Contacts of the helix formed by residues 116 - 136 (chain B) in PDB entry 1SMN
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 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B ASN* 3.7 6.8 + - - -
84B LYS* 3.0 33.7 + - - +
86B ASP* 3.1 35.3 + - - -
114B GLN 3.2 1.6 + - - -
115B LYS* 1.3 71.0 - - - +
117B ASP* 1.3 57.5 + - - +
119B ASN* 4.2 0.4 - - - -
120B GLN* 2.7 48.4 + - - +
196B LYS* 3.7 6.1 - - - -
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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
----------------------------------------------------------
84B LYS* 6.3 2.7 - - - -
115B LYS* 3.3 4.6 - - + +
116B SER* 1.3 79.1 - - - +
118B LEU* 1.3 57.9 + - - +
121B GLY* 3.0 25.6 + - - -
122B ALA 4.4 0.5 + - - -
192B GLN 5.9 0.4 - - - +
194B THR 3.9 9.1 - - - +
195B PRO* 4.4 1.8 - - + +
196B LYS* 2.7 65.8 + - - +
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Residues in contact with LEU 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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114B GLN* 3.9 11.9 - - + +
115B LYS* 3.2 9.7 + - + +
117B ASP* 1.3 77.8 - - - +
119B ASN* 1.3 67.1 + - - +
121B GLY 3.0 10.9 + - - -
122B ALA* 4.6 2.0 - - + +
123B TRP* 3.2 37.8 + - + +
170B TYR* 3.7 31.6 - - + -
190B PHE* 3.7 34.3 - - + -
191B ASP 3.8 14.6 - - - +
192B GLN* 4.0 20.0 - - - +
194B THR* 3.9 22.3 + - + +
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Residues in contact with ASN 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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86B ASP* 3.0 35.5 + - + +
87B ARG 4.8 1.3 + - - +
88B GLY* 3.8 11.5 - - - -
89B HIS 4.8 1.2 + - - -
114B GLN* 2.9 32.8 + - + +
115B LYS 2.9 17.1 + - - +
116B SER 3.8 2.9 - - - +
118B LEU* 1.3 79.3 - - - +
120B GLN* 1.3 66.8 + - - +
123B TRP* 4.1 6.3 - - - +
124B ALA* 3.4 23.4 + - - +
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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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86B ASP* 2.7 26.1 + - - -
116B SER* 2.7 23.0 + - - +
117B ASP 4.0 0.4 - - - -
119B ASN* 1.3 84.9 - - - +
121B GLY* 1.3 57.8 + - - +
124B ALA* 4.1 9.3 - - - +
125B ARG* 4.1 6.6 + - - -
196B LYS* 3.2 32.2 + - - +
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Residues in contact with GLY 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 ASP 3.0 13.6 + - - -
118B LEU 3.0 5.3 + - - -
120B GLN* 1.3 79.4 - - - +
122B ALA* 1.3 66.4 + - - -
123B TRP 3.2 1.9 + - - -
124B ALA* 3.2 2.1 + - - +
125B ARG* 3.1 44.4 + - - -
196B LYS* 3.5 9.4 - - - -
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Residues in contact with ALA 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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117B ASP 4.4 1.2 + - - -
118B LEU* 3.6 4.6 + - + +
121B GLY* 1.3 71.2 - - - -
123B TRP* 1.3 57.7 + - - +
125B ARG* 3.4 16.1 + - - +
126B LEU* 2.9 30.7 + - - +
190B PHE* 3.7 29.4 - - + -
194B THR* 4.4 15.3 - - + -
195B PRO 5.2 1.6 + - - -
196B LYS 4.3 1.0 + - - -
198B ALA* 3.8 17.3 - - + +
199B ASP 4.9 0.2 - - - -
200B PHE* 3.8 10.5 - - + +
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Residues in contact with TRP 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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89B HIS 3.7 17.9 + - - -
90B GLN* 4.7 4.5 - - - -
114B GLN* 3.6 29.2 + - - -
118B LEU* 3.2 30.9 + - + +
119B ASN* 4.1 6.7 - - - +
122B ALA* 1.3 79.9 - - - +
124B ALA* 1.3 58.1 + - - +
126B LEU* 3.4 7.6 + - + +
127B GLU* 3.0 52.8 + - - +
146B THR* 3.5 25.8 - - - -
170B TYR* 3.7 34.3 - + + -
171B TRP 4.0 7.4 - - - -
172B LYS* 3.9 25.1 - - + -
190B PHE* 3.7 33.9 - + - -
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Residues in contact with ALA 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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119B ASN 3.4 18.7 + - - +
120B GLN* 4.1 11.9 - - - +
121B GLY 3.2 7.5 + - - +
123B TRP* 1.3 74.9 - - - +
125B ARG* 1.3 62.1 + - - +
127B GLU* 3.2 16.5 + - - +
128B ASP* 2.9 37.0 + - - +
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Residues in contact with ARG 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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120B GLN 4.1 5.6 + - - -
121B GLY* 3.1 30.6 + - - -
122B ALA* 3.5 12.8 - - - +
124B ALA* 1.3 78.6 - - - +
126B LEU* 1.3 61.2 + - - +
128B ASP* 3.3 12.8 + - + +
129B GLN* 3.1 26.2 + - - +
196B LYS* 2.7 27.1 + - - +
197B GLY* 3.4 10.5 + - - -
198B ALA 2.8 26.9 + - - -
199B ASP* 5.8 0.6 - - - +
200B PHE* 4.0 17.4 - - + +
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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
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122B ALA 2.9 18.1 + - - +
123B TRP* 3.8 7.6 - - + +
125B ARG* 1.3 72.5 - - - +
127B GLU* 1.3 68.6 + - - +
