Contacts of the helix formed by residues 131 - 152 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F THR* 2.4 20.9 + - - +
130F ARG* 1.3 71.9 - - - +
132F ASP* 1.3 67.3 + - - +
133F LEU* 2.9 8.2 - - - +
134F PHE* 2.8 31.5 + - - +
135F LYS* 3.9 9.4 + - - +
349F LYS* 5.8 2.2 + - - -
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Residues in contact with ASP 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F MET* 3.8 5.6 - - + +
129F THR* 2.7 46.6 + - + +
131F ASP* 1.3 86.0 - - - +
133F LEU* 1.3 61.3 + - - +
135F LYS* 3.0 26.5 + - + +
136F ILE* 3.2 18.7 + - + +
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Residues in contact with LEU 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F VAL* 5.0 8.7 - - + +
123F PRO 4.7 7.2 - - - +
124F ARG* 4.5 21.8 - - - +
128F MET* 4.1 15.6 + - + +
129F THR 3.8 1.2 + - - -
130F ARG* 4.2 22.4 - - + -
131F ASP* 2.9 8.1 - - - +
132F ASP* 1.3 77.1 - - - +
134F PHE* 1.3 73.2 + - + +
136F ILE* 3.6 12.7 - - - +
137F ASN* 3.0 35.7 + - + +
162F ASN* 5.4 9.0 - - + +
163F PRO* 5.9 2.0 - - + -
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Residues in contact with PHE 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F ASP* 2.8 15.6 + - - +
133F LEU* 1.3 88.3 - - + +
135F LYS* 1.3 67.3 + - + +
137F ASN* 3.4 2.7 + - - +
138F ALA* 2.8 51.7 + - + +
163F PRO* 3.9 26.0 - - + -
166F SER* 3.8 28.9 - - - -
167F THR* 5.5 0.9 - - + -
170F ILE* 4.3 9.2 - - + -
349F LYS* 3.8 53.6 - - + +
353F PHE* 4.4 12.3 - + + -
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Residues in contact with LYS 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F ASP* 4.7 7.9 - - - +
132F ASP* 3.0 21.0 + - + +
134F PHE* 1.3 88.1 - - + +
136F ILE* 1.3 61.4 + - + +
138F ALA* 3.9 4.4 - - - +
139F GLY* 3.1 19.8 + - - -
353F PHE* 4.3 13.7 - - + -
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Residues in contact with ILE 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F VAL* 3.5 26.7 - - + -
128F MET* 3.4 39.9 - - + -
132F ASP* 3.2 16.2 + - + +
133F LEU* 3.6 11.4 - - - +
134F PHE 3.2 0.2 - - - -
135F LYS* 1.3 77.1 - - + +
137F ASN* 1.3 59.2 + - - +
139F GLY* 3.1 3.3 + - - -
140F ILE* 2.9 44.1 + - + +
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Residues in contact with ASN 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F ALA 4.2 4.6 + - - -
121F GLY* 3.3 22.9 - - - -
122F VAL* 3.0 37.2 + - - +
133F LEU* 3.0 23.1 + - + +
134F PHE* 4.0 3.4 - - - +
136F ILE* 1.3 73.5 - - - +
138F ALA* 1.3 60.6 + - - +
140F ILE* 3.1 6.9 + - - +
141F VAL* 2.8 37.2 + - + +
161F SER* 4.8 1.4 - - - -
162F ASN* 3.3 35.6 + - - +
163F PRO* 5.5 0.7 - - + -
167F THR* 5.6 0.2 - - - -
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Residues in contact with ALA 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F PHE* 2.8 32.4 + - + +
135F LYS 3.9 0.7 - - - +
137F ASN* 1.3 73.1 - - - +
139F GLY* 1.3 57.1 + - - +
141F VAL* 3.2 6.4 + - - +
142F LYS* 2.8 28.2 + - - +
167F THR* 5.4 3.5 - - - +
170F ILE* 3.7 23.4 - - + +
353F PHE* 3.5 35.0 - - + -
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Residues in contact with GLY 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F LYS 3.1 15.2 + - - -
136F ILE 3.5 3.8 - - - -
138F ALA* 1.3 75.0 - - - +
140F ILE* 1.3 61.8 + - - +
142F LYS* 3.3 6.8 + - - +
143F THR* 2.8 34.9 + - - +
353F PHE* 3.6 10.9 - - - -
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Residues in contact with ILE 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F ALA* 3.9 17.0 - - + +
121F GLY* 3.9 17.9 - - - +
122F VAL* 3.9 18.4 - - + -
136F ILE* 2.9 40.0 + - + +
137F ASN* 3.1 7.6 + - - +
139F GLY* 1.3 76.3 - - - +
141F VAL* 1.3 63.4 + - + +
143F THR* 4.1 5.0 + - - -
144F LEU* 3.2 41.1 + - + +
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Residues in contact with VAL 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F VAL* 5.8 0.7 - - - -
120F ALA 5.3 0.4 - - - +
137F ASN 2.8 23.0 + - - +
138F ALA* 3.5 6.1 - - - +
140F ILE* 1.3 77.9 - - + +
142F LYS* 1.3 65.2 + - - +
144F LEU* 3.2 6.8 + - + +
145F CYS* 2.9 38.8 + - - -
159F LEU* 4.1 13.2 - - + -
161F SER* 3.4 35.9 - - - +
167F THR* 3.9 32.1 - - + +
170F ILE* 4.5 8.7 - - + -
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Residues in contact with LYS 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F ALA 2.8 17.8 + - - +
139F GLY* 3.5 8.5 - - - +
