Contacts of the helix formed by residues 143 - 161 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B TYR* 6.4 1.3 - - + -
78B SER* 3.8 23.8 - - - +
79B ARG* 5.8 0.2 - - - -
80B GLU* 4.6 4.3 - - - +
140B GLY 3.4 12.8 + - - +
141B SER 3.2 5.6 - - - +
142B ASP* 1.3 88.2 - - - +
144B LEU* 1.3 64.6 + - - +
145B VAL* 4.0 17.0 - - + -
146B THR* 3.2 12.2 + - - +
147B ARG* 3.3 7.8 + - - +
174B PHE* 3.7 31.2 - - + -
1D GLC 4.8 10.1 - - - +
2D GLC 5.1 3.1 - - - +
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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
----------------------------------------------------------
78B SER* 5.1 3.9 - - - +
80B GLU* 3.8 10.0 + - - +
100B LYS* 4.1 30.7 - - + +
101B PRO 3.9 5.6 - - - +
102B TYR* 3.4 48.7 - - + +
142B ASP 3.1 4.6 + - - +
143B LEU* 1.3 67.7 - - - +
145B VAL* 1.3 68.7 + - - +
146B THR 2.9 2.0 - - - -
147B ARG* 2.8 33.3 + - + +
148B ASP* 2.8 45.7 + - - +
2D GLC 6.0 0.2 - - - +
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN* 3.9 12.1 - - - +
143B LEU* 4.0 22.9 - - + -
144B LEU* 1.3 75.2 - - - +
146B THR* 1.3 72.4 + - - +
148B ASP* 3.5 3.8 + - - +
149B ARG* 3.0 62.4 + - - +
174B PHE* 5.1 1.1 - - + -
199B THR* 5.9 0.7 - - - -
1D GLC 4.0 17.9 - - - +
2D GLC 3.5 34.7 + - - +
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Residues in contact with THR 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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136B PHE* 3.8 22.8 - - + -
138B GLY* 3.9 8.3 - - - -
139B GLY 3.1 34.0 + - - +
140B GLY 3.7 8.9 + - - +
141B SER* 4.6 5.8 - - - -
143B LEU* 3.2 11.9 + - - +
144B LEU 2.9 0.4 - - - -
145B VAL* 1.3 86.9 - - - +
147B ARG* 1.3 57.9 + - - +
149B ARG* 3.3 6.0 + - - +
150B LEU* 2.8 31.9 + - + +
171B HIS* 4.5 7.9 - - + -
174B PHE* 4.1 6.1 - - - -
199B THR* 4.8 5.5 + - + -
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU* 4.2 18.6 - - - +
102B TYR* 3.6 33.9 - - - -
141B SER 3.5 17.7 + - - +
142B ASP* 3.5 27.4 + - - +
143B LEU 3.3 3.0 + - - +
144B LEU* 2.8 30.1 + - + +
146B THR* 1.3 74.9 - - - +
148B ASP* 1.3 59.3 + - - +
150B LEU* 3.4 11.2 - - + +
151B ALA* 2.9 28.5 + - - +
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Residues in contact with ASP 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS* 2.9 37.4 + - - +
112B ASP* 4.9 2.4 - - - +
115B ASN* 4.1 18.9 + - + +
116B TYR* 3.9 20.6 + - + +
144B LEU* 2.8 34.7 + - - +
145B VAL* 3.9 4.0 - - - +
147B ARG* 1.3 72.4 - - - +
149B ARG* 1.3 60.6 + - - +
151B ALA* 3.2 6.6 + - - +
152B GLY* 2.8 28.6 + - - -
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASN* 3.1 38.4 + - + +
119B ALA* 3.2 23.9 - - - +
136B PHE* 3.9 2.9 - - - -
145B VAL* 3.0 37.1 + - - +
146B THR 4.0 1.8 - - - +
148B ASP* 1.3 75.5 - - - +
150B LEU* 1.3 64.0 + - - +
153B MSE 3.5 3.1 + - - +
197B MSE 3.6 20.5 - - + +
199B THR* 3.0 35.7 + - + -
227B PHE* 3.7 44.6 - - + +
245B VAL* 4.3 8.5 - - - +
1D GLC 2.9 32.3 + - - -
2D GLC 3.2 13.7 + - - -
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Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PHE* 3.6 38.2 - - + -
146B THR* 2.8 15.1 + - + +
147B ARG* 3.4 16.4 - - + +
149B ARG* 1.3 77.1 - - - +
151B ALA* 1.3 58.8 + - - +
153B MSE 3.1 5.2 + - + +
154B SER* 2.9 41.0 + - - +
164B LEU* 4.9 3.4 - - + -
169B ILE* 4.3 21.5 - - + -
171B HIS* 4.4 17.9 - - + +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR* 3.7 14.4 - - + -
147B ARG 2.9 17.2 + - - +
148B ASP* 3.6 7.2 - - - +
150B LEU* 1.3 76.1 - - - +
152B GLY* 1.3 64.7 + - - +
154B SER* 3.8 5.7 - - - -
155B ASP* 3.0 33.0 + - - +
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Residues in contact with GLY 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR* 3.5 36.0 - - - -
