Contacts of the helix formed by residues 117 - 137 (chain B) in PDB entry 3M9M
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 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ILE* 3.9 10.1 - - - -
115B VAL* 3.8 2.4 - - - +
116B ARG* 1.3 79.1 - - - +
118B TYR* 1.3 61.4 + - - +
119B ARG* 3.1 33.6 + - - +
120B GLU* 2.6 35.7 + - - +
121B ALA* 2.9 25.8 + - - +
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 4.3 2.1 + - - -
2B ILE* 3.6 31.1 - - + +
117B ASP* 1.3 72.6 - - - +
119B ARG* 1.3 58.6 + - - +
121B ALA* 3.6 3.6 - - + +
122B TYR* 2.9 28.9 + - - +
144B ILE* 4.0 18.8 - - + -
145B SER* 3.0 19.9 + - - -
146B LYS* 2.9 36.4 + - - +
165B VAL* 3.7 25.4 - - + +
167B ASP* 3.5 33.4 - - + -
168B ASP* 3.7 13.4 + - - -
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 5.4 4.4 - - - +
117B ASP* 3.1 16.4 + - - +
118B TYR* 1.3 76.8 - - - +
120B GLU* 1.3 78.5 + - - +
122B TYR* 3.7 5.7 + - - +
123B ASN* 2.4 54.9 + - - +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B VAL* 3.6 18.5 - - + +
116B ARG* 2.9 58.6 + - - +
117B ASP* 2.6 30.9 + - - +
119B ARG* 1.3 94.5 + - - +
121B ALA* 1.3 67.1 + - - +
123B ASN* 3.2 8.9 + - - +
124B LEU* 2.9 23.2 + - - +
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Residues in contact with ALA 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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2B ILE* 3.9 14.8 - - + -
4B LEU* 4.8 0.3 - - - +
111B ILE* 4.2 10.4 - - + +
115B VAL* 4.0 8.7 - - + +
117B ASP 2.9 16.1 + - - +
118B TYR* 3.6 9.2 - - - +
119B ARG 3.3 0.2 - - - -
120B GLU* 1.3 77.1 - - - +
122B TYR* 1.3 62.4 + - - +
124B LEU* 3.0 5.7 + - - +
125B GLY 2.9 18.5 + - - -
144B ILE* 3.4 35.9 - - + +
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TYR 2.9 18.6 + - - +
119B ARG* 3.8 7.6 - - - +
120B GLU 3.3 0.2 - - - -
121B ALA* 1.3 78.2 - - - +
123B ASN* 1.3 70.2 + - - +
125B GLY 3.3 1.0 + - - -
126B LEU* 3.2 42.8 + - + +
144B ILE* 3.4 10.2 - - + +
163B ILE* 3.3 49.5 - - + +
164B LYS* 4.7 2.7 - - - -
165B VAL* 4.3 16.8 - - + -
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Residues in contact with ASN 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 ARG* 2.4 51.1 + - - +
120B GLU* 3.2 9.9 + - - +
121B ALA 3.2 0.8 - - - -
122B TYR* 1.3 83.4 - - - +
124B LEU* 1.3 66.0 + - - +
126B LEU* 3.4 9.8 + - - +
127B GLU* 3.0 23.9 + - - +
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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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4B LEU* 4.8 0.7 - - + -
95B TYR* 3.7 35.2 - - + +
111B ILE* 3.8 27.6 - - + -
114B LYS* 4.7 4.9 - - + +
115B VAL* 3.6 25.1 - - + -
120B GLU 2.9 13.1 + - - +
121B ALA 3.4 8.5 - - - +
123B ASN* 1.3 76.0 - - - +
125B GLY* 1.3 62.9 + - - +
127B GLU* 3.4 18.6 + - - +
128B ILE* 2.9 39.4 + - + +
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Residues in contact with GLY 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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4B LEU* 4.3 13.2 - - - +
121B ALA 2.9 12.6 + - - -
122B TYR 3.7 0.2 - - - -
123B ASN 3.1 0.6 - - - -
124B LEU* 1.3 75.8 - - - +
126B LEU* 1.3 49.7 + - - +
128B ILE* 2.7 28.9 + - - +
129B LYS* 2.8 20.2 + - - +
142B VAL* 4.3 8.0 - - - +
163B ILE* 3.6 18.8 - - - -
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 3.2 43.7 + - + +
123B ASN* 3.8 12.1 - - - +
125B GLY* 1.3 73.7 - - - +
127B GLU* 1.3 65.5 + - - +
129B LYS* 3.7 18.7 - - - +
130B ASN* 2.8 42.6 + - - +
163B ILE* 3.3 18.3 - - + +
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Residues in contact with GLU 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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95B TYR* 3.2 29.7 + - + +
123B ASN 3.0 15.4 + - - +
124B LEU* 3.4 21.1 - - + +
125B GLY 3.1 0.2 - - - -
126B LEU* 1.3 76.2 - - - +
128B ILE* 1.3 57.6 + - - +
130B ASN* 3.5 8.4 - - - +
131B LYS* 2.9 30.1 + - + +
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Residues in contact with ILE 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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4B LEU* 3.5 35.2 - - + -
