Contacts of the helix formed by residues 133 - 152 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C VAL* 3.3 40.2 - - + +
123C PRO* 3.7 14.8 - - + +
124C ARG* 3.7 35.7 - - + +
128C MET* 4.1 11.0 - - + -
129C THR 4.7 0.2 - - - +
130C ARG* 3.2 18.6 + - - +
131C ASP 3.0 0.8 - - - -
132C ASP* 1.3 76.7 - - - +
134C PHE* 1.3 63.6 + - - +
135C LYS 3.5 1.3 + - - -
136C ILE* 3.7 4.3 + - - +
137C ASN* 3.0 35.4 + - - +
162C ASN* 4.1 23.8 - - + +
163C PRO* 4.4 0.9 - - - -
1313C CIT 5.4 0.4 - - - +
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Residues in contact with PHE 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C ASP* 3.0 19.5 + - - +
132C ASP 3.1 1.4 - - - -
133C LEU* 1.3 76.8 - - - +
135C LYS* 1.3 64.3 + - + +
138C ALA* 2.7 45.2 + - + +
163C PRO* 4.0 17.2 - - + +
166C SER* 3.7 31.2 - - - -
167C THR* 5.7 0.4 - - + -
170C ILE* 3.9 12.8 - - + -
349C LYS* 3.4 45.1 - - + +
350C GLY* 4.3 0.7 - - - -
353C PHE* 3.8 41.5 - + + -
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Residues in contact with LYS 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C ASP 4.7 3.5 + - - +
133C LEU 3.6 0.4 - - - -
134C PHE* 1.3 86.8 - - + +
136C ILE* 1.3 65.7 + - + +
138C ALA* 4.3 2.2 - - - +
139C GLY* 3.7 12.0 + - - -
353C PHE* 5.2 7.4 - - + -
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C VAL* 4.1 25.4 - - + -
133C LEU 3.7 5.1 + - - +
134C PHE 3.3 0.2 - - - -
135C LYS* 1.3 77.5 - - + +
137C ASN* 1.3 73.8 + - - +
139C GLY* 3.4 3.5 + - - -
140C ILE* 3.3 36.7 + - + +
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Residues in contact with ASN 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C GLY* 3.5 15.0 - - - -
122C VAL* 3.0 46.9 + - - +
133C LEU* 3.0 23.7 + - - +
134C PHE 4.3 0.2 - - - +
136C ILE* 1.3 76.7 - - - +
138C ALA* 1.3 66.0 - - - +
140C ILE* 3.2 7.5 + - - +
141C VAL* 2.9 30.7 + - + +
161C SER* 4.8 0.8 - - - -
162C ASN* 2.7 39.4 + - - +
163C PRO* 4.9 1.1 - - + -
167C THR* 5.1 2.0 - - + -
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C PHE* 2.7 36.3 + - + +
135C LYS 4.3 1.1 - - - +
137C ASN* 1.3 73.1 - - - +
139C GLY* 1.3 57.0 + - - +
141C VAL* 3.2 5.1 + - - +
142C LYS* 2.9 30.0 + - - +
167C THR* 5.0 3.3 - - - +
170C ILE* 3.7 23.4 - - + +
353C PHE* 3.7 31.4 - - + -
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Residues in contact with GLY 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LYS 3.7 7.1 + - - -
136C ILE 3.4 7.6 + - - -
137C ASN 3.2 0.6 - - - -
138C ALA* 1.3 79.6 - - - +
140C ILE* 1.3 58.6 + - - +
142C LYS* 3.2 7.7 + - - +
143C THR* 2.9 31.3 + - - +
353C PHE* 3.9 12.0 - - - -
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Residues in contact with ILE 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C ALA* 3.9 15.7 - - + +
121C GLY* 4.3 13.7 - - - +
122C VAL* 4.8 4.5 - - + +
136C ILE* 3.3 31.5 + - + +
137C ASN* 3.2 17.5 + - - +
139C GLY* 1.3 74.5 - - - +
141C VAL* 1.3 66.1 + - + +
143C THR* 3.5 7.1 + - - +
144C LEU* 3.1 43.0 + - + +
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Residues in contact with VAL 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C VAL* 5.6 0.7 - - + -
120C ALA 5.3 0.4 - - - +
137C ASN 2.9 20.5 + - - +
138C ALA* 3.6 5.2 - - - +
140C ILE* 1.3 77.8 - - + +
142C LYS* 1.3 58.7 + - - +
144C LEU* 3.3 7.0 + - + +
145C CYS* 2.8 47.1 + - - +
159C LEU* 4.0 12.3 - - + -
161C SER* 3.6 33.2 - - - +
167C THR* 3.9 36.1 - - + +
170C ILE* 4.4 9.0 - - + -
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Residues in contact with LYS 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C ALA 2.9 13.8 + - - +
139C GLY* 3.4 10.8 - - - +
141C VAL* 1.3 78.8 - - - +
143C THR* 1.3 66.0 + - + +
145C CYS* 3.2 2.1 + - - +
146C GLU* 3.0 49.9 + - - +
170C ILE* 4.6 2.4 - - + +
174C VAL* 4.1 11.6 - - + +
353C PHE* 4.2 19.5 + - + -
354C ILE* 3.7 30.4 + - + +