119B ALA* 3.7 3.8 - - - -
120B ARG* 3.1 27.8 - - - +
148B ASP 2.8 16.5 + - - -
151B ALA* 1.3 72.5 - - - +
153B MSE 1.3 62.1 + - - +
155B ASP* 3.5 0.7 + - - +
156B ALA 3.2 10.4 + - - -
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Residues in contact with MSE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ALA* 3.7 10.6 - - - +
122B VAL* 5.0 2.2 - - + -
123B ALA* 4.1 17.9 - - + -
126B LEU* 4.7 5.6 - - + -
134B ILE* 3.3 38.6 - - + +
135B ALA 3.9 5.8 - - - +
136B PHE* 4.0 25.8 - - + -
149B ARG 3.5 12.1 + - - +
150B LEU* 3.1 9.6 + - + +
152B GLY* 1.3 71.8 - - - +
154B SER* 1.3 60.4 + - - +
155B ASP 3.0 1.7 + - - -
156B ALA* 3.0 2.8 + - - +
157B LEU* 2.9 40.3 + - + +
164B LEU* 5.2 4.9 - - - -
197B MSE 3.2 42.6 - - + +
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 2.9 30.5 + - - +
151B ALA* 3.9 5.6 - - - -
153B MSE 1.3 75.6 - - - +
155B ASP* 1.3 58.2 + - - +
157B LEU* 3.9 10.2 + - - +
158B LYS* 3.2 42.1 + - - +
164B LEU* 4.8 15.7 - - - +
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Residues in contact with ASP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 2.6 31.3 + - - +
159A LEU* 3.6 22.6 - - + +
116B TYR* 2.7 24.4 + - - +
120B ARG* 4.4 4.7 - - - +
151B ALA* 3.0 18.8 + - - +
152B GLY 3.7 2.7 - - - +
154B SER* 1.3 77.2 + - - +
156B ALA* 1.3 66.0 + - - +
157B LEU 3.1 1.3 - - - -
158B LYS* 3.0 10.2 + - - +
159B LEU* 2.9 30.7 + - + +
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Residues in contact with ALA 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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120B ARG* 3.9 23.1 - - - +
123B ALA* 3.5 29.8 - - + -
124B GLU* 4.5 9.6 - - + +
127B ILE* 5.7 1.3 - - + +
152B GLY 3.2 10.0 + - - +
153B MSE 3.0 3.6 + - - +
155B ASP* 1.3 79.6 - - - +
157B LEU* 1.3 65.0 + - - +
159B LEU* 3.4 6.4 + - - +
160B ALA* 2.9 23.3 + - - +
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Residues in contact with LEU 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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123B ALA* 4.8 9.9 - - + -
127B ILE* 4.0 25.1 - - + -
134B ILE* 4.5 22.0 - - + +
153B MSE 2.9 24.0 + - + +
154B SER* 3.9 5.2 - - - +
156B ALA* 1.3 79.1 - - - +
158B LYS* 1.3 50.7 + - - +
160B ALA* 2.8 6.6 + - - +
161B ASP 2.5 32.7 + - - -
162B ILE* 3.1 35.8 + - + +
163B VAL 4.8 0.7 - - - +
164B LEU* 2.8 42.0 - - + -
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Residues in contact with LYS 158 (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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159A LEU* 3.5 33.9 - - + +
154B SER* 3.2 31.7 + - - +
155B ASP* 3.0 11.8 + - - +
157B LEU* 1.3 78.9 - - - +
159B LEU* 1.3 64.2 + - - +
161B ASP* 3.0 16.2 + - - +
162B ILE 4.3 6.3 - - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP* 3.6 30.3 - - + +
158A LYS* 4.5 25.0 - - + +
159A LEU* 3.2 38.6 - - + +
120B ARG* 4.0 21.5 - - - +
155B ASP* 2.9 19.6 + - + +
156B ALA* 3.8 5.6 - - - +
158B LYS* 1.3 75.9 - - - +
160B ALA* 1.3 61.9 + - - +
161B ASP* 3.4 1.6 + - - +
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Residues in contact with ALA 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 4.3 18.8 - - + -
156B ALA 2.9 14.8 + - - +
157B LEU* 2.9 16.2 - - - +
159B LEU* 1.3 77.9 - - - +
161B ASP* 1.3 66.2 + - - +
162B ILE* 3.5 23.4 - - + +
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Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU 2.5 10.7 + - - -
158B LYS 3.0 14.1 + - - +
159B LEU 4.7 1.2 - - - +
160B ALA* 1.3 78.6 - - - +
162B ILE* 1.3 65.6 + - + -
163B VAL* 3.8 10.9 - - - +
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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