Contacts of the helix formed by residues 143 - 160 (chain A) in PDB entry 3K4H
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 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PRO* 5.5 9.6 - - + -
77A TYR* 4.6 10.1 - - + -
78A SER 3.6 15.3 - - - +
79A ARG* 3.8 33.0 - - + +
140A GLY* 3.8 14.6 - - - +
141A SER 3.1 8.3 - - - +
142A ASP* 1.3 86.5 + - - +
144A LEU* 1.3 65.9 + - - +
145A VAL* 3.4 11.9 - - + -
146A THR* 3.4 9.8 + - - +
147A ARG* 3.2 17.0 + - - +
174A PHE* 4.3 26.9 - - + -
1C GLC 5.0 8.5 - - - +
2C GLC 5.9 0.4 - - - +
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Residues in contact with LEU 144 (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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78A SER* 3.0 38.0 + - - +
79A ARG 4.3 1.1 - - - +
80A GLU* 4.2 13.0 - - - +
100A LYS* 3.5 38.4 - - + +
102A TYR* 3.6 49.6 - - + +
142A ASP 4.8 0.7 - - - +
143A LEU* 1.3 73.2 - - - +
145A VAL* 1.3 65.9 + - - +
147A ARG* 3.2 24.3 + - + +
148A ASP* 2.9 32.1 + - - +
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Residues in contact with VAL 145 (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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78A SER 4.9 0.6 + - - -
100A LYS 6.0 0.8 - - - +
115A ASN* 3.5 17.0 - - - +
143A LEU* 4.5 14.4 - - + -
144A LEU* 1.3 77.0 - - - +
146A THR* 1.3 65.0 + - - +
148A ASP* 3.6 2.9 + - - +
149A ARG* 3.0 69.4 + - - +
174A PHE* 5.3 4.0 - - + -
199A THR* 6.2 0.4 - - - -
1C GLC 4.2 23.3 - - - +
2C GLC 3.4 29.8 + - - +
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Residues in contact with THR 146 (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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136A PHE* 3.7 14.2 - - + -
138A GLY* 4.3 1.1 - - - -
139A GLY* 3.9 20.2 + - - +
140A GLY 3.3 23.2 + - - +
141A SER* 4.9 0.9 - - - -
143A LEU* 3.4 10.3 + - - +
144A LEU 3.1 0.6 - - - -
145A VAL* 1.3 81.1 - - - +
147A ARG* 1.3 66.9 + - - +
149A ARG* 4.7 3.6 - - - -
150A LEU* 2.9 23.9 + - - +
171A HIS* 3.6 33.4 - - + +
174A PHE* 4.6 5.2 - - - -
199A THR* 4.9 6.4 + - + -
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Residues in contact with ARG 147 (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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80A GLU* 2.7 40.8 + - - +
102A TYR* 4.7 12.9 + - - -
141A SER* 3.5 25.5 + - - +
142A ASP* 4.2 10.1 + - - +
143A LEU 3.2 7.9 + - - +
144A LEU* 3.2 27.6 + - + +
146A THR* 1.3 78.7 - - - +
148A ASP* 1.3 59.7 + - - +
150A LEU* 3.5 8.5 - - + +
151A ALA* 2.8 29.8 + - - +
171A HIS* 6.4 0.2 - - - -
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Residues in contact with ASP 148 (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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100A LYS* 2.6 51.8 + - - +
112A ASP* 4.6 4.2 - - - +
115A ASN* 4.0 20.7 + - + +
116A TYR* 3.9 20.6 - - - +
144A LEU* 2.9 22.5 + - - +
145A VAL* 3.9 4.6 - - - +
147A ARG* 1.3 77.0 - - - +
149A ARG* 1.3 60.5 + - - +
151A ALA* 2.9 8.8 + - - +
152A GLY* 2.9 28.2 + - - -
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Residues in contact with ARG 149 (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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115A ASN* 2.7 41.8 + - + +
119A ALA* 3.2 23.2 - - + +
136A PHE* 3.8 2.9 - - - -
145A VAL* 3.0 31.4 + - - +
146A THR 4.0 0.9 - - - +
148A ASP* 1.3 75.9 - - - +
150A LEU* 1.3 66.9 + - - +
153A MSE 3.3 5.7 + - - -
197A MSE 3.5 10.1 - - + +
199A THR* 3.0 45.4 + - + -
227A PHE* 3.4 45.1 - - + -
245A VAL* 3.8 7.5 - - - +
1C GLC 2.8 30.5 + - - -
2C GLC 3.5 12.1 + - - -
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Residues in contact with LEU 150 (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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136A PHE* 3.3 39.6 - - + -
146A THR* 2.9 18.7 + - + +
147A ARG* 3.5 9.0 - - + +
149A ARG* 1.3 76.7 - - - +
151A ALA* 1.3 63.8 + - - +
153A MSE 3.9 4.6 - - + +
154A SER* 2.9 35.7 + - - -
164A LEU* 4.7 2.2 - - + -
169A ILE* 4.2 32.3 - - + -
171A HIS* 4.5 12.6 - - + +
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Residues in contact with ALA 151 (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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116A TYR* 3.7 16.6 - - + -
