - -
115B SER* 1.3 81.7 - - - +
117B ALA* 1.3 65.3 + - - +
118B ASP* 2.9 24.1 + - - +
119B LEU* 3.0 31.3 + - + +
120B ARG* 3.0 26.3 + - - +
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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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116B ASP* 1.3 73.2 + - - +
118B ASP* 1.3 56.8 + - - +
120B ARG* 3.3 33.5 + - - +
121B ASN* 2.8 29.0 + - - +
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Residues in contact with ASP 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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116B ASP* 2.9 11.2 + - - +
117B ALA* 1.3 78.1 - - - +
119B LEU* 1.3 63.3 + - + +
121B ASN* 3.2 13.4 + - - +
122B ARG* 2.8 63.6 + - - +
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Residues in contact with LEU 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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34B ALA* 3.7 27.6 - - + -
60B ARG* 4.8 5.6 - - - +
112B MSE 3.5 33.0 - - + +
113B LEU* 3.9 12.8 - - + -
116B ASP* 3.0 38.5 + - + +
118B ASP* 1.3 81.1 - - - +
120B ARG* 1.3 55.4 + - - +
122B ARG* 4.6 10.1 - - - -
123B PHE* 2.7 58.1 + - + +
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Residues in contact with ARG 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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113B LEU* 2.9 50.7 + - + +
114B ALA* 3.1 21.8 + - - +
115B SER 4.4 0.6 - - - -
116B ASP 3.0 16.8 + - - +
117B ALA* 3.4 32.2 - - - +
119B LEU* 1.3 76.7 - - - +
121B ASN* 1.3 63.9 + - - +
124B LEU* 2.8 52.7 + - + +
125B PRO* 4.1 0.5 - - - +
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Residues in contact with ASN 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 ALA 2.8 17.4 + - - +
118B ASP* 3.2 16.2 + - - +
120B ARG* 1.3 78.2 - - - +
122B ARG* 1.3 65.6 + - - +
125B PRO* 4.3 9.7 - - - +
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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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60B ARG* 3.8 23.6 - - - +
61B ALA* 3.5 18.9 - - + +
118B ASP* 2.8 47.8 + - - +
119B LEU* 3.8 7.6 - - - +
121B ASN* 1.3 83.9 - - - +
123B PHE* 1.3 72.6 + - + +
125B PRO* 4.5 4.4 - - - +
126B ALA 5.7 0.2 + - - -
209B EDO 3.2 27.4 + - - +
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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
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29B LEU* 6.0 0.2 - - + -
34B ALA* 4.3 11.0 - - + -
37B MSE 4.4 5.6 - - + -
60B ARG* 3.6 53.2 - - + -
61B ALA* 3.8 20.2 - - + +
64B ILE* 3.7 32.3 - - + +
109B LEU* 5.6 1.8 - - + -
112B MSE 5.4 2.9 - - - -
113B LEU* 4.0 19.7 - - + -
119B LEU* 2.7 42.2 + - + +
122B ARG* 1.3 90.5 - - + +
124B LEU* 1.3 64.8 + - - +
125B PRO* 3.3 3.6 - - - -
126B ALA* 3.3 5.5 + - - +
127B TYR* 3.0 21.7 + - - +
209B EDO 5.1 1.3 - - - -
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Residues in contact with LEU 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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113B LEU* 5.0 7.8 - - + +
120B ARG* 2.8 46.7 + - + +
123B PHE* 1.3 72.7 - - - +
125B PRO* 1.4 70.4 - - + +
127B TYR* 4.2 22.2 - - + -
128B ASN* 2.8 33.2 + - + +
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Residues in contact with PRO 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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125A PRO* 3.7 35.7 - - + -
120B ARG 4.1 4.3 - - - +
121B ASN 4.3 10.8 - - - +
122B ARG 4.5 4.0 - - - +
123B PHE* 3.6 3.8 - - - -
124B LEU* 1.4 94.0 - - + +
126B ALA* 1.3 56.6 + - - +
128B ASN* 4.0 3.6 - - + +
129B ALA* 2.9 33.8 + - - +
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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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61B ALA* 3.1 41.0 - - + +
62B ASP* 5.0 2.9 - - - +
64B ILE* 4.8 0.7 - - + -
65B GLY* 3.9 12.1 - - - +
123B PHE 3.3 6.2 + - - +
124B LEU 3.3 0.4 - - - -
125B PRO* 1.3 77.0 - - - +
127B TYR* 1.3 65.7 + - - +
129B ALA* 4.7 1.1 - - - -
130B ASN* 2.9 36.4 + - - +
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Residues in contact with TYR 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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64B ILE* 4.0 11.6 - - + +
68B VAL* 3.9 19.1 - - + +
71B TRP* 5.5 2.7 - + - -
106B ALA 4.7 2.8 + - - -
109B LEU* 3.8 37.7 - - + -
110B PHE* 3.6 34.9 + + - +
113B LEU* 3.5 29.8 - - + -
123B PHE 3.0 17.2 + - - +
124B LEU* 3.6 15.0 - - + +
126B ALA* 1.3 78.0 - - - +
128B ASN* 1.3 66.5 + - - +
131B GLY* 3.4 20.8 + - - -
174B LEU* 5.8 0.7 - - - +
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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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124B LEU* 2.8 32.1 + - + +
125B PRO* 4.0 3.6 - - + +
127B TYR* 1.3 77.6 - - + +
129B ALA* 1.3 66.2 + - - +
130B ASN 3.3 0.7 + - - -
131B GLY* 3.7 3.5 + - - -
132B ILE* 5.0 8.7 + - - +
133B GLU* 3.3 30.8 + - - +
136B ARG* 5.7 3.8 - - - +
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Residues in contact with ALA 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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129A ALA* 3.9 28.0 - - + -
133A GLU* 5.7 1.8 - - - +
137A ARG* 5.4 1.0 + - - -
125B PRO 2.9 18.7 + - - +
126B ALA* 4.7 0.9 - - - -
127B TYR 3.4 0.2 - - - -
128B ASN* 1.3 78.4 + - - +
130B ASN* 1.3 70.4 + - - +
131B GLY 3.5 0.2 - - - -
133B GLU* 4.7 7.8 - - - +
134B ARG* 3.3 22.9 + - - +
137B ARG* 4.8 3.1 + - - -
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Residues in contact with ASN 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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133A GLU* 5.2 7.3 + - - +
137A ARG* 5.0 7.6 + - - -
65B GLY* 3.5 34.7 - - - +
68B VAL* 3.5 9.2 - - + +
69B GLU* 3.6 24.8 - - + +
72B ILE* 3.4 22.5 - - - +
126B ALA* 2.9 30.0 + - - +
128B ASN 3.2 0.4 - - - -
129B ALA* 1.3 89.9 - - - +
131B GLY* 1.3 60.0 + - - +
134B ARG* 3.7 9.0 + - - +
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Residues in contact with GLY 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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68B VAL* 3.3 18.8 - - - -
72B ILE* 4.2 9.3 - - - +
101B VAL* 6.1 0.4 - - - -
127B TYR 3.4 11.5 + - - -
128B ASN 3.7 1.7 + - - -
129B ALA 3.5 2.2 - - - -
130B ASN* 1.3 78.3 - - - +
132B ILE* 1.3 54.1 - - - -
133B GLU 3.0 5.6 - - - -
134B ARG* 2.8 34.5 + - - +
135B SER* 3.4 4.7 + - - -
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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