Contacts of the helix formed by residues 116 - 136 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ASN* 4.8 3.7 + - - -
84A LYS* 3.0 24.4 + - - +
86A ASP* 3.1 37.5 - - - -
114A GLN 3.2 1.8 + - - -
115A LYS* 1.3 71.9 - - - +
117A ASP* 1.3 64.4 + - - +
119A ASN* 4.1 1.3 - - - -
120A GLN* 2.8 45.5 + - - +
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Residues in contact with ASP 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LYS* 3.2 4.7 - - + +
116A SER* 1.3 84.9 + - - +
118A LEU* 1.3 61.1 + - - +
121A GLY* 3.2 19.4 + - - -
122A ALA 4.4 0.2 + - - -
194A THR 4.0 8.8 - - - +
195A PRO* 4.3 2.2 - - + +
196A LYS* 3.6 55.8 + - - +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLN* 3.9 11.7 - - + +
115A LYS* 3.0 9.0 + - - +
117A ASP* 1.3 80.0 - - - +
119A ASN* 1.3 64.5 + - - +
121A GLY 3.0 10.4 + - - -
122A ALA* 3.6 3.7 + - + +
123A TRP* 3.2 43.8 + - + +
170A TYR* 3.7 30.7 - - + -
190A PHE* 3.9 27.6 - - + -
191A ASP 3.7 16.2 - - - +
192A GLN* 3.8 20.6 - - - +
194A THR* 4.0 20.5 + - - +
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Residues in contact with ASN 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASP* 3.2 33.4 + - - +
87A ARG 5.4 1.0 + - - -
88A GLY* 3.7 13.5 - - - -
89A HIS 4.8 1.0 + - - -
114A GLN* 2.9 37.7 + - + +
115A LYS 2.9 15.4 + - - +
116A SER* 3.8 3.6 - - - +
118A LEU* 1.3 79.1 - - - +
120A GLN* 1.3 64.3 + - - +
123A TRP* 4.1 6.9 - - - +
124A ALA* 3.4 24.1 + - - +
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Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ASP* 2.9 26.4 + - - -
116A SER* 2.8 24.5 + - - +
119A ASN* 1.3 83.2 - - - +
121A GLY* 1.3 60.9 + - - +
124A ALA* 4.1 9.6 - - - +
125A ARG* 4.3 5.2 + - - +
196A LYS* 3.3 32.0 + - - +
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Residues in contact with GLY 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASP 3.2 14.5 + - - -
118A LEU 3.0 5.5 + - - -
120A GLN* 1.3 78.9 - - - +
122A ALA* 1.3 66.1 + - - -
123A TRP 3.3 0.7 - - - -
124A ALA* 3.1 3.1 + - - +
125A ARG* 3.0 36.9 + - - +
196A LYS* 3.5 17.9 - - - -
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Residues in contact with ALA 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ASP 4.4 1.6 + - - -
118A LEU* 3.6 4.1 + - + +
121A GLY* 1.3 70.5 - - - +
123A TRP* 1.3 57.9 + - - +
125A ARG* 3.3 9.3 + - - +
126A LEU* 3.0 30.7 + - - +
190A PHE* 3.9 28.0 - - + -
194A THR* 4.2 17.5 - - + -
195A PRO 5.1 1.0 + - - -
196A LYS 4.4 1.0 + - - -
198A ALA* 3.7 22.9 - - + +
200A PHE* 3.8 13.1 - - + +
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Residues in contact with TRP 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A HIS 3.6 17.2 + - - -
90A GLN* 4.6 5.4 - - - -
114A GLN* 3.7 26.6 + - - -
118A LEU* 3.2 31.2 + - + +
119A ASN* 4.1 7.9 - - - +
122A ALA* 1.3 79.1 - - - +
124A ALA* 1.3 57.3 + - - +
126A LEU* 3.4 6.7 + - + +
127A GLU* 3.0 52.8 + - - +
146A THR* 3.4 26.5 - - - -
170A TYR* 3.6 35.2 - + + -
171A TRP 3.9 7.0 - - - -
172A LYS* 3.8 23.6 - - + -
190A PHE* 3.6 34.5 - + - -
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASN 3.4 18.9 + - - +
120A GLN* 4.1 12.1 - - - +
121A GLY 3.1 7.6 + - - +
123A TRP* 1.3 78.5 - - - +
125A ARG* 1.3 60.7 + - + +
127A GLU* 3.2 15.0 + - - +
128A ASP* 3.0 34.7 + - - +
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLN 4.3 4.0 + - - -
121A GLY* 3.0 29.7 + - - +
122A ALA* 3.5 11.6 - - - +
123A TRP 3.3 0.2 - - - -
124A ALA* 1.3 73.4 - - + +
126A LEU* 1.3 64.9 + - - +
128A ASP* 3.2 14.0 + - - +
129A GLN* 3.0 26.4 + - + +
196A LYS* 2.7 28.9 + - - +
197A GLY* 3.5 9.8 + - - -
198A ALA 2.9 28.5 + - - -
199A ASP* 5.5 1.4 - - - +
200A PHE* 4.1 17.8 - - + +
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Residues in contact with LEU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ALA 3.0 16.7 + - - +
123A TRP* 3.8 7.0 - - + +
125A ARG* 1.3 74.5 - - - +
127A GLU* 1.3 63.5 + - - +
129A GLN* 3.2 0.9 + - - -
130A GLU* 2.8 26.3 + - + +
