Contacts of the helix formed by residues 131 - 152 (chain A) in PDB entry 1SMK
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 131 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A THR 2.6 17.4 + - - +
130A ARG* 1.3 72.7 - - - +
132A ASP* 1.3 58.6 + - - +
133A LEU* 2.8 9.7 + - - +
134A PHE* 3.2 21.3 + - - +
135A LYS* 3.4 25.6 + - - +
349A LYS* 3.2 29.7 + - - -
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Residues in contact with ASP 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 2.4 59.5 + - + +
131A ASP* 1.3 68.0 - - - +
133A LEU* 1.3 62.4 + - - +
135A LYS* 3.5 26.9 + - - +
136A ILE* 3.4 27.4 + - - +
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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
----------------------------------------------------------
122A VAL* 3.5 27.8 - - + +
123A PRO 3.6 3.4 - - - +
124A ARG* 3.3 41.5 - - + +
128A MET* 3.3 36.1 - - + -
129A THR* 4.7 9.0 - - - +
130A ARG* 4.2 2.2 - - - +
131A ASP* 2.8 8.9 - - - +
132A ASP* 1.3 76.0 - - - +
134A PHE* 1.3 59.1 + - + +
135A LYS 3.0 0.9 - - - -
136A ILE* 2.6 32.3 + - + +
137A ASN* 3.0 24.0 + - - +
162A ASN 6.1 0.4 - - - +
163A PRO* 6.5 1.3 - - + -
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Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ASP* 3.2 23.6 + - - +
133A LEU* 1.3 83.9 - - + +
135A LYS* 1.3 65.0 + - + +
137A ASN* 4.6 5.4 - - - -
138A ALA* 2.8 47.8 + - + +
163A PRO* 3.7 27.6 - - + -
166A SER* 3.7 28.5 - - - -
167A THR* 5.4 1.1 - - + -
170A ILE* 4.3 12.3 - - + -
349A LYS* 3.7 49.6 - - + +
353A PHE* 4.4 14.4 - + + -
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Residues in contact with LYS 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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131A ASP* 3.4 24.2 + - - +
132A ASP* 3.6 26.6 + - - +
133A LEU 2.9 0.8 + - - -
134A PHE* 1.3 86.5 - - + +
136A ILE* 1.3 57.9 + - + +
138A ALA* 3.9 3.6 - - - +
139A GLY* 2.9 24.6 + - - -
353A PHE* 4.2 14.4 - - + -
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Residues in contact with ILE 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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122A VAL* 3.6 42.8 - - + -
128A MET* 5.2 5.6 - - + -
130A ARG* 6.3 0.4 - - - +
132A ASP* 3.6 22.0 - - - +
133A LEU* 2.6 19.4 + - + +
135A LYS* 1.3 73.5 - - + +
137A ASN* 1.3 58.6 + - - +
139A GLY* 3.1 3.5 + - - -
140A ILE* 2.8 39.1 + - + +
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Residues in contact with ASN 137 (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 ALA 5.0 1.2 + - - +
121A GLY* 4.0 14.5 - - - -
122A VAL* 3.0 40.2 + - - +
133A LEU* 3.0 20.8 + - - +
134A PHE* 3.9 9.0 - - - +
136A ILE* 1.3 74.7 - - - +
138A ALA* 1.3 61.1 + - - +
140A ILE* 3.1 6.9 + - - +
141A VAL* 2.8 36.4 + - + +
161A SER* 5.1 1.0 - - - -
162A ASN* 2.9 35.1 + - - +
163A PRO* 5.3 1.1 - - + -
167A THR* 5.3 3.1 - - + -
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Residues in contact with ALA 138 (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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134A PHE* 2.8 30.2 + - + +
137A ASN* 1.3 69.5 - - - +
139A GLY* 1.3 66.7 + - - +
141A VAL* 3.3 4.5 + - - +
142A LYS* 2.9 24.6 + - - +
167A THR* 5.1 2.0 - - - +
170A ILE* 3.7 22.5 - - + +
353A PHE* 3.4 39.1 - - + -
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Residues in contact with GLY 139 (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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135A LYS 2.9 16.3 + - - -
136A ILE* 3.1 4.9 + - - -
138A ALA* 1.3 76.5 - - - +
140A ILE* 1.3 61.7 + - - +
142A LYS* 3.1 21.2 + - - +
143A THR* 3.2 16.8 + - - +
353A PHE* 3.6 11.2 - - - -
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Residues in contact with ILE 140 (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 ALA* 3.9 19.7 - - + +
121A GLY* 4.2 6.1 - - - +
122A VAL* 4.0 25.4 - - + +
136A ILE* 2.8 36.9 + - + +
137A ASN* 3.1 8.5 + - - +
139A GLY* 1.3 71.2 - - - +
141A VAL* 1.3 67.6 + - + +
142A LYS 3.0 1.8 + - - -
143A THR* 3.3 7.8 + - - -
144A LEU* 3.2 42.4 + - + +
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Residues in contact with VAL 141 (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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118A VAL* 5.9 0.4 - - - -
120A ALA 5.1 1.3 - - - +
137A ASN 2.8 23.4 + - - +
138A ALA* 3.8 5.4 - - - +
140A ILE* 1.3 74.7 - - + +
142A LYS* 1.3 63.3 + - - +
144A LEU* 4.0 6.2 - - - +
145A CYS* 3.0 39.3 + - - +
159A LEU* 3.9 11.9 - - + -
161A SER* 3.4 34.5 - - - +
167A THR* 3.9 35.9 - - + +
170A ILE* 4.2 10.1 - - + -
171A ALA* 4.5 0.2 - - + -
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Residues in contact with LYS 142 (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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138A ALA 2.9 13.9 + - - +
139A GLY* 3.1 12.8 - - - +
