Contacts of the helix formed by residues 124 - 139 (chain B) in PDB entry 4D10
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 GLN 124 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120B SER 4.6 6.3 + - - +
121B THR 4.7 2.6 + - - -
122B SER 3.6 12.7 + - - -
123B LYS* 1.3 99.1 + - - +
125B MET* 1.3 68.7 + - + +
126B ASP* 3.2 11.5 + - + +
127B LEU* 3.4 3.7 + - - +
128B LEU* 3.3 23.9 + - - +
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Residues in contact with MET 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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124B GLN* 1.3 77.9 - - + +
126B ASP* 1.3 80.3 + - - +
127B LEU 2.9 6.8 + - - -
128B LEU* 4.2 4.4 - - - +
129B GLN* 3.0 46.1 + - + +
158B LEU* 3.4 51.8 - - + +
161B GLU* 4.5 10.1 - - + +
162B ARG* 3.8 33.4 - - + -
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Residues in contact with ASP 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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124B GLN* 3.2 9.8 + - + +
125B MET* 1.3 91.3 - - - +
127B LEU* 1.3 65.9 + - + +
130B GLU* 3.0 15.1 - - - +
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Residues in contact with LEU 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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85B PHE* 4.0 40.8 - - + -
119B ILE* 5.5 0.9 - - + -
123B LYS* 3.9 38.6 - - + -
124B GLN 3.4 4.4 + - - +
126B ASP* 1.3 85.1 - - + +
128B LEU* 1.3 64.7 + - - +
129B GLN 3.3 1.8 - - - -
130B GLU* 3.3 18.2 + - - +
131B PHE* 3.1 31.2 + - + -
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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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116B LEU* 3.9 13.7 - - + +
119B ILE* 3.7 32.9 - - + +
120B SER* 3.8 30.5 - - - +
123B LYS 5.0 0.7 - - - +
124B GLN* 3.3 22.2 + - - +
125B MET* 4.2 1.1 - - - +
127B LEU* 1.3 78.7 - - - +
129B GLN* 1.3 56.8 + - - +
131B PHE* 3.2 12.4 + - + +
132B TYR* 3.0 62.4 + - + +
158B LEU* 4.3 19.5 - - + -
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B MET* 3.0 45.7 + - + +
128B LEU* 1.3 76.3 - - - +
130B GLU* 1.3 71.8 + - - +
132B TYR* 3.4 4.1 + - - +
133B GLU* 2.9 53.5 + - - +
155B LEU* 3.8 6.5 - - + +
158B LEU* 3.8 25.5 - - + +
159B TYR* 3.8 23.0 + - + -
162B ARG* 3.9 18.2 - - - +
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Residues in contact with GLU 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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89B MET* 6.1 5.6 - - - -
125B MET 4.1 0.7 - - - +
126B ASP* 3.0 28.4 - - - +
127B LEU* 3.3 11.2 + - - +
128B LEU 3.3 0.4 - - - -
129B GLN* 1.3 92.7 + - - +
131B PHE* 1.3 66.5 + - + +
133B GLU* 3.3 18.2 + - - +
134B THR* 3.0 34.0 + - + +
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Residues in contact with PHE 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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85B PHE* 4.7 17.5 - + + -
88B MET* 3.5 34.1 - - + -
89B MET* 4.0 36.8 - - + -
92B TYR* 4.5 13.9 - + + -
116B LEU* 4.9 10.5 - - + -
119B ILE* 4.4 17.0 - - + -
127B LEU* 3.1 47.3 - - + -
128B LEU* 3.2 10.7 + - - +
130B GLU* 1.3 80.1 - - + +
132B TYR* 1.3 57.1 + - - +
134B THR* 2.8 18.5 + - - -
135B THR* 2.7 30.3 + - - +
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Residues in contact with TYR 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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116B LEU* 3.7 34.8 + - + +
120B SER* 5.6 3.1 - - - -
128B LEU* 3.0 51.8 + - + +