6B VAL* 4.7 7.9 - - + -
92B LEU* 3.4 31.9 - - + -
95B TYR* 3.7 40.6 - - + -
109B LEU* 4.2 1.3 - - + -
124B LEU* 2.9 19.2 + - + +
125B GLY* 2.7 14.9 + - - +
127B GLU* 1.3 68.3 - - - +
129B LYS* 1.3 69.2 + - + +
131B LYS* 3.1 8.9 + - - +
132B ILE* 3.0 31.8 + - + +
142B VAL* 5.1 5.4 - - + -
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Residues in contact with LYS 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 GLY 2.8 10.2 + - - +
126B LEU* 3.7 18.8 - - + +
128B ILE* 1.3 75.7 - - - +
130B ASN* 1.3 66.8 - - - +
132B ILE* 3.1 8.4 + - - +
133B LEU* 2.9 21.9 + - - +
138B ILE 4.9 1.0 - - - +
139B THR* 5.4 0.7 - - - +
140B VAL* 2.7 39.1 + - + +
142B VAL* 3.6 24.2 - - + -
161B ASN* 3.0 25.9 + - - -
162B GLY* 3.2 31.3 + - - +
163B ILE* 4.1 18.2 - - + -
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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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126B LEU* 2.8 40.0 + - - +
127B GLU* 3.5 7.5 - - - +
129B LYS* 1.3 74.4 - - - +
131B LYS* 1.3 69.5 + - - +
133B LEU* 2.6 26.2 + - - +
134B GLU* 2.7 26.2 + - + +
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Residues in contact with LYS 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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91B LEU* 4.3 22.6 - - + +
94B GLU* 5.6 4.3 + - - -
95B TYR* 3.2 41.3 - - + +
127B GLU 2.9 13.3 + - - +
128B ILE* 3.4 8.3 - - - +
130B ASN* 1.3 72.4 - - - +
132B ILE* 1.3 60.9 + - + +
134B GLU* 2.9 20.1 + - - +
135B LYS* 2.9 60.7 + - + +
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Residues in contact with ILE 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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6B VAL* 4.4 7.9 - - + -
88B ILE* 3.8 35.0 - - + -
91B LEU* 4.1 17.5 - - + -
92B LEU* 4.6 5.6 - - + -
128B ILE* 3.0 30.5 + - + +
129B LYS* 3.2 7.6 - - - +
131B LYS* 1.3 77.3 - - + +
133B LEU* 1.3 57.2 + - - +
136B GLU* 2.9 28.5 + - + +
137B LYS 3.4 3.3 + - - -
138B ILE* 3.0 31.2 - - + +
140B VAL* 3.9 32.3 - - + -
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Residues in contact with LEU 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 LYS 2.9 11.8 + - - +
130B ASN* 2.6 23.0 + - - +
132B ILE* 1.3 73.0 - - - +
134B GLU* 1.3 59.6 + - + +
137B LYS* 3.0 45.5 + - + +
138B ILE 4.1 5.2 - - - +
139B THR* 4.0 25.4 - - + -
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Residues in contact with GLU 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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130B ASN* 2.7 26.7 + - + +
131B LYS* 3.2 29.8 + - - +
133B LEU* 1.3 77.3 - - + +
135B LYS* 1.3 68.0 + - + +
137B LYS* 4.3 6.2 + - - -
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Residues in contact with LYS 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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91B LEU* 3.8 28.5 - - + -
131B LYS* 2.9 53.6 + - + +
134B GLU* 1.3 78.3 - - + +
136B GLU* 1.3 68.5 + - + +
137B LYS* 5.2 2.1 - - - +
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Residues in contact with GLU 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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18B VAL* 4.1 2.9 - - - +
84B VAL* 4.5 5.6 - - + +
87B ARG* 2.6 59.8 + - + +
88B ILE* 4.1 21.5 - - + -
91B LEU* 4.5 6.2 - - + +
132B ILE 2.9 12.9 + - - +
135B LYS* 1.3 87.2 - - + +
137B LYS* 1.3 87.7 + - - +
138B ILE* 3.0 22.2 + - + +
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Residues in contact with LYS 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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14B GLN* 3.8 5.9 + - - -
18B VAL* 3.5 38.6 - - + +
132B ILE 3.4 0.2 + - - -
133B LEU* 3.0 35.9 + - + +
134B GLU 5.1 4.6 + - - -
135B LYS 3.8 2.6 + - - +
136B GLU* 1.3 96.6 - - - +
138B ILE* 1.3 59.1 + - - +
139B THR* 4.2 1.0 + - - +
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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
------------------------------------------------------------
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