129B GLN* 3.2 1.4 + - - -
130B GLU* 2.8 25.9 + - + +
172B LYS* 4.1 25.6 - - + +
174B ILE* 4.3 6.1 - - + -
188B PHE* 3.6 43.3 - - + -
190B PHE* 3.6 30.1 - - + -
200B PHE* 3.9 18.3 - - + -
241B MET* 3.7 18.8 - - + -
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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
----------------------------------------------------------
89B HIS* 4.1 11.6 + - - +
90B GLN 4.7 0.7 - - - +
92B PRO* 3.6 29.1 - - + +
95B SER* 4.5 0.9 + - - -
123B TRP* 3.0 40.1 + - - +
124B ALA* 3.2 17.0 + - - +
126B LEU* 1.3 76.5 - - - +
128B ASP* 1.3 63.4 + - - +
130B GLU* 3.3 10.5 + - - +
131B ARG* 3.1 40.1 + - - +
172B LYS* 3.6 19.0 + - - +
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Residues in contact with ASP 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 ALA* 2.9 23.0 + - - +
125B ARG* 3.5 13.0 - - - +
126B LEU 3.2 0.2 - - - -
127B GLU* 1.3 76.7 - - - +
129B GLN* 1.3 69.3 + - - +
131B ARG* 2.6 36.5 + - - +
132B LYS* 3.0 36.5 + - - +
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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
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125B ARG 3.1 19.4 + - - +
126B LEU 3.9 2.7 - - - +
128B ASP* 1.3 78.0 - - - +
130B GLU* 1.3 61.5 + - - +
132B LYS* 3.3 44.4 + - - +
133B LEU* 3.3 17.5 + - - +
200B PHE* 3.7 23.8 - - + -
240B LEU 5.0 0.9 - - - +
241B MET* 3.6 43.6 - - + +
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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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44B TYR* 2.6 30.0 + - - -
46B ILE* 4.0 13.3 - - + +
92B PRO* 4.3 4.4 - - - +
95B SER* 5.2 0.6 + - - +
126B LEU* 2.8 14.7 + - + +
127B GLU* 3.6 10.6 - - - +
129B GLN* 1.3 76.2 - - - +
131B ARG* 1.3 63.9 + - - +
133B LEU* 3.4 21.6 + - - +
142B VAL* 4.0 18.2 - - + +
144B THR* 2.7 23.2 + - - +
172B LYS* 2.9 31.8 + - - +
174B ILE* 4.4 8.3 - - + -
241B MET* 3.7 16.0 - - + +
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Residues in contact with ARG 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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46B ILE* 4.7 7.9 - - + -
51B PRO* 4.6 16.6 - - + -
92B PRO* 4.7 3.2 - - - +
94B ALA* 3.5 23.1 - - - +
95B SER* 2.9 60.1 + - - +
127B GLU* 3.1 28.4 + - - +
128B ASP* 2.6 40.1 + - - +
130B GLU* 1.3 77.2 - - - +
132B LYS* 1.3 65.4 + - + +
133B LEU 3.1 0.9 + - - -
134B ILE* 3.2 27.9 + - + +
135B ASP* 4.7 1.4 - - - +
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Residues in contact with LYS 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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128B ASP* 3.0 24.3 + - - +
129B GLN* 3.3 39.1 + - - +
131B ARG* 1.3 75.6 - - + +
133B LEU* 1.3 64.9 + - - +
135B ASP* 2.9 35.3 + - + +
136B ARG* 3.9 4.3 + - - +
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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 GLN 3.3 10.7 + - - +
130B GLU* 3.4 21.3 - - - +
131B ARG 3.1 0.6 - - - -
132B LYS* 1.3 76.8 - - - +
134B ILE* 1.3 58.2 + - - +
136B ARG* 3.0 33.9 + - - +
139B ILE* 3.5 29.7 - - + +
142B VAL* 3.9 17.0 - - + -
174B ILE* 4.7 1.3 - - + -
176B ILE* 4.2 9.9 - - + -
237B LEU* 4.1 27.8 - - + -
240B LEU* 4.3 21.3 - - + +
241B MET* 4.0 24.7 - - + -
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Residues in contact with ILE 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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46B ILE* 3.9 22.9 - - + +
47B THR* 3.5 26.5 - - - +
48B LYS* 2.8 43.3 + - + +
51B PRO* 4.5 11.7 - - + -
130B GLU 4.3 0.6 + - - -
131B ARG* 3.2 21.1 + - + +
132B LYS 3.1 0.6 - - - -
133B LEU* 1.3 77.4 - - - +
135B ASP* 1.3 66.7 + - - +
136B ARG 3.2 0.4 - - - -
139B ILE* 3.7 10.8 - - + +
140B SER* 3.6 32.8 - - - +
141B SER* 3.6 15.0 - - - +
142B VAL* 4.2 4.0 - - + +
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Residues in contact with ASP 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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48B LYS* 4.4 1.5 + - - +
131B ARG 4.7 0.2 - - - -
132B LYS* 2.9 34.0 + - + +
134B ILE* 1.3 86.5 - - - +
136B ARG* 1.3 65.0 + - + +
137B ALA* 3.4 2.4 + - - -
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Residues in contact with ARG 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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225A ASP* 2.9 32.9 + - - -
226A VAL* 3.9 16.0 - - - +
48B LYS* 2.8 24.3 + - - -
132B LYS 4.6 3.8 + - - +
133B LEU* 3.0 20.3 + - - +
135B ASP* 1.3 77.4 - - + +
137B ALA* 1.3 59.3 + - - +
138B ASP* 3.3 13.7 - - - +
139B ILE* 3.1 34.0 + - + +
240B LEU* 3.2 48.9 + - - +
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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
------------------------------------------------------------
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