172A LYS* 4.0 28.5 - - + +
174A ILE* 4.3 6.7 - - + -
188A PHE* 3.8 31.0 - - + -
190A PHE* 3.6 31.2 - - + -
200A PHE* 4.0 21.9 - - + -
241A MET* 3.6 25.6 - - + -
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A HIS* 4.1 10.6 + - - +
90A GLN 4.7 0.5 - - - +
92A PRO* 3.5 30.3 - - + +
95A SER* 4.3 1.0 + - - -
123A TRP* 3.0 40.5 + - - +
124A ALA* 3.5 16.9 - - - +
126A LEU* 1.3 77.5 - - - +
128A ASP* 1.3 61.0 + - - +
130A GLU* 3.7 10.8 - - - +
131A ARG* 3.1 40.0 + - - +
172A LYS* 3.6 19.0 + - - +
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Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ALA* 3.0 21.7 + - - +
125A ARG* 3.2 17.4 + - - +
127A GLU* 1.3 75.7 - - - +
129A GLN* 1.3 64.1 + - - +
131A ARG* 2.7 37.4 + - - +
132A LYS* 3.0 42.0 + - - +
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Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ARG* 3.0 18.5 + - + +
126A LEU 3.9 1.1 - - - +
128A ASP* 1.3 76.6 - - - +
130A GLU* 1.3 65.9 + - - +
132A LYS* 3.3 35.6 + - - +
133A LEU* 3.2 24.4 + - - +
200A PHE* 3.7 23.6 - - + -
240A LEU 5.0 1.0 - - - +
241A MET* 3.7 44.8 - - + +
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Residues in contact with GLU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TYR* 2.6 27.1 + - - -
46A ILE* 3.8 17.2 - - + +
92A PRO* 4.4 3.8 - - - +
95A SER* 5.3 0.4 + - - -
126A LEU* 2.8 15.7 + - + +
127A GLU* 3.7 11.6 - - - +
129A GLN* 1.3 77.1 - - - +
131A ARG* 1.3 62.3 + - - +
133A LEU* 3.3 22.6 + - - +
142A VAL* 4.0 18.2 - - + +
144A THR* 2.9 21.8 + - - +
172A LYS* 2.9 31.2 + - - -
174A ILE* 4.6 7.6 - - + -
241A MET* 3.7 14.1 - - + +
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Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.7 7.2 - - - -
51A PRO* 4.4 18.2 - - + -
92A PRO* 4.8 3.0 - - - +
94A ALA* 3.7 24.1 - - - +
95A SER* 2.7 63.3 + - - +
127A GLU* 3.1 24.1 + - - +
128A ASP* 2.7 37.8 + - - +
129A GLN 3.3 0.2 - - - -
130A GLU* 1.3 77.0 - - - +
132A LYS* 1.3 63.6 + - + +
133A LEU 3.3 0.3 + - - -
134A ILE* 3.2 27.0 + - + +
135A ASP* 4.7 1.6 - - - +
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Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ASP* 3.0 28.5 + - - +
129A GLN* 3.3 36.8 + - - +
131A ARG* 1.3 76.0 - - + +
133A LEU* 1.3 64.0 + - - +
134A ILE 3.1 0.2 - - - -
135A ASP* 3.0 33.5 + - + +
136A ARG* 4.0 3.8 + - - +
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLN 3.2 11.6 + - - +
130A GLU* 3.5 21.1 - - - +
131A ARG 3.2 0.8 - - - -
132A LYS* 1.3 76.2 - - - +
134A ILE* 1.3 56.5 + - - +
136A ARG* 3.0 34.1 + - - +
139A ILE* 3.5 30.3 - - + +
142A VAL* 3.9 16.6 - - + -
174A ILE* 4.7 1.8 - - + -
176A ILE* 4.3 8.3 - - + -
237A LEU* 4.2 27.8 - - + -
240A LEU* 4.2 22.4 - - + +
241A MET* 4.0 25.6 - - + -
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Residues in contact with ILE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.8 20.4 - - + +
47A THR* 3.5 28.5 - - - +
48A LYS* 2.6 43.6 + - + +
51A PRO* 4.6 10.1 - - + -
130A GLU 4.3 0.6 + - - -
131A ARG* 3.2 19.6 + - + +
132A LYS 3.1 1.2 - - - -
133A LEU* 1.3 77.9 - - - +
135A ASP* 1.3 63.4 + - - +
136A ARG 3.3 0.4 - - - -
139A ILE* 3.8 7.0 - - + +
140A SER 3.6 33.4 - - - +
141A SER* 3.7 15.3 - - - +
142A VAL* 4.1 6.7 - - + +
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Residues in contact with ASP 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 4.3 1.8 + - - -
131A ARG 4.7 0.9 - - - -
132A LYS* 3.0 30.2 + - + +
134A ILE* 1.3 88.6 - - - +
136A ARG* 1.3 65.9 + - - +
137A ALA* 3.4 2.6 + - - -
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 3.0 17.9 + - - -
132A LYS 4.7 3.4 - - - +
133A LEU* 3.0 19.4 + - - +
135A ASP* 1.3 78.8 - - - +
137A ALA* 1.3 68.4 + - - +
138A ASP* 3.8 14.1 - - - +
139A ILE* 3.2 33.8 + - + +
240A LEU* 3.3 47.8 + - - +
225B ASP* 2.9 31.9 + - - -
226B VAL* 3.8 18.2 - - - +
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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