Contacts of the helix formed by residues 155 - 171 (chain B) in PDB entry 4MDH
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 THR 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ASN* 4.9 2.7 - - - +
153B CYS* 3.7 3.7 + - - -
154B LEU* 1.3 78.9 - - - +
156B ARG* 1.3 56.9 + - - +
157B LEU 3.0 3.1 - - - -
158B ASP* 2.7 28.9 + - - +
159B HIS* 2.9 11.5 + - - +
182B ILE* 4.0 18.6 - - + +
184B GLY 4.7 0.7 - - - +
186B HIS* 4.2 28.3 - - + +
252B HIS* 4.5 2.2 - - - -
267B SER* 3.6 3.9 + - - -
268B MET* 3.6 19.9 + - - -
269B GLY* 3.7 3.2 + - - +
286B SER* 3.0 35.0 + - - +
335B NAD 5.6 0.2 - - - -
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B LEU* 3.7 8.9 - - + +
155B THR* 1.3 78.8 + - - +
157B LEU* 1.3 54.1 + - - +
158B ASP 3.2 0.2 - - - -
159B HIS* 3.5 23.6 + - - -
160B ASN* 2.7 54.0 + - - +
163B LYS* 5.7 4.8 - - - +
247B LYS* 5.4 0.8 - - - +
248B ALA* 3.7 23.1 - - - +
251B ASP* 3.5 31.7 + - + +
252B HIS* 4.4 8.8 - - + +
255B ASP* 2.3 39.0 + - - +
266B VAL* 3.6 22.0 - - - +
267B SER 4.2 13.8 + - - +
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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
----------------------------------------------------------
58A ASP* 5.5 1.1 - - + +
154B LEU* 3.9 5.4 - - + +
155B THR 2.9 1.2 + - - -
156B ARG* 1.3 76.6 - - - +
158B ASP* 1.3 59.6 + - - +
160B ASN* 3.3 6.4 + - + +
161B ARG* 3.1 70.9 + - + +
186B HIS* 5.2 0.4 - - + -
241B SER* 5.3 0.4 - - - -
244B SER* 4.0 28.9 - - - +
245B ALA* 3.7 21.8 - - + -
248B ALA* 3.6 16.0 - - + +
334B SO4 4.6 0.4 - - - +
335B NAD 3.6 36.3 - - + +
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B THR* 2.7 10.7 + - - +
157B LEU* 1.3 75.8 - - - +
159B HIS* 1.3 57.6 + - - +
161B ARG* 3.5 24.1 + - - +
162B ALA* 3.2 21.7 + - - +
182B ILE* 3.2 19.1 - - + +
186B HIS* 2.7 38.1 + - - +
190B GLN* 3.0 41.1 + - - +
226B VAL* 3.7 12.6 - - + +
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Residues in contact with HIS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B THR 2.9 5.6 + - - +
156B ARG* 3.4 33.2 + - - +
158B ASP* 1.3 75.4 - - - +
160B ASN* 1.3 74.4 + - - +
161B ARG 3.5 0.3 + - - -
162B ALA* 3.6 4.0 - - - +
163B LYS* 3.4 35.5 + - + +
179B ASN* 5.8 0.4 - - - -
180B VAL* 3.3 29.8 + - + +
182B ILE* 3.0 16.2 - - + +
264B GLU* 5.9 1.4 + - - -
265B PHE 4.1 4.3 - - - -
266B VAL* 3.8 15.7 - - + +
267B SER* 2.5 38.7 + - - +
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Residues in contact with ASN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASP 4.0 18.3 + - - +
156B ARG* 2.7 43.8 + - - +
157B LEU* 3.3 8.9 + - + +
159B HIS* 1.3 77.7 - - - +
161B ARG* 1.3 66.1 + - + +
162B ALA 3.4 0.2 - - - -
163B LYS* 3.5 15.0 + - - +
164B ALA* 3.1 21.1 + - - +
174B SER* 5.4 0.9 - - - -
244B SER 5.5 0.4 + - - -
247B LYS* 3.9 13.9 + - - +
248B ALA* 3.8 14.1 - - - +
251B ASP* 3.0 24.8 + - - +
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Residues in contact with ARG 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASP* 3.8 26.8 + - + +
157B LEU* 3.1 54.3 + - + +
158B ASP* 3.7 21.9 + - - +
160B ASN* 1.3 75.9 - - - +
162B ALA* 1.3 57.3 + - - +
164B ALA* 3.0 6.2 + - - +
165B GLN* 2.9 30.9 + - + +
226B VAL* 4.5 14.1 + - + -
229B ARG* 3.1 31.4 + - + +
230B GLY* 3.6 33.8 - - - +
233B VAL* 4.6 1.8 - - - +
241B SER* 3.0 32.1 + - - -
244B SER* 4.5 1.6 + - - -
334B SO4 3.8 10.1 + - - -
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ASP 3.2 15.2 + - - +
159B HIS 3.6 7.4 - - - +
161B ARG* 1.3 77.4 - - - +
163B LYS* 1.4 55.0 - - - +
165B GLN* 3.3 4.9 + - - +
166B ILE* 3.0 34.1 + - - +
180B VAL* 3.6 22.9 - - + -
182B ILE* 4.0 4.7 - - + -
192B PRO* 4.7 3.1 - - + -
222B PHE* 3.5 12.9 - - + -
226B VAL* 3.8 18.3 - - + +
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Residues in contact with LYS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG* 5.7 4.6 - - - +
