Contacts of the helix formed by residues 161 - 175 (chain B) in PDB entry 1MHP
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 PRO 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B ILE* 5.1 0.2 - - - -
160B TYR* 1.3 114.0 - - + +
162B TRP* 1.3 65.6 + - - +
163B GLU* 4.1 19.3 - - + +
164B SER* 3.0 32.3 + - - +
165B VAL* 3.8 2.8 + - - +
321B GLU* 4.1 14.1 - - + +
322B LEU* 4.2 13.7 - - + -
31X ARG* 5.3 2.9 - - - +
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Residues in contact with TRP 162 (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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153B LEU* 4.5 12.8 - - + -
154B ASP 3.5 24.2 - - - -
155B GLY* 3.9 7.0 - - - -
159B ILE* 3.9 10.3 - - + -
160B TYR* 4.1 4.4 - - - +
161B PRO* 1.3 70.5 - - - +
163B GLU* 1.3 64.4 + - - +
165B VAL* 2.9 40.2 + - + +
166B ILE* 3.0 37.0 + - + +
189B GLN* 3.9 27.6 - - - -
216B ILE* 2.9 32.3 + - + -
217B VAL* 4.4 1.1 - - - -
218B GLN* 3.2 58.3 - - + +
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PRO* 3.1 22.2 + - + +
162B TRP* 1.3 77.2 - - - +
164B SER* 1.3 64.6 + - - +
166B ILE* 3.3 10.7 + - - +
167B ALA* 2.9 29.1 + - - +
322B LEU* 6.6 0.2 - - - -
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Residues in contact with SER 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PRO* 3.0 26.3 + - - +
163B GLU* 1.3 82.7 - - - +
165B VAL* 1.3 58.2 + - - +
167B ALA* 3.2 7.8 + - - +
168B PHE* 2.9 28.1 + - - +
321B GLU* 3.7 32.3 - - - +
322B LEU* 3.5 23.8 - - - +
324B LEU* 4.5 1.6 - - - +
325B VAL* 5.2 2.1 - - - +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 4.1 27.1 - - + -
154B ASP 5.2 1.8 - - - +
159B ILE* 3.7 32.5 - - + -
161B PRO 4.5 1.1 - - - +
162B TRP* 2.9 32.3 + - + +
164B SER* 1.3 75.9 - - - +
166B ILE* 1.3 59.9 + - + +
168B PHE* 3.1 22.9 - - + +
169B LEU* 3.1 9.9 + - + +
255B VAL* 5.9 5.2 - - + -
285B ILE* 6.3 0.7 - - + -
321B GLU* 4.3 9.6 - - + +
324B LEU* 4.1 22.7 - - + -
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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
----------------------------------------------------------
153B LEU* 6.5 0.2 - - + -
162B TRP* 3.0 50.5 + - + +
163B GLU* 3.7 9.4 - - - +
164B SER 3.2 0.2 - - - -
165B VAL* 1.3 75.2 - - + +
167B ALA* 1.3 60.1 + - - +
168B PHE 3.1 1.8 - - - -
169B LEU* 3.0 12.2 + - + +
170B ASN* 2.8 26.5 + - - +
213B ALA* 4.2 7.9 - - + +
214B ASN* 3.7 47.6 - - - +
216B ILE* 3.3 16.2 - - + +
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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 GLU 2.9 17.2 + - - +
164B SER* 3.2 9.4 + - - +
166B ILE* 1.3 76.2 - - - +
168B PHE* 1.3 62.3 + - - +
170B ASN* 3.3 7.0 + - - +
171B ASP* 3.0 33.1 + - - +
214B ASN* 5.9 0.7 - - - +
325B VAL* 4.6 13.2 - - + -
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Residues in contact with PHE 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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151B ILE* 5.6 0.7 - - + -
153B LEU* 5.4 1.8 - - + -
164B SER 2.9 12.3 + - - +
165B VAL* 3.1 15.3 - - + +
166B ILE 3.1 0.2 - - - -
167B ALA* 1.3 78.3 - - - +
169B LEU* 1.3 78.6 + - + +
172B LEU* 3.0 33.8 + - + +
253B VAL* 5.0 2.7 - - + -
255B VAL* 4.1 21.3 - - + -
283B ILE* 3.7 15.9 - - + -
324B LEU* 3.6 51.1 - - + -