141F VAL* 1.3 79.4 - - - +
143F THR* 1.3 65.0 + - + +
145F CYS* 3.3 2.9 + - - +
146F GLU* 2.9 47.8 + - - +
170F ILE* 4.7 1.3 - - - -
174F VAL* 4.1 13.8 - - + +
177F LYS* 4.7 14.1 - - - +
353F PHE* 4.2 13.0 + - + -
354F ILE* 3.6 35.4 + - + +
356F SER 6.0 0.4 + - - -
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Residues in contact with THR 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLN* 3.6 21.9 + - - -
106F LEU* 4.5 4.4 - - - +
139F GLY* 2.8 20.8 + - - +
140F ILE* 4.1 5.5 + - - +
142F LYS* 1.3 79.0 - - + +
144F LEU* 1.3 69.5 + - - +
146F GLU* 3.3 21.2 + - - +
147F GLY* 3.1 17.7 + - - -
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Residues in contact with LEU 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LEU* 3.6 29.6 - - + +
76F TYR* 4.3 11.4 - - + +
106F LEU* 3.9 26.0 - - + -
110F LEU* 4.3 2.9 - - - +
118F VAL* 4.0 17.5 - - + -
120F ALA* 3.5 31.4 - - + -
140F ILE* 3.2 27.3 + - + +
141F VAL* 3.2 6.8 + - - +
143F THR* 1.3 87.1 + - - +
145F CYS* 1.3 62.4 - - - +
147F GLY* 3.1 4.0 + - - -
148F ILE* 3.0 27.1 + - + +
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Residues in contact with CYS 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F VAL* 2.9 28.0 + - - +
142F LYS* 3.3 1.3 + - - +
144F LEU* 1.3 73.4 - - - +
146F GLU* 1.3 55.8 + - - +
148F ILE* 2.7 18.3 + - - +
149F ALA* 2.6 33.4 + - - +
157F VAL* 5.8 2.2 - - - -
159F LEU* 5.3 5.2 - - - -
171F ALA* 3.4 34.3 - - - -
174F VAL* 3.5 23.3 - - + -
175F PHE* 3.5 17.8 - - + -
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Residues in contact with GLU 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F LYS* 2.9 43.1 - - - +
143F THR* 3.3 21.5 - - - +
145F CYS* 1.3 76.5 - - - +
147F GLY* 1.3 63.2 + - - +
149F ALA* 3.6 5.7 - - - +
150F LYS* 2.9 26.8 + - - +
174F VAL* 3.7 16.8 - - + +
177F LYS* 4.4 11.1 + - - +
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Residues in contact with GLY 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F GLN* 6.0 0.2 - - - -
106F LEU* 4.2 10.5 - - - -
110F LEU* 3.3 13.0 - - - -
143F THR 3.1 12.2 + - - -
144F LEU 3.1 4.9 + - - -
145F CYS 3.0 0.8 - - - -
146F GLU* 1.3 79.0 - - - +
148F ILE* 1.3 56.4 + - - +
150F LYS* 4.5 6.3 - - - -
151F CYS* 2.8 39.6 + - - +
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Residues in contact with ILE 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F LEU* 4.6 2.7 - - + -
110F LEU* 3.9 13.9 - - + -
116F ILE* 3.5 44.2 - - + -
118F VAL* 4.6 10.8 - - + -
144F LEU* 3.1 17.5 - - + +
145F CYS* 2.7 22.6 + - - +
147F GLY* 1.3 73.9 - - - +
149F ALA* 1.3 61.1 + - - +
152F CYS* 2.7 47.5 + - - +
153F PRO* 4.9 2.0 - - + -
155F ALA 5.5 0.2 - - - +
157F VAL* 4.1 21.3 - - + -
175F PHE* 4.0 16.2 - - + -
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Residues in contact with ALA 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F CYS 2.6 17.4 + - - +
146F GLU* 3.6 9.0 - - - +
148F ILE* 1.3 71.7 - - - +
150F LYS* 1.3 62.2 + - - +
153F PRO* 3.2 26.4 - - - +
174F VAL 5.0 0.7 - - - +
175F PHE* 3.9 10.9 - - + -
178F ALA* 3.6 23.8 - - + -
180F THR* 3.5 29.5 - - + +
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Residues in contact with LYS 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F GLU* 3.3 35.4 + - - +
146F GLU 2.9 17.3 + - - +
147F GLY* 3.7 5.2 - - - +
149F ALA* 1.3 81.0 - - - +
151F CYS* 1.3 69.0 + - - +
153F PRO* 3.8 5.0 - - - +
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Residues in contact with CYS 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F LEU* 6.2 0.2 - - - -
107F GLU* 3.5 40.4 - - - -
110F LEU* 3.7 19.1 - - + -
111F THR* 4.0 23.5 + - - +
112F GLY 4.3 2.9 + - - -
147F GLY* 2.8 25.7 + - - +
150F LYS* 1.3 90.3 - - - +
152F CYS* 1.3 59.7 + - - +
153F PRO* 3.7 2.1 - - - +
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Residues in contact with CYS 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F LEU* 3.5 34.1 - - - +
112F GLY 4.9 1.3 - - - +
113F MET* 4.4 9.0 - - - +
116F ILE* 3.1 36.3 - - - -
148F ILE* 2.7 28.8 + - - +
151F CYS* 1.3 75.5 - - - +
153F PRO* 1.3 59.3 - - - +
154F ARG 2.9 12.3 + - - +
155F ALA* 3.0 22.2 + - + +
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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
------------------------------------------------------------
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