Contacts of the helix formed by residues 133 - 152 (chain D) 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 LEU 133 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D VAL* 4.4 12.6 - - + +
123D PRO* 4.8 3.4 - - + +
124D ARG* 4.6 23.1 - - + +
130D ARG* 4.0 17.3 + - + +
131D ASP* 2.9 21.3 - - - +
132D ASP* 1.3 75.3 - - - +
134D PHE* 1.3 74.4 + - - +
135D LYS 3.0 1.1 - - - -
136D ILE* 2.8 30.0 + - + +
137D ASN* 3.0 41.0 + - - +
162D ASN* 4.3 20.6 - - + +
163D PRO* 4.4 3.4 - - + -
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Residues in contact with PHE 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ASP 3.7 6.0 + - - +
132D ASP* 2.8 9.6 - - - +
133D LEU* 1.3 88.3 - - + +
135D LYS* 1.3 60.6 + - + +
137D ASN* 4.7 0.4 - - - +
138D ALA* 2.6 41.9 + - + +
163D PRO* 3.9 24.9 - - + -
166D SER* 3.5 27.6 - - - -
167D THR* 5.3 0.7 - - + -
170D ILE* 4.2 22.2 - - + -
349D LYS* 3.4 63.0 - - + +
353D PHE* 4.1 21.8 - + + -
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Residues in contact with LYS 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ARG* 5.5 5.8 - - - +
132D ASP* 3.4 32.8 - - + +
134D PHE* 1.3 88.7 - - + +
136D ILE* 1.3 68.4 + - + +
138D ALA* 3.7 2.8 - - - +
139D GLY* 3.1 14.4 + - - -
353D PHE* 4.4 9.7 - - - -
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D VAL* 4.0 21.8 - - + -
133D LEU* 2.8 22.5 + - + +
135D LYS* 1.3 79.3 - - + +
137D ASN* 1.3 66.4 + - - +
139D GLY* 2.9 13.2 + - - -
140D ILE* 3.0 32.8 + - + +
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Residues in contact with ASN 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ALA 5.3 0.2 - - - -
121D GLY* 3.1 12.8 - - - -
122D VAL* 3.1 39.5 + - - +
133D LEU* 3.0 40.8 + - + +
134D PHE* 4.3 2.0 - - - +
136D ILE* 1.3 79.4 - - - +
138D ALA* 1.3 56.3 + - - +
140D ILE* 3.2 7.7 + - - +
141D VAL* 2.8 39.7 + - + +
161D SER* 5.4 2.9 - - - -
162D ASN* 3.2 26.1 + - - +
163D PRO* 5.0 1.3 - - + -
167D THR* 5.1 1.3 - - + -
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PHE* 2.6 37.1 + - + +
135D LYS 3.7 3.1 - - - +
137D ASN* 1.3 74.1 - - - +
139D GLY* 1.3 56.1 + - - +
141D VAL* 3.5 5.0 + - - +
142D LYS* 3.0 27.2 + - - +
167D THR* 5.1 2.2 - - - +
170D ILE* 3.7 29.5 - - + +
353D PHE* 3.6 24.3 - - + -
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Residues in contact with GLY 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LYS 3.1 9.7 + - - -
136D ILE 2.9 7.2 + - - -
138D ALA* 1.3 75.2 - - - +
140D ILE* 1.3 64.1 + - - +
142D LYS* 2.9 10.9 + - - +
143D THR* 2.9 30.9 + - - +
353D PHE* 3.9 9.6 - - - -
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Residues in contact with ILE 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D ALA* 3.9 15.7 - - + +
121D GLY* 4.3 23.3 - - - +
122D VAL* 4.8 5.2 - - + -
136D ILE* 3.0 36.1 + - + +
137D ASN* 3.5 9.2 - - - +
139D GLY* 1.3 75.9 - - - +
141D VAL* 1.3 64.8 + - + +
143D THR* 3.0 23.6 + - - +
144D LEU* 3.1 33.0 + - + +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D VAL* 6.0 0.2 - - - -
137D ASN 2.8 21.8 + - - +
138D ALA* 3.7 5.6 - - - +
140D ILE* 1.3 78.7 - - + +
142D LYS* 1.3 64.7 + - - +
144D LEU* 3.8 6.8 - - - +
145D CYS* 2.9 42.5 + - - +
159D LEU* 3.8 19.5 - - + -
161D SER* 3.6 31.6 - - - +
167D THR* 3.6 27.6 - - + +
170D ILE* 4.3 9.6 - - + -
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Residues in contact with LYS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D ALA 3.0 15.1 + - - +
139D GLY* 2.9 12.9 + - - +
141D VAL* 1.3 80.8 - - - +
143D THR* 1.3 66.8 + - + +
145D CYS* 3.3 2.4 + - - +
146D GLU* 3.0 52.0 + - - +
170D ILE* 4.8 1.6 - - + -
174D VAL* 4.2 13.1 - - + +
177D LYS* 5.3 8.4 - - - +
353D PHE* 4.0 22.0 - - + -
354D ILE* 4.0 24.7 - - + -
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Residues in contact with THR 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLN* 4.4 18.8 + - - +
106D LEU* 4.8 4.2 - - - +