147A ARG 2.8 21.3 + - - +
148A ASP* 2.9 10.0 + - - +
150A LEU* 1.3 73.9 - - - +
152A GLY* 1.3 57.0 + - - +
154A SER* 3.5 5.6 + - - -
155A ASP* 3.0 35.6 + - - +
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Residues in contact with GLY 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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116A TYR* 3.5 37.1 - - - -
120A ARG* 3.2 26.9 - - - +
148A ASP 2.9 11.6 + - - -
149A ARG 4.1 1.3 - - - -
151A ALA* 1.3 73.9 - - - +
153A MSE 1.3 62.7 + - - +
155A ASP 3.7 0.2 + - - -
156A ALA* 3.2 13.5 + - - +
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Residues in contact with MSE 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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119A ALA* 3.9 3.4 - - - +
123A ALA* 3.9 20.8 - - + +
134A ILE* 3.4 40.4 - - - +
135A ALA 4.0 5.8 - - - +
136A PHE* 3.8 35.7 - - + -
149A ARG 3.3 14.7 + - - +
150A LEU* 3.9 7.4 - - + +
152A GLY* 1.3 73.1 - - - +
154A SER* 1.3 64.3 + - - +
156A ALA* 3.3 3.5 + - - +
157A LEU* 3.0 42.5 + - + +
164A LEU* 3.8 27.8 - - + -
197A MSE 3.9 23.8 - - + +
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Residues in contact with SER 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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150A LEU* 2.9 24.0 + - - -
151A ALA* 3.6 7.0 - - - -
153A MSE 1.3 81.1 - - - +
155A ASP* 1.3 64.0 + - - +
157A LEU* 3.2 5.1 + - - +
158A LYS* 3.0 44.6 + - - +
164A LEU* 4.0 26.0 - - - +
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Residues in contact with ASP 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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116A TYR* 2.5 24.6 + - - +
120A ARG* 4.4 4.9 - - - +
151A ALA* 3.0 17.7 + - - +
152A GLY 4.1 2.0 - - - +
154A SER* 1.3 73.6 + - - +
156A ALA* 1.3 60.7 + - - +
158A LYS* 3.1 16.6 + - - +
159A LEU* 2.8 41.6 + - + +
120B ARG* 2.4 33.5 + - - +
159B LEU* 3.6 17.5 - - + +
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Residues in contact with ALA 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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120A ARG* 4.0 22.8 - - - +
123A ALA* 3.6 22.0 - - + -
124A GLU* 4.6 8.2 - - + +
127A ILE* 3.8 14.3 - - + +
152A GLY 3.2 17.5 + - - +
153A MSE 3.5 5.2 - - - +
155A ASP* 1.3 78.3 - - - +
157A LEU* 1.3 62.5 + - - +
159A LEU* 3.4 7.3 + - - +
160A ALA* 3.3 17.2 + - - +
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Residues in contact with LEU 157 (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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123A ALA* 4.8 5.2 - - + -
127A ILE* 3.6 24.9 - - + -
134A ILE* 3.7 33.0 - - + +
153A MSE 3.0 33.2 + - + +
154A SER 3.6 6.3 - - - +
155A ASP 3.2 0.2 - - - -
156A ALA* 1.3 77.9 - - - +
158A LYS* 1.3 57.4 + - + +
160A ALA 3.3 1.7 + - - -
161A ASP 3.2 4.3 + - - -
162A ILE* 2.7 51.7 + - + +
163A VAL 4.1 8.7 - - - +
164A LEU* 3.7 35.2 - - + -
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Residues in contact with LYS 158 (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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154A SER* 3.0 35.3 + - - +
155A ASP* 3.1 17.5 + - - +
157A LEU* 1.3 76.4 - - + +
159A LEU* 1.3 61.7 + - - +
161A ASP* 3.4 17.1 + - - +
162A ILE 4.3 6.7 - - - +
164A LEU* 6.3 4.5 - - + -
159B LEU* 4.5 21.2 - - + +
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Residues in contact with LEU 159 (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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120A ARG* 3.6 39.7 - - - +
155A ASP* 2.8 25.0 + - + +
156A ALA* 3.8 6.1 - - - +
157A LEU 3.2 0.2 - - - -
158A LYS* 1.3 77.1 - - - +
160A ALA* 1.3 58.1 + - - +
161A ASP* 3.2 3.9 + - - +
155B ASP* 3.6 19.1 - - + +
158B LYS* 3.5 41.3 - - + +
159B LEU* 3.2 29.6 - - + -
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Residues in contact with ALA 160 (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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127A ILE* 4.1 17.0 - - + -
156A ALA 3.3 14.6 + - - +
157A LEU 3.3 0.6 + - - +
158A LYS 3.3 0.2 - - - -
159A LEU* 1.3 76.3 - - - +
161A ASP* 1.3 69.2 + - - +
162A ILE* 3.4 25.3 + - + +
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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