Contacts of the helix formed by residues 139 - 157 (chain B) in PDB entry 3KTC
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 SER 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256A TYR* 6.5 0.2 - - - -
305A GLN* 6.5 0.2 - - - -
308A GLN* 3.6 20.0 + - - +
344A EDO 4.5 6.9 + - - -
138B VAL* 1.3 70.7 - - - +
140B HIS* 1.3 58.5 + - - +
141B LYS* 3.6 6.1 + - - +
142B ASN* 3.0 42.2 + - - -
143B LEU* 2.8 32.1 + - - +
344B EDO 2.9 11.9 + - - -
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Residues in contact with HIS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A SER* 3.6 20.4 + - - -
213A ALA* 4.0 7.2 - - + -
214A ASP* 3.6 45.4 + - + +
217A GLN* 4.4 10.1 - - + -
253A GLU* 2.9 28.4 + - - -
257A VAL* 4.5 9.6 - - + -
132B TRP* 3.9 18.6 - + - -
134B TYR 6.1 0.4 - - - -
135B PRO* 6.4 0.9 - - + -
136B PHE 5.8 0.4 - - - -
138B VAL* 3.4 28.4 + - + +
139B SER* 1.3 71.5 - - - +
141B LYS* 1.3 64.0 + - - +
143B LEU* 4.0 3.8 - - - +
144B TRP* 3.2 26.0 + - - +
341B EDO 4.1 5.3 + - - -
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Residues in contact with LYS 141 (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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217A GLN* 3.6 29.3 + - - +
221A ASP* 2.9 36.1 + - - +
261A ASN* 5.5 0.4 - - - -
344A EDO 3.7 33.9 - - - +
139B SER* 3.2 6.7 + - - +
140B HIS* 1.3 80.3 - - - +
142B ASN* 1.3 70.8 + - - +
144B TRP* 4.0 2.4 - - - +
145B LYS* 3.1 29.4 + - + +
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Residues in contact with ASN 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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309A GLU* 4.6 8.9 + - - -
344A EDO 5.0 2.1 + - - -
139B SER* 3.0 26.0 + - - +
141B LYS* 1.3 86.4 - - - +
143B LEU* 1.3 65.0 + - - +
145B LYS* 3.7 10.7 - - - +
146B LEU* 3.0 28.1 + - + +
344B EDO 3.7 20.3 + - - +
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Residues in contact with LEU 143 (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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311A GLN* 4.3 5.4 - - - +
94B THR* 3.6 28.8 - - - +
131B GLY* 3.8 29.2 - - - +
132B TRP* 4.4 7.0 - - + -
138B VAL* 4.0 20.9 - - + -
139B SER 2.8 17.9 + - - +
140B HIS* 4.0 4.5 - - - +
142B ASN* 1.3 77.8 - - - +
144B TRP* 1.3 57.5 + - - +
146B LEU* 3.3 6.4 + - + +
147B ALA* 3.0 26.4 + - - +
177B THR* 3.9 21.8 - - + -
341B EDO 5.0 5.2 - - - +
344B EDO 3.4 23.4 - - - -
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Residues in contact with TRP 144 (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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214A ASP* 5.1 0.2 - - - +
218A LEU* 3.8 20.2 - - + +
221A ASP* 6.1 0.9 - - - -
140B HIS 3.2 16.2 + - - +
141B LYS* 4.1 2.2 - - - +
143B LEU* 1.3 77.2 - - - +
145B LYS* 1.3 61.3 + - - +
147B ALA* 3.3 13.8 + - + +
148B VAL* 2.9 48.5 + - + +
177B THR* 3.7 21.1 - - + -
178B TRP* 3.7 43.1 - + - -
183B ARG* 3.4 56.8 - - + +
186B LEU* 5.4 1.9 - - + +
187B GLY* 3.8 15.9 - - - -
190B ASP* 4.4 11.2 + - - -
341B EDO 4.7 0.9 - - - -
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Residues in contact with LYS 145 (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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141B LYS* 3.1 25.7 + - + +
142B ASN* 3.7 12.3 - - - +
143B LEU 3.2 0.2 - - - -
144B TRP* 1.3 77.8 - - - +
146B LEU* 1.3 56.8 + - + +
148B VAL* 4.8 3.6 - - - -
149B ASP* 2.8 71.1 + - - +
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Residues in contact with LEU 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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311A GLN* 4.9 1.3 - - - +
93B PHE* 3.8 14.1 - - - +
94B THR* 4.1 23.8 - - + +
95B ASN 4.6 0.2 - - - +
96B PRO* 6.0 0.2 - - + -
101B ARG* 3.7 44.6 - - - +
142B ASN 3.0 18.4 + - - +
143B LEU* 3.3 7.4 + - - +
145B LYS* 1.3 76.1 - - + +
147B ALA* 1.3 58.6 + - - +
149B ASP* 4.8 2.9 - - + -
150B GLY* 2.9 29.2 + - - +
344B EDO 4.1 21.3 - - - +
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Residues in contact with ALA 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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93B PHE* 4.4 10.3 - - + -
94B THR* 4.0 15.0 - - + +
130B ASP* 5.7 0.4 - - - +
143B LEU 3.0 12.7 + - - +
144B TRP* 3.3 27.1 + - + +
146B LEU* 1.3 77.5 - - - +
148B VAL* 1.3 61.5 + - - +
151B MSE 3.2 23.9 + - - +
177B THR* 4.2 8.1 - - - +
178B TRP* 4.0 21.2 + - - +