129B GLN* 3.4 9.6 - - - +
131B PHE* 1.3 77.5 - - - +
133B GLU* 1.3 57.1 + - - +
135B THR* 3.3 7.4 + - - -
136B LEU* 3.0 33.0 + - - +
151B THR* 3.5 37.9 - - + +
154B LYS* 3.3 45.0 + - + +
155B LEU* 3.7 17.3 - - + -
158B LEU* 3.7 13.2 - - + -
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Residues in contact with GLU 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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129B GLN* 2.9 41.4 + - - +
130B GLU* 3.5 19.9 - - - +
132B TYR* 1.3 75.7 - - - +
134B THR* 1.3 57.3 + - + +
136B LEU* 3.4 7.6 + - - +
137B GLU* 2.8 42.2 + - - +
155B LEU* 3.8 16.8 - - + +
159B TYR* 3.0 27.7 + - - +
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Residues in contact with THR 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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89B MET* 5.2 10.9 - - + +
92B TYR* 4.5 9.5 - - - -
93B LYS* 4.3 25.6 - - - +
96B LEU* 3.9 12.7 - - - +
130B GLU* 3.0 18.8 + - + +
131B PHE* 2.8 26.5 + - - -
133B GLU* 1.3 72.2 - - + +
135B THR* 1.3 59.5 + - - +
137B GLU* 3.7 16.0 - - - +
138B ALA* 2.9 31.2 + - - +
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Residues in contact with THR 135 (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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92B TYR* 3.0 21.9 + - - +
96B LEU* 4.3 10.0 - - + +
112B ILE* 3.9 29.6 - - + +
116B LEU* 4.9 4.8 - - + +
131B PHE 2.7 23.0 + - - -
132B TYR* 3.5 9.2 - - - -
134B THR* 1.3 77.6 + - - +
136B LEU* 1.3 57.2 + - - +
138B ALA* 3.4 2.8 + - - +
139B LEU* 3.1 51.6 + - + +
151B THR* 4.4 12.8 - - + +
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Residues in contact with LEU 136 (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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132B TYR 3.0 20.3 + - - +
133B GLU* 3.8 4.0 - - - +
135B THR* 1.3 73.2 - - - +
137B GLU* 1.3 64.5 + - - +
139B LEU* 3.5 11.2 + - + +
140B LYS* 4.4 0.7 + - - +
148B TRP* 3.3 74.1 - - + +
151B THR* 3.8 30.1 - - + +
152B ASN* 3.4 28.9 - - - +
155B LEU* 3.8 22.7 - - + -
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Residues in contact with GLU 137 (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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133B GLU* 2.8 30.8 + - - +
134B THR* 3.7 21.7 - - - +
135B THR 3.3 0.2 - - - -
136B LEU* 1.3 75.1 - - + +
138B ALA* 1.3 57.5 + - - +
140B LYS* 4.3 11.8 + - - +
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Residues in contact with ALA 138 (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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96B LEU* 3.8 43.0 - - + +
99B ILE* 4.4 8.0 - - + +
100B ARG* 3.1 18.5 + - - -
134B THR 2.9 16.8 + - - +
135B THR 4.0 0.4 - - - +
136B LEU 3.3 0.2 - - - -
137B GLU* 1.3 73.7 - - - +
139B LEU* 1.3 56.8 + - - +
140B LYS* 3.1 11.4 + - - +
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Residues in contact with LEU 139 (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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96B LEU* 5.8 0.2 - - + -
99B ILE* 3.9 34.1 - - + -
100B ARG* 4.1 2.0 - - - +
112B ILE* 5.3 8.5 - - + -
135B THR* 3.1 39.7 + - + +
136B LEU* 3.5 12.9 + - + +
137B GLU 3.5 1.0 - - - -
138B ALA* 1.3 74.7 - - - +
140B LYS* 1.3 58.4 + - - +
141B ASP 2.9 9.5 + - - +
144B ASN* 2.9 31.1 + - - +
147B LEU* 4.1 34.8 - - + +
148B TRP* 3.5 20.3 - - + -
151B THR* 4.9 2.9 - - - +
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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