Contacts of the helix formed by residues 132 - 152 (chain B) 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 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ARG* 2.6 39.6 + - + +
131B ASP* 1.3 102.0 - - - +
133B LEU* 1.3 64.1 + - - +
134B PHE* 2.9 11.7 + - + -
135B LYS* 3.4 40.6 + - - +
136B ILE* 4.5 3.1 + - - +
349B LYS* 5.3 4.3 - - - +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 4.4 16.2 - - + +
123B PRO 5.7 4.5 - - - +
124B ARG* 6.4 0.9 - - - -
130B ARG* 3.5 32.6 - - + +
131B ASP 5.0 0.2 - - - +
132B ASP* 1.3 72.0 - - - +
134B PHE* 1.3 74.9 + - - +
136B ILE* 2.7 27.2 + - - +
137B ASN* 3.0 39.3 + - - +
162B ASN* 3.9 28.0 - - + +
163B PRO* 4.7 3.8 - - + -
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Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 3.9 16.6 - - - +
132B ASP* 2.9 9.4 - - + -
133B LEU* 1.3 85.0 - - + +
135B LYS* 1.3 74.8 + - + +
137B ASN* 4.8 2.9 - - - -
138B ALA* 2.7 33.7 + - + +
163B PRO* 4.3 20.6 - - + -
166B SER* 3.7 24.9 - - - -
167B THR* 6.0 0.9 - - + -
170B ILE* 4.3 8.1 - - + -
349B LYS* 3.4 51.6 - - + -
350B GLY* 4.3 1.1 - - - -
353B PHE* 3.7 32.1 - + + -
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ASP 4.9 2.2 - - - +
132B ASP* 3.4 30.6 + - - +
133B LEU 3.0 0.8 + - - -
134B PHE* 1.3 88.1 - - + +
136B ILE* 1.3 66.2 + - + +
138B ALA* 3.8 3.0 - - - +
139B GLY* 3.0 19.6 + - - -
353B PHE* 4.3 10.4 - - + -
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B VAL* 3.6 43.5 - - + -
125B LYS* 5.4 9.0 - - - -
131B ASP 6.0 0.7 - - - +
132B ASP 5.0 2.2 - - - +
133B LEU* 2.7 20.7 + - - +
135B LYS* 1.3 72.0 - - + +
137B ASN* 1.3 68.2 + - - +
139B GLY* 2.8 12.8 + - - -
140B ILE* 2.8 23.5 + - + +
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ALA 4.5 1.6 + - - -
121B GLY* 3.7 17.2 - - - -
122B VAL* 3.0 41.6 + - - +
133B LEU* 3.0 24.6 + - - +
134B PHE* 4.0 3.1 - - - +
136B ILE* 1.3 76.1 - - - +
138B ALA* 1.3 53.0 + - - +
140B ILE* 3.0 10.0 + - - +
141B VAL* 2.7 44.2 + - + +
161B SER* 4.6 0.8 - - - -
162B ASN* 2.7 41.2 + - - +
163B PRO* 5.1 1.1 - - + -
167B THR* 5.1 0.9 - - + -
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B PHE* 2.7 31.6 + - + +
135B LYS 3.8 0.2 - - - +
137B ASN* 1.3 73.1 - - - +
139B GLY* 1.3 62.9 + - - +
141B VAL* 3.3 6.2 + - - +
142B LYS* 2.9 24.4 + - - +
167B THR* 5.2 2.6 - - + +
170B ILE* 3.6 27.2 - - + +
353B PHE* 3.5 30.1 - - + -
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LYS 3.0 11.4 + - - -
136B ILE 2.8 8.8 + - - -
138B ALA* 1.3 75.4 - - - +
140B ILE* 1.3 62.4 + - - +
142B LYS* 3.1 14.4 + - - +
143B THR* 3.1 21.6 + - - +
353B PHE* 3.8 10.9 - - - -
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ALA* 4.1 15.0 - - + +
121B GLY* 4.0 23.8 - - - +
122B VAL* 4.3 7.6 - - + +
136B ILE* 2.8 34.3 + - + +
137B ASN* 3.3 7.6 - - - +
139B GLY* 1.3 75.3 - - - +
141B VAL* 1.3 64.6 + - + +
143B THR* 3.0 10.5 + - - +
144B LEU* 3.0 44.0 + - + +
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 5.7 0.7 - - + -
137B ASN 2.7 24.1 + - - +
138B ALA* 3.6 6.5 - - - +
140B ILE* 1.3 76.3 - - + +
142B LYS* 1.3 57.6 + - - +
144B LEU* 3.4 6.0 + - - +
145B CYS* 2.8 53.5 + - - -
159B LEU* 4.3 11.4 - - + -
161B SER* 3.6 32.5 - - - +
167B THR* 3.9 35.7 - - + +
170B ILE* 4.3 9.2 - - + -
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B ALA 2.9 13.1 + - - +
139B GLY* 3.1 9.6 + - - +
141B VAL* 1.3 77.1 - - - +
143B THR* 1.3 60.7 + - + +
145B CYS* 3.2 2.6 + - - +
146B GLU* 2.8 57.7 + - - +
170B ILE* 4.7 1.3 - - + +
174B VAL* 3.9 25.5 - - + +
177B LYS* 6.0 1.8 - - - +
353B PHE* 4.5 11.3 + - + -
354B ILE* 3.8 26.4 + - + +
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Residues in contact with THR 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLN* 4.6 17.9 + - - +