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Residues in contact with VAL 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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144B TRP* 2.9 61.2 + - + +
145B LYS* 4.1 3.6 - - - +
147B ALA* 1.3 71.4 - - - +
149B ASP* 1.3 69.2 + - - +
151B MSE 3.2 3.3 + - - +
152B ARG* 3.0 45.2 + - - +
178B TRP* 4.5 7.2 - - + -
187B GLY* 4.4 9.9 - - - -
190B ASP* 4.0 16.2 - - + +
191B ILE* 3.8 14.4 - - + +
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Residues in contact with ASP 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 LYS* 2.8 62.0 + - - +
146B LEU* 4.4 2.9 - - + +
148B VAL* 1.3 75.6 - - - +
150B GLY* 1.3 58.4 + - - +
152B ARG* 2.9 29.9 + - - +
153B ASP* 2.9 37.1 + - - +
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Residues in contact with GLY 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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93B PHE* 3.5 23.2 - - - -
105B PHE* 5.3 1.4 - - - -
146B LEU 2.9 18.4 + - - -
149B ASP* 1.3 76.9 - - - +
151B MSE 1.3 63.4 + - - +
153B ASP* 3.3 11.2 + - - +
154B LEU* 3.1 19.4 + - - +
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Residues in contact with MSE 151 (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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93B PHE* 3.6 24.7 - - + -
125B VAL* 3.6 35.4 - - + -
147B ALA 3.2 20.3 + - - +
148B VAL 3.2 3.6 + - - +
150B GLY* 1.3 77.0 - - - +
152B ARG* 1.3 60.9 + - - +
154B LEU* 3.3 9.4 + - - +
155B ALA* 3.0 24.5 + - - +
163B PHE* 4.9 7.9 - - - -
165B ILE* 3.6 34.1 - - + -
178B TRP* 3.9 21.1 - - + +
191B ILE* 3.5 24.9 - - + -
196B VAL* 4.4 7.0 - - + -
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Residues in contact with ARG 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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148B VAL* 3.0 23.2 + - - +
149B ASP* 2.9 35.6 + - - +
151B MSE 1.3 77.2 - - - +
153B ASP* 1.3 60.0 + - - +
156B GLY* 2.8 30.0 + - - -
190B ASP* 3.0 28.7 + - - +
191B ILE* 3.0 36.8 + - + +
193B LEU* 3.8 13.9 - - + +
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Residues in contact with ASP 153 (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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105B PHE* 3.8 15.1 - - + -
149B ASP* 2.9 20.7 + - - +
150B GLY* 3.6 11.6 - - - +
152B ARG* 1.3 79.4 + - - +
154B LEU* 1.3 63.0 + - - +
156B GLY* 4.0 0.6 - - - -
157B ALA* 3.2 24.9 + - - +
335B MG 4.1 18.0 - - - -
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Residues in contact with LEU 154 (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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93B PHE* 4.3 10.5 - - + -
105B PHE* 3.8 19.2 - - + -
108B MSE 3.7 49.1 - - + -
109B HIS* 3.8 14.6 - - - +
123B VAL* 5.4 0.2 - - + -
125B VAL* 4.4 7.0 - - + -
150B GLY 3.1 14.0 + - - +
151B MSE 3.7 11.0 - - - +
152B ARG 3.3 0.2 - - - -
153B ASP* 1.3 79.9 - - - +
155B ALA* 1.3 62.0 + - - +
157B ALA* 3.3 2.4 + - - +
158B ASN* 3.0 33.3 + - - +
163B PHE* 3.5 33.7 - - + -
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Residues in contact with ALA 155 (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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151B MSE 3.0 14.5 + - + +
154B LEU* 1.3 76.9 - - - +
156B GLY* 1.3 61.8 + - - +
158B ASN 3.1 12.0 + - - -
159B PRO* 3.5 1.6 - - - +
163B PHE* 3.8 18.2 - - + -
193B LEU* 3.8 7.9 - - + -
195B ASN* 3.0 30.6 + - - +
196B VAL* 3.4 33.9 - - + -
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Residues in contact with GLY 156 (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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152B ARG* 2.8 22.8 + - - -
153B ASP* 4.0 1.1 - - - -
155B ALA* 1.3 74.5 - - - +
157B ALA* 1.3 57.3 + - - +
158B ASN 3.2 1.2 + - - -
159B PRO* 3.6 13.5 - - - +
193B LEU* 3.5 16.4 - - - +
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Residues in contact with ALA 157 (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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105B PHE* 4.1 13.7 - - + -
109B HIS* 4.0 16.7 - - + -
116B ARG* 5.0 0.3 + - - -
153B ASP 3.2 18.6 + - - +
154B LEU 3.7 5.8 - - - +
155B ALA 3.2 0.8 - - - -
156B GLY* 1.3 74.8 - - - +
158B ASN* 1.3 71.3 + - - +
159B PRO* 3.5 6.0 - - - +
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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