159B HIS* 3.4 34.2 + - + +
160B ASN* 3.5 18.3 + - - +
162B ALA* 1.4 75.7 - - - +
164B ALA* 1.3 64.8 + - - +
165B GLN 3.2 0.4 - - - -
166B ILE* 3.9 2.5 - - - +
167B ALA* 3.1 24.1 + - - +
174B SER* 3.1 37.0 + - - +
175B ASP* 4.6 8.7 + - - +
177B VAL* 2.9 37.8 + - + +
180B VAL* 4.0 19.5 - - + +
264B GLU* 5.6 3.7 + - - -
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Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 3.5 20.9 - - + +
58A ASP* 3.4 23.6 - - - +
160B ASN 3.1 8.8 + - - +
161B ARG 3.0 9.9 + - - +
163B LYS* 1.3 78.2 - - - +
165B GLN* 1.3 60.5 - - - +
167B ALA* 3.7 2.1 - - - +
168B LEU* 3.1 40.0 + - + +
174B SER* 4.1 11.0 - - - -
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Residues in contact with GLN 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ASP* 5.0 1.2 - - - +
161B ARG* 2.9 14.8 + - + +
162B ALA 3.4 9.6 - - - +
163B LYS 3.2 0.2 - - - -
164B ALA* 1.3 76.4 - - - +
166B ILE* 1.3 66.4 + - - +
168B LEU* 3.4 21.9 + - - +
169B LYS* 3.2 20.6 + - - +
217B TRP* 4.6 12.4 - - + -
222B PHE* 3.5 17.0 - - + -
225B THR* 3.4 35.1 + - + +
226B VAL* 4.1 10.3 - - + -
229B ARG* 3.7 24.4 + - - -
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Residues in contact with ILE 166 (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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162B ALA 3.0 18.7 + - - +
163B LYS* 3.9 6.5 - - - +
164B ALA 3.3 0.2 - - - -
165B GLN* 1.3 80.8 - - - +
167B ALA* 1.3 64.1 + - - +
169B LYS* 3.1 12.8 + - - +
170B LEU* 3.2 34.8 + - + +
177B VAL* 4.2 25.1 - - + -
180B VAL* 5.2 1.6 - - + -
194B VAL* 4.0 7.2 - - + -
199B VAL* 4.6 0.7 - - + -
208B VAL* 3.6 32.5 - - + -
212B VAL* 4.9 2.0 - - + -
217B TRP* 4.7 3.8 - - + -
218B LEU* 3.9 20.4 - - + -
222B PHE* 3.9 18.2 - - + -
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Residues in contact with ALA 167 (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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163B LYS 3.1 18.2 + - - +
164B ALA* 3.7 5.4 - - - +
166B ILE* 1.3 76.1 - - - +
168B LEU* 1.3 55.0 + - + +
171B GLY* 2.7 32.7 + - - -
172B VAL* 3.1 38.0 + - - +
173B THR* 3.7 3.1 - - - +
174B SER* 3.6 21.3 - - - +
177B VAL* 4.4 1.3 - - + +
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Residues in contact with LEU 168 (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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57A GLN* 3.6 43.7 - - + +
164B ALA* 3.1 20.9 + - + +
165B GLN* 3.8 25.8 - - - +
166B ILE 3.2 0.4 + - - -
167B ALA* 1.3 81.5 - - + +
169B LYS* 1.3 64.3 + - - +
171B GLY* 3.3 8.8 + - - -
229B ARG* 5.1 0.2 - - - +
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Residues in contact with LYS 169 (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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165B GLN 3.2 9.4 + - - +
166B ILE* 3.1 10.2 + - - +
168B LEU* 1.3 81.0 - - - +
170B LEU* 1.3 73.6 + - + +
171B GLY 3.5 0.3 + - - -
212B VAL* 4.1 17.0 + - + -
214B ASP* 3.5 22.3 + - - +
217B TRP* 3.9 50.8 - - + -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 3.2 35.7 + - + +
169B LYS* 1.3 81.8 - - + +
171B GLY* 1.3 63.9 + - - +
172B VAL* 3.4 16.7 - - + +
199B VAL* 4.0 26.0 - - + -
201B LEU* 5.1 11.7 - - + +
208B VAL 5.1 0.4 - - - +
211B ALA* 3.7 18.2 - - + +
212B VAL* 3.2 43.7 - - + +
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Residues in contact with GLY 171 (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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167B ALA 2.7 11.2 + - - -
168B LEU 3.3 6.5 + - - -
169B LYS 3.3 4.2 + - - -
170B LEU* 1.3 80.4 - - - +
172B VAL* 1.3 60.2 + - - +
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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
------------------------------------------------------------
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