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Residues in contact with THR 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C GLN* 3.2 24.8 + - - +
106C LEU* 4.3 3.8 - - - +
139C GLY 2.9 21.1 - - - +
140C ILE* 3.9 8.2 + - - +
142C LYS* 1.3 75.8 - - + +
144C LEU* 1.3 69.4 + - - +
146C GLU* 3.1 19.0 + - - +
147C GLY* 3.1 17.8 + - - -
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 4.0 27.3 - - + +
76C TYR* 4.1 24.0 - - + +
106C LEU* 4.3 12.3 - - + -
110C LEU* 4.6 2.4 - - - +
118C VAL* 3.7 18.2 - - + -
120C ALA* 3.5 32.1 - - + -
140C ILE* 3.1 27.3 + - + +
141C VAL* 3.7 5.6 - - - +
143C THR* 1.3 82.6 + - - +
145C CYS* 1.3 65.8 + - - +
147C GLY* 3.0 4.0 + - - -
148C ILE* 3.0 27.4 + - + +
161C SER* 5.6 0.2 - - - +
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Residues in contact with CYS 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C VAL* 6.4 1.1 - - - -
141C VAL* 2.8 32.4 + - - +
142C LYS 3.8 3.4 - - - +
144C LEU* 1.3 72.2 - - - +
146C GLU* 1.3 61.5 + - - +
148C ILE* 3.1 11.2 + - - -
149C ALA* 2.8 31.2 + - - +
157C VAL* 5.7 2.9 - - - -
159C LEU* 5.0 4.3 - - - -
171C ALA* 3.5 32.8 - - - -
174C VAL* 3.8 17.0 - - + -
175C PHE* 3.4 23.5 - - + -
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Residues in contact with GLU 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C LYS* 3.0 50.6 + - + +
143C THR* 3.1 20.0 + - - +
145C CYS* 1.3 76.4 - - - +
147C GLY* 1.3 62.2 + - - +
149C ALA* 3.5 6.0 + - - +
150C LYS* 3.2 22.3 + - - +
174C VAL* 3.8 18.0 - - + +
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Residues in contact with GLY 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C GLN* 5.7 0.7 - - - -
106C LEU* 4.2 9.9 - - - -
110C LEU* 3.4 14.1 - - - -
143C THR 3.1 9.0 + - - -
144C LEU 3.0 8.2 + - - -
146C GLU* 1.3 76.2 - - - +
148C ILE* 1.3 58.9 + - - +
150C LYS* 3.2 5.1 + - - -
151C CYS* 2.8 39.4 + - - +
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Residues in contact with ILE 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C LEU* 4.1 7.9 - - + -
110C LEU* 4.0 21.8 - - + -
116C ILE* 3.8 23.6 - - + -
118C VAL* 4.4 4.9 - - + -
144C LEU* 3.0 20.0 + - + +
145C CYS* 3.1 20.2 + - - +
147C GLY* 1.3 77.9 - - - +
149C ALA* 1.3 63.2 + - - +
152C CYS* 2.9 52.9 + - - +
153C PRO* 5.1 2.0 - - + -
155C ALA 5.6 0.2 - - - +
157C VAL* 4.1 28.5 - - + -
175C PHE* 4.1 15.5 - - + -
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Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C CYS 2.8 16.8 + - - +
146C GLU* 3.6 9.0 - - - +
148C ILE* 1.3 77.7 - - - +
150C LYS* 1.3 58.3 + - - +
153C PRO* 3.4 22.2 - - - +
174C VAL* 5.0 0.9 - - + -
175C PHE* 3.9 11.4 - - + -
178C ALA* 3.7 29.4 - - + -
180C THR* 3.6 23.4 - - - +
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Residues in contact with LYS 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C GLU* 3.2 29.8 + - + +
146C GLU 3.2 15.7 + - - +
147C GLY* 3.7 5.2 - - - +
148C ILE 3.1 0.4 - - - -
149C ALA* 1.3 80.5 - - - +
151C CYS* 1.3 69.7 + - - +
153C PRO* 4.4 4.1 - - - +
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Residues in contact with CYS 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 5.8 0.2 - - - -
107C GLU* 3.6 38.4 - - - -
110C LEU* 3.5 21.8 - - + -
111C THR* 3.9 26.6 + - - +
112C GLY 4.3 2.1 + - - -
147C GLY* 2.8 28.0 + - - +
150C LYS* 1.3 91.2 - - - +
152C CYS* 1.3 59.0 + - - +
153C PRO* 3.6 4.6 - - - +
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Residues in contact with CYS 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C LEU* 3.5 38.6 - - - +
112C GLY 4.8 1.3 - - - +
113C MET 4.1 8.3 - - - +
116C ILE* 3.7 30.1 - - - -
148C ILE* 2.9 26.4 + - - +
151C CYS* 1.3 78.1 - - - +
153C PRO* 1.3 60.6 - - - +
154C ARG 3.1 11.1 + - - +
155C ALA* 3.3 19.3 + - + +
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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