Contacts of the helix formed by residues 139 - 157 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A VAL* 1.3 70.7 - - - +
140A HIS* 1.3 57.3 + - - +
141A LYS* 3.7 5.9 + - - +
142A ASN* 3.0 42.9 + - - -
143A LEU* 2.9 32.1 + - - +
256B TYR* 6.5 0.2 - - - -
260B ILE* 6.0 0.9 - - - +
305B GLN* 6.3 0.7 - - - -
308B GLN* 3.6 28.4 + - - +
339B EDO 4.4 7.3 + - - -
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Residues in contact with HIS 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TRP* 3.9 18.6 - + - -
134A TYR 6.1 0.4 - - - -
135A PRO* 6.4 0.9 - - + -
136A PHE 5.8 0.4 - - - -
138A VAL* 3.4 30.1 + - + +
139A SER* 1.3 70.6 + - - +
141A LYS* 1.3 64.0 + - - +
143A LEU* 4.0 3.7 - - - +
144A TRP* 3.1 26.5 + - - +
339A EDO 4.4 4.4 + - - -
211B SER* 3.6 20.2 + - - -
213B ALA* 3.8 17.9 - - + -
214B ASP* 3.6 36.1 + - + +
217B GLN* 4.4 11.0 - - + +
253B GLU* 2.9 28.0 + - - -
257B VAL* 4.6 9.2 - - + +
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 3.2 5.8 + - - +
140A HIS* 1.3 80.3 - - - +
142A ASN* 1.3 65.1 + - - +
144A TRP* 3.9 2.8 - - - +
145A LYS* 3.0 34.7 + - + +
217B GLN* 3.7 29.8 + - - +
221B ASP* 2.9 35.5 + - - +
261B ASN* 5.1 0.4 - - - +
339B EDO 3.7 31.2 - - - +
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Residues in contact with ASN 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A SER* 3.0 28.8 + - - +
141A LYS* 1.3 85.6 - - - +
143A LEU* 1.3 65.0 + - - +
145A LYS* 3.3 11.4 + - - +
146A LEU* 3.0 30.8 + - + +
309B GLU* 4.6 14.2 + - - +
339B EDO 4.9 4.5 + - - -
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Residues in contact with LEU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A THR* 3.6 28.8 - - - +
131A GLY* 3.8 29.8 - - - +
132A TRP* 4.4 6.3 - - + -
138A VAL* 4.0 24.9 - - + -
139A SER 2.9 18.4 + - - +
140A HIS* 4.0 5.4 - - - +
142A ASN* 1.3 78.2 - - - +
144A TRP* 1.3 61.4 + - - +
146A LEU* 3.3 9.3 + - + +
147A ALA* 3.0 21.3 + - - +
177A THR* 3.9 21.5 - - + -
339A EDO 5.4 4.3 - - - +
311B GLN* 4.2 18.6 - - - +
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Residues in contact with TRP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A HIS 3.1 16.2 + - - +
141A LYS* 4.1 2.7 - - - +
143A LEU* 1.3 79.7 - - - +
145A LYS* 1.3 58.8 + - - +
147A ALA* 3.3 14.0 + - + +
148A VAL* 2.9 46.6 + - + +
177A THR* 3.7 20.4 - - + -
178A TRP* 3.7 44.0 - + - -
183A ARG* 3.5 56.3 - - + +
186A LEU* 5.4 2.1 - - + +
187A GLY* 3.7 16.4 - - - -
190A ASP* 4.5 10.6 + - - -
339A EDO 4.6 0.2 - - - -
214B ASP* 5.0 0.4 - - - +
218B LEU* 3.9 20.1 - - + +
221B ASP* 5.9 2.9 - - - -
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 3.0 23.8 + - + +
142A ASN* 3.6 12.3 - - - +
144A TRP* 1.3 78.8 - - - +
146A LEU* 1.3 57.5 + - + +
148A VAL* 4.8 3.8 - - - -
149A ASP* 2.8 71.3 + - - +
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.7 15.8 - - - +
94A THR* 4.1 24.2 - - + +
95A ASN 4.5 0.4 - - - +
101A ARG* 3.8 44.6 - - - +
142A ASN* 3.0 19.8 + - + +
143A LEU* 3.6 11.2 - - - +
145A LYS* 1.3 76.5 - - + +
147A ALA* 1.3 63.7 + - - +
149A ASP* 4.8 3.4 - - + -
150A GLY* 2.9 23.0 + - - -
311B GLN* 4.8 7.0 - - - +
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 4.4 9.8 - - + -
94A THR* 4.0 15.0 - - + +
130A ASP* 5.8 0.2 - - - +
143A LEU 3.0 13.4 + - - +
144A TRP* 3.5 26.5 - - + +
145A LYS 3.2 0.2 - - - -
146A LEU* 1.3 78.2 - - - +
148A VAL* 1.3 61.1 + - - +
150A GLY* 4.2 0.2 - - - -
151A MSE 3.1 24.8 + - - +
177A THR* 4.2 7.6 - - - +
178A TRP* 4.0 21.3 + - - +
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TRP* 2.9 57.8 + - + +