139D GLY* 2.9 18.3 + - - +
140D ILE* 3.0 12.6 + - - +
142D LYS* 1.3 74.8 - - + +
144D LEU* 1.3 74.6 + - - +
146D GLU* 2.8 34.3 + - - +
147D GLY* 3.0 9.9 + - - -
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 4.2 24.7 - - + -
76D TYR* 4.3 20.4 - - + +
106D LEU* 4.2 20.0 - - + -
110D LEU* 4.2 1.7 - - - +
118D VAL* 3.9 14.8 - - + -
120D ALA* 3.4 33.7 - - + -
140D ILE* 3.1 26.6 + - + +
141D VAL* 3.8 4.7 - - - +
143D THR* 1.3 85.1 + - - +
145D CYS* 1.3 59.1 + - - +
147D GLY* 3.1 3.8 + - - +
148D ILE* 2.9 34.5 + - + +
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Residues in contact with CYS 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D VAL* 6.5 0.9 - - - -
141D VAL* 2.9 37.8 + - - +
142D LYS 3.8 3.6 - - - +
143D THR 3.3 0.2 - - - -
144D LEU* 1.3 74.8 - - - +
146D GLU* 1.3 57.1 + - - +
148D ILE* 4.1 9.6 - - - -
149D ALA* 3.0 24.4 + - - +
157D VAL* 5.9 2.9 - - - -
159D LEU* 4.8 4.9 - - - -
171D ALA* 3.5 31.0 - - - -
174D VAL* 3.9 16.1 - - + +
175D PHE* 3.0 31.5 - - + -
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Residues in contact with GLU 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D LYS* 3.0 43.0 + - - +
143D THR* 2.8 21.4 + - - +
145D CYS* 1.3 74.4 - - - +
147D GLY* 1.3 66.0 + - - +
149D ALA* 3.5 5.2 + - - +
150D LYS* 3.1 25.2 + - - +
174D VAL* 3.5 20.4 - - + +
177D LYS* 5.3 7.1 + - - +
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Residues in contact with GLY 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D GLN* 6.0 0.7 - - - -
106D LEU* 4.4 11.9 - - - -
107D GLU* 6.3 0.2 - - - -
110D LEU* 3.2 15.1 - - - +
143D THR 3.0 10.4 + - - -
144D LEU 3.1 4.4 + - - -
146D GLU* 1.3 78.7 - - - +
148D ILE* 1.3 55.2 + - - +
150D LYS* 3.3 6.1 + - - -
151D CYS* 2.8 37.2 + - - -
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Residues in contact with ILE 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 4.3 7.6 - - + -
110D LEU* 3.6 12.8 - - + -
116D ILE* 3.7 37.9 - - + -
118D VAL* 4.7 3.6 - - + -
144D LEU* 2.9 18.8 + - + +
145D CYS* 3.5 17.9 - - - +
146D GLU 3.1 0.2 - - - -
147D GLY* 1.3 74.0 - - - +
149D ALA* 1.3 62.3 + - - +
152D CYS* 2.7 56.5 + - - +
153D PRO* 5.1 2.2 - - + -
155D ALA 5.4 0.2 - - - +
157D VAL* 4.3 25.1 - - + -
175D PHE* 4.0 15.5 - - + -
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Residues in contact with ALA 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D CYS 3.0 16.7 + - - +
146D GLU* 4.1 4.9 - - - +
148D ILE* 1.3 76.3 - - - +
150D LYS* 1.3 59.5 + - - +
153D PRO* 3.3 26.3 - - - +
174D VAL 5.2 0.7 - - - +
175D PHE* 3.9 9.8 - - + -
178D ALA* 3.8 20.9 - - + -
180D THR* 3.0 35.3 - - - +
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Residues in contact with LYS 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLU* 3.9 27.1 + - + +
146D GLU 3.1 17.9 + - - +
147D GLY* 3.6 6.7 - - - +
148D ILE 3.0 0.6 - - - -
149D ALA* 1.3 80.2 - - - +
151D CYS* 1.3 66.5 + - - +
153D PRO* 4.5 2.1 - - - +
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Residues in contact with CYS 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLU* 3.8 42.2 - - - -
110D LEU* 3.6 18.4 - - + -
111D THR* 3.8 25.8 - - - +
112D GLY 3.9 3.6 + - - -
147D GLY* 2.8 22.0 + - - +
150D LYS* 1.3 95.7 - - - +
152D CYS* 1.3 61.5 + - - +
153D PRO* 3.6 4.3 - - - +
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Residues in contact with CYS 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D LEU* 3.5 31.6 - - - +
112D GLY* 4.8 0.9 - - - +
113D MET* 3.9 11.0 - - - +
116D ILE* 3.0 37.5 - - - -
148D ILE* 2.7 28.2 + - - +
151D CYS* 1.3 75.0 - - - +
153D PRO* 1.3 59.5 - - - +
154D ARG 3.0 5.8 - - - -
155D ALA* 2.8 32.0 + - + +
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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
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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