140A ILE 3.0 0.2 - - - -
141A VAL* 1.3 80.9 - - - +
143A THR* 1.3 60.8 + - + +
145A CYS* 3.2 2.6 + - - +
146A GLU* 2.9 55.3 + - - +
170A ILE* 4.7 1.5 - - + +
174A VAL* 4.0 12.7 - - + +
177A LYS* 6.1 1.0 - - - +
353A PHE* 4.4 10.1 - - + -
354A ILE* 3.8 33.7 + - + +
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Residues in contact with THR 143 (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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103A GLN* 4.4 17.4 + - - +
106A LEU* 4.4 3.9 - - - +
139A GLY 3.2 16.5 + - - +
140A ILE* 3.5 7.5 + - - +
142A LYS* 1.3 74.9 - - + +
144A LEU* 1.3 78.7 + - - +
146A GLU* 2.9 20.7 + - - +
147A GLY* 2.9 20.4 + - - -
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Residues in contact with LEU 144 (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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50A LEU* 4.0 22.6 - - + +
76A TYR* 4.0 27.6 - - + +
106A LEU* 4.0 16.2 - - + -
110A LEU* 4.4 1.9 - - - +
118A VAL* 4.0 15.9 - - + -
120A ALA* 3.4 34.1 - - + -
140A ILE* 3.2 25.2 + - + +
141A VAL* 4.1 4.0 - - - +
143A THR* 1.3 85.0 + - - +
145A CYS* 1.3 59.9 + - - +
147A GLY* 3.1 2.8 + - - -
148A ILE* 2.8 34.5 + - + +
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Residues in contact with CYS 145 (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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141A VAL* 3.0 32.9 + - - +
142A LYS 3.6 3.6 - - - +
144A LEU* 1.3 75.1 - - - +
146A GLU* 1.3 60.7 + - - +
148A ILE* 4.1 9.9 - - - -
149A ALA* 2.8 31.2 + - - +
157A VAL* 5.7 3.4 - - - -
159A LEU* 5.2 3.8 - - - -
171A ALA* 3.5 32.1 - - - -
174A VAL* 4.0 16.8 - - + -
175A PHE* 3.4 22.6 - - + -
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Residues in contact with GLU 146 (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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142A LYS* 2.9 49.3 + - - +
143A THR* 2.9 22.6 + - - +
145A CYS* 1.3 77.5 - - - +
147A GLY* 1.3 62.4 + - - +
149A ALA* 3.4 5.6 + - - +
150A LYS* 3.0 24.6 + - - +
174A VAL* 3.7 17.6 - - + +
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Residues in contact with GLY 147 (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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103A GLN* 6.0 0.9 - - - -
106A LEU* 4.3 9.2 - - - -
110A LEU* 3.3 14.6 - - - -
143A THR 2.9 12.5 + - - -
144A LEU 3.1 3.3 + - - -
146A GLU* 1.3 76.4 - - - +
148A ILE* 1.3 55.0 + - - +
150A LYS* 3.1 6.4 + - - -
151A CYS* 2.7 43.6 + - - +
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Residues in contact with ILE 148 (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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50A LEU* 4.2 8.1 - - + -
110A LEU* 3.8 22.9 - - + -
116A ILE* 3.9 25.4 - - + -
118A VAL* 4.5 4.5 - - + -
144A LEU* 2.8 21.7 + - + +
145A CYS* 3.6 15.9 - - - +
147A GLY* 1.3 76.8 - - - +
149A ALA* 1.3 61.6 + - - +
152A CYS* 2.9 48.6 + - - +
153A PRO* 3.2 8.8 - - + -
155A ALA* 5.3 0.2 - - + -
157A VAL* 4.1 33.4 - - + -
175A PHE* 4.1 11.2 - - + -
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Residues in contact with ALA 149 (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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145A CYS 2.8 17.1 + - - +
146A GLU* 3.6 8.1 - - - +
148A ILE* 1.3 78.2 - - - +
150A LYS* 1.3 59.4 + - - +
153A PRO* 3.5 21.1 - - - +
174A VAL 5.1 0.7 - - - +
175A PHE* 3.8 12.1 - - + -
178A ALA* 3.8 22.2 - - + -
180A THR* 3.6 31.4 - - - +
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Residues in contact with LYS 150 (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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107A GLU* 2.8 30.0 + - - +
146A GLU 3.0 16.3 + - - +
147A GLY* 3.6 5.4 - - - +
149A ALA* 1.3 79.9 - - - +
151A CYS* 1.3 67.4 + - - +
153A PRO* 4.1 4.2 - - - +
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Residues in contact with CYS 151 (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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107A GLU* 3.6 41.3 - - - -
110A LEU* 3.7 19.3 - - + -
111A THR* 3.9 25.7 + - - +
112A GLY 4.4 2.6 + - - -
147A GLY* 2.7 27.6 + - - +
150A LYS* 1.3 87.2 - - - +
152A CYS* 1.3 57.9 + - - +
153A PRO* 3.4 7.3 - - - +
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Residues in contact with CYS 152 (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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110A LEU* 3.6 35.2 - - - +
112A GLY 4.8 1.3 - - - +
113A MET 4.1 9.0 - - - +
116A ILE* 3.8 31.4 - - - -
148A ILE* 2.9 32.2 + - - +
151A CYS* 1.3 74.7 - - - +
153A PRO* 1.3 57.8 - - - +
154A ARG 3.0 5.2 - - - -
155A ALA* 2.9 29.4 + - + +
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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
------------------------------------------------------------
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