106B LEU* 4.4 5.3 - - - +
139B GLY 3.1 13.0 + - - +
140B ILE* 3.0 12.5 + - - +
142B LYS* 1.3 77.9 - - + +
144B LEU* 1.3 72.6 + - - +
146B GLU* 3.1 19.8 + - - +
147B GLY* 3.0 19.2 + - - -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 3.9 24.0 - - + +
76B TYR* 4.2 19.7 - - + +
106B LEU* 4.0 22.0 - - + -
110B LEU* 4.5 1.7 - - - +
118B VAL* 3.8 18.2 - - + -
120B ALA* 3.6 31.4 - - + -
140B ILE* 3.0 25.4 + - + +
141B VAL* 3.7 4.9 - - - +
143B THR* 1.3 84.5 + - - +
145B CYS* 1.3 60.7 + - - +
147B GLY* 3.1 4.2 + - - -
148B ILE* 2.8 32.9 + - + +
161B SER* 5.6 0.2 - - - +
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Residues in contact with CYS 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL* 6.5 0.7 - - - -
141B VAL* 2.8 38.5 + - - +
142B LYS 3.7 3.4 - - - +
144B LEU* 1.3 71.0 - - - +
146B GLU* 1.3 61.5 + - - +
148B ILE* 3.1 10.2 + - - -
149B ALA* 2.8 27.5 + - - +
157B VAL* 6.0 2.2 - - - -
159B LEU* 5.4 5.2 - - - -
171B ALA* 3.4 30.7 - - - -
174B VAL* 3.7 15.3 - - + -
175B PHE* 3.1 29.5 - - + -
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B LYS* 2.8 55.0 + - + +
143B THR* 3.1 26.4 - - - +
145B CYS* 1.3 76.1 - - - +
147B GLY* 1.3 67.1 + - - +
149B ALA* 3.1 5.3 + - - +
150B LYS* 3.0 24.5 + - - +
174B VAL* 3.7 17.3 - - + -
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Residues in contact with GLY 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLN* 6.1 0.4 - - - -
106B LEU* 4.4 8.1 - - - -
107B GLU* 6.0 1.3 - - - -
110B LEU* 3.4 16.4 - - - -
143B THR 3.0 13.4 + - - -
144B LEU 3.1 4.0 + - - -
146B GLU* 1.3 76.8 - - - +
148B ILE* 1.3 52.1 + - - +
150B LYS* 3.0 6.9 + - - -
151B CYS* 2.7 42.4 + - - +
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Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 3.8 20.2 - - + -
110B LEU* 4.0 15.9 - - + -
116B ILE* 3.5 37.2 - - + -
118B VAL* 4.4 8.3 - - + -
144B LEU* 2.8 23.6 + - + +
145B CYS* 3.1 17.2 + - - +
147B GLY* 1.3 71.8 - - - +
149B ALA* 1.3 57.3 + - - +
152B CYS* 2.9 47.1 + - - +
153B PRO* 5.4 0.9 - - + -
155B ALA 5.4 0.2 - - - +
157B VAL* 4.1 23.3 - - + -
175B PHE* 4.3 10.1 - - + -
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Residues in contact with ALA 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B CYS 2.8 20.2 + - - +
146B GLU* 3.5 7.4 - - - +
148B ILE* 1.3 74.1 - - - +
150B LYS* 1.3 59.2 + - - +
153B PRO* 3.5 13.1 - - - +
174B VAL 5.0 0.7 - - - +
175B PHE* 3.6 14.1 - - + -
178B ALA* 3.7 21.3 - - + -
180B THR* 3.4 39.8 - - - +
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Residues in contact with LYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU* 3.0 31.0 + - - +
146B GLU 3.0 16.1 + - - +
147B GLY* 3.6 5.4 - - - +
149B ALA* 1.3 80.9 - - - +
151B CYS* 1.3 65.7 + - - +
153B PRO* 4.1 4.7 - - - +
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Residues in contact with CYS 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU* 3.6 46.4 - - - -
110B LEU* 3.6 21.1 - - + -
111B THR* 4.0 25.4 + - - +
112B GLY 4.5 1.7 + - - -
147B GLY* 2.7 25.1 + - - +
150B LYS* 1.3 82.2 - - - +
152B CYS* 1.3 60.4 + - - +
153B PRO* 3.5 5.2 - - - +
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Residues in contact with CYS 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 3.6 32.1 - - - +
112B GLY 4.8 1.8 - - - +
113B MET* 4.1 9.9 - - - +
116B ILE* 3.0 37.2 - - - -
148B ILE* 2.9 22.6 + - - +
151B CYS* 1.3 80.7 - - - +
153B PRO* 1.3 57.9 - - - +
154B ARG 3.1 2.9 - - - -
155B ALA* 2.8 35.6 + - + +
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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