325B VAL* 4.5 8.2 - - - +
327B ILE* 4.3 4.3 - - + -
328B VAL* 3.7 23.0 - - + +
331B LEU* 3.6 30.3 - - + -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 3.9 34.5 - - + -
153B LEU* 3.4 34.1 - - + -
165B VAL 3.1 13.8 + - - +
166B ILE* 3.0 16.0 + - + +
168B PHE* 1.3 88.5 - - + +
170B ASN* 1.3 57.8 + - - +
172B LEU* 3.1 2.9 + - + -
173B LEU* 2.7 46.0 + - + +
187B ILE* 3.6 19.1 - - + -
213B ALA* 4.3 17.5 - - + +
216B ILE* 4.5 6.7 - - + -
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Residues in contact with ASN 170 (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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211A VAL* 4.3 12.2 - - - +
215A LYS* 5.8 0.6 - - - +
166B ILE 2.8 12.7 + - - +
167B ALA* 3.5 11.9 - - - +
169B LEU* 1.3 76.0 - - - +
171B ASP* 1.3 69.7 + - - +
174B LYS* 2.8 40.2 + - - +
210B LEU* 3.2 26.1 + - - +
213B ALA* 5.6 1.3 - - - +
214B ASN* 2.7 38.4 + - - +
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Residues in contact with ASP 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* 3.0 20.4 + - - +
168B PHE* 4.8 0.2 - - - -
170B ASN* 1.3 83.6 - - - +
172B LEU* 1.3 63.4 + - - +
174B LYS* 3.5 25.7 + - - +
175B ARG* 3.3 30.8 + - - +
325B VAL* 4.5 16.9 - - - +
328B VAL* 3.8 28.2 - - + +
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Residues in contact with LEU 172 (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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149B ILE* 6.5 0.4 - - + -
151B ILE* 4.4 21.1 - - + -
168B PHE* 3.0 33.6 + - + +
169B LEU* 3.5 4.0 - - + +
171B ASP* 1.3 79.9 - - - +
173B LEU* 1.3 62.5 + - + +
175B ARG* 3.5 15.7 + - - +
176B MET* 3.2 30.6 - - + +
253B VAL* 5.0 10.5 - - + -
328B VAL* 4.1 12.3 - - + +
331B LEU* 4.2 26.7 - - + -
332B GLY* 4.2 27.8 - - - +
335B ILE* 5.4 4.0 - - + -
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Residues in contact with LEU 173 (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 ILE* 4.1 9.6 - - + -
169B LEU* 2.7 63.6 + - + +
170B ASN 3.9 0.9 - - - +
172B LEU* 1.3 73.4 - - + +
174B LYS* 1.3 58.2 + - - +
176B MET* 2.8 50.4 + - + +
178B ILE* 4.0 7.9 - - + +
185B VAL* 3.8 34.3 - - + -
187B ILE* 4.8 1.8 - - + -
206B THR* 4.0 0.9 - - - +
209B VAL* 4.0 19.3 - - + -
210B LEU* 4.4 14.1 - - + -
213B ALA* 4.7 8.5 - - + -
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Residues in contact with LYS 174 (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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207A GLU* 5.4 6.0 - - - +
170B ASN* 2.8 30.2 + - - +
171B ASP* 3.5 25.6 + - - +
173B LEU* 1.3 72.7 - - - +
175B ARG* 1.3 91.7 + - + +
176B MET 3.1 8.9 + - - +
206B THR* 4.3 6.0 - - - +
210B LEU* 3.6 29.3 - - + +
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Residues in contact with ARG 175 (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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171B ASP* 3.3 18.2 + - - +
172B LEU* 3.5 10.1 + - - +
173B LEU 3.0 1.4 + - - -
174B LYS* 1.3 111.7 - - + +
176B MET* 1.3 60.1 + - + +
177B ASP* 4.8 2.7 - - - +
328B VAL* 3.9 34.1 - - - +
329B LYS* 4.3 30.9 - - - +
332B GLY* 5.4 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
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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