145A LYS* 4.1 3.4 - - - +
147A ALA* 1.3 71.8 - - - +
149A ASP* 1.3 65.6 + - - +
151A MSE 3.3 3.3 + - - +
152A ARG* 3.0 49.0 + - - +
178A TRP* 4.5 4.7 - - + -
187A GLY* 4.4 8.1 - - - -
190A ASP* 4.0 17.7 - - + +
191A ILE* 3.7 18.2 - - + +
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Residues in contact with ASP 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LYS* 2.8 63.6 + - - +
146A LEU* 4.3 3.8 - - + +
148A VAL* 1.3 74.4 - - - +
150A GLY* 1.3 57.1 + - - +
152A ARG* 3.0 30.4 + - - +
153A ASP* 2.8 39.5 + - - +
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Residues in contact with GLY 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.5 24.9 - - - -
105A PHE* 5.4 1.2 - - - -
146A LEU 2.9 17.6 + - - -
149A ASP* 1.3 77.0 - - - +
151A MSE 1.3 61.3 + - - +
153A ASP* 3.4 10.8 + - - +
154A LEU* 3.1 18.9 + - - +
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Residues in contact with MSE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.7 24.5 - - + -
125A VAL* 3.6 31.4 - - + -
127A PRO* 5.2 0.4 - - + -
147A ALA 3.1 19.8 + - - +
148A VAL 3.6 4.0 - - - +
149A ASP 3.3 0.2 - - - -
150A GLY* 1.3 72.3 - - - +
152A ARG* 1.3 65.9 + - - +
154A LEU* 3.3 7.9 + - - +
155A ALA* 2.9 24.7 + - - +
163A PHE* 5.1 5.2 - - - -
165A ILE* 3.6 38.8 - - + -
178A TRP* 3.8 21.3 - - + +
191A ILE* 3.5 24.7 - - + -
196A VAL* 4.3 9.6 - - + -
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Residues in contact with ARG 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A VAL* 3.0 24.4 + - - +
149A ASP* 3.0 37.2 + - - +
151A MSE 1.3 76.8 - - - +
153A ASP* 1.3 60.6 + - - +
156A GLY* 2.8 29.8 + - - -
190A ASP* 3.0 27.5 + - - +
191A ILE* 3.0 38.9 + - + +
193A LEU* 4.0 10.3 - - + -
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Residues in contact with ASP 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 3.8 14.2 - - + -
149A ASP* 2.8 27.1 + - - +
150A GLY* 3.6 9.0 - - - +
151A MSE 3.3 0.2 - - - -
152A ARG* 1.3 81.3 + - - +
154A LEU* 1.3 61.2 + - - +
156A GLY* 4.1 0.7 - - - -
157A ALA* 3.2 23.9 + - - +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 4.2 10.5 - - + -
105A PHE* 3.9 19.2 - - + -
108A MSE 3.7 48.7 - - + -
109A HIS* 3.8 14.6 - - - +
123A VAL* 5.5 0.2 - - + -
125A VAL* 4.4 7.0 - - + -
150A GLY 3.1 11.7 + - - +
151A MSE 3.6 10.5 - - - +
152A ARG 3.3 0.2 - - - -
153A ASP* 1.3 80.1 - - - +
155A ALA* 1.3 61.2 + - - +
157A ALA* 3.2 4.5 + - - +
158A ASN* 3.0 35.5 + - - +
163A PHE* 3.5 35.0 - - + -
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A MSE 2.9 15.3 + - + +
154A LEU* 1.3 78.0 - - - +
156A GLY* 1.3 62.2 + - - +
158A ASN 3.1 11.4 + - - -
159A PRO* 3.5 1.6 - - - +
163A PHE* 3.8 17.7 - - + -
193A LEU* 3.6 11.7 - - + -
195A ASN* 3.0 27.1 + - - +
196A VAL* 3.4 33.2 - - + -
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Residues in contact with GLY 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ARG* 2.8 22.4 + - - -
153A ASP* 4.1 0.9 - - - -
155A ALA* 1.3 74.5 - - - +
157A ALA* 1.3 59.5 + - - +
158A ASN 3.2 1.0 + - - -
159A PRO* 3.6 13.6 - - - +
193A LEU* 3.5 15.8 - - - +
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Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 4.1 17.7 - - + -
109A HIS* 3.9 11.7 - - + -
116A ARG* 5.0 0.5 + - - -
153A ASP 3.2 18.1 + - - +
154A LEU 3.7 5.4 - - - +
155A ALA 3.2 0.8 - - - -
156A GLY* 1.3 77.1 - - - +
158A ASN* 1.3 70.4 + - - +
159A PRO* 3.6 6.1 - - - +
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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