Contacts of the helix formed by residues 161 - 177 (chain B) in PDB entry 3MQ6
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 VAL 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 LEU 3.7 0.2 + - - -
160B LEU* 1.3 73.9 - - - +
162B PRO* 1.3 69.0 - - + +
163B GLU* 4.3 8.7 - - + +
164B SER* 2.8 43.8 + - - +
165B GLN 3.2 6.8 + - - -
228B GLY 3.4 4.3 - - - +
229B ARG* 3.5 31.2 - - - +
230B VAL 2.9 19.0 + - - +
231B GLN* 4.0 30.7 - - - +
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Residues in contact with PRO 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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160B LEU 3.6 2.2 - - - +
161B VAL* 1.3 86.2 - - + +
163B GLU* 1.3 64.8 + - - +
165B GLN* 3.0 23.2 + - + +
166B GLU* 3.1 28.9 + - + +
228B GLY* 3.4 16.8 - - - +
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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
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161B VAL* 3.1 10.6 + - + +
162B PRO* 1.3 80.5 - - - +
164B SER* 1.3 61.1 - - - +
166B GLU* 3.6 25.3 + - - +
167B VAL* 3.4 18.5 + - + +
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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
----------------------------------------------------------
160B LEU* 4.1 13.7 - - - -
161B VAL* 2.8 19.6 + - - +
163B GLU* 1.3 74.8 - - - +
165B GLN* 1.3 66.6 + - - +
166B GLU 3.2 2.0 - - - -
167B VAL* 3.3 18.4 + - - +
168B ILE* 3.3 18.7 + - - +
231B GLN* 4.9 0.2 + - - -
232B PRO* 3.2 38.6 - - - +
268B LEU* 4.1 8.9 - - - +
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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
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157B VAL* 3.4 35.0 + - + +
158B SER* 3.7 18.0 + - - +
160B LEU* 2.8 31.5 + - + +
161B VAL 3.2 4.6 + - - +
162B PRO* 3.0 13.7 + - + +
164B SER* 1.3 77.3 - - - +
166B GLU* 1.3 58.7 + - + +
168B ILE* 3.3 8.8 + - - +
169B GLU* 2.9 36.1 + - + +
228B GLY* 4.3 4.4 - - - -
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Residues in contact with GLU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PRO* 3.1 24.3 + - + +
163B GLU* 3.8 23.6 - - - +
164B SER 3.2 0.4 - - - -
165B GLN* 1.3 75.6 - - + +
167B VAL* 1.3 59.9 + - + +
169B GLU* 3.3 6.4 + - - +
170B GLU* 2.9 34.9 + - - +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLU* 3.4 17.7 - - + +
164B SER* 3.5 8.7 - - - +
165B GLN 3.3 0.2 - - - -
166B GLU* 1.3 77.4 - - + +
168B ILE* 1.3 57.2 + - + +
170B GLU* 3.5 10.8 + - - +
171B PHE* 3.0 29.9 + - + +
267B LYS* 4.5 19.5 - - + +
268B LEU* 3.9 23.8 - - + -
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Residues in contact with ILE 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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156B TRP* 5.0 1.1 - - + -
157B VAL* 3.9 22.0 - - + -
160B LEU* 3.7 30.1 - - + -
164B SER 3.4 10.8 - - - +
165B GLN* 3.3 7.1 + - - +
166B GLU 3.2 0.2 - - - -
167B VAL* 1.3 76.9 - - + +
169B GLU* 1.3 61.9 + - - +
171B PHE* 3.0 10.0 + - - +
172B ARG* 2.8 63.5 + - + +
263B LEU* 4.4 31.0 - - + -
267B LYS* 5.9 2.5 - - + -
268B LEU* 4.1 15.7 - - + -
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Residues in contact with GLU 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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157B VAL* 5.4 3.0 - - + +
165B GLN* 2.9 23.1 + - + +
166B GLU* 3.9 5.6 - - - +
168B ILE* 1.3 76.5 - - - +
170B GLU* 1.3 57.0 + - - +
172B ARG* 2.9 36.8 + - - +
173B ALA* 2.8 30.2 + - - +
176B ARG* 3.3 26.7 + - - -
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLU* 2.9 18.6 + - - +
167B VAL* 3.8 8.8 - - - +
169B GLU* 1.3 76.0 - - - +
171B PHE* 1.3 62.3 + - - +
173B ALA* 3.7 8.9 - - - +
174B GLY* 3.3 16.5 + - - -
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Residues in contact with PHE 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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299A LEU* 4.3 24.9 - - + -
167B VAL* 3.0 16.0 + - + +
168B ILE* 3.2 11.9 - - - +
170B GLU* 1.3 76.8 - - - +
172B ARG* 1.3 69.0 + - + +
174B GLY* 3.3 4.0 + - - -
175B LEU* 3.2 36.9 + - + +
182B LEU* 4.1 13.5 - - + -
262B LEU* 4.3 2.2 - - + -
263B LEU* 3.8 31.0 - - + -
267B LYS* 3.6 43.1 - - + -
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Residues in contact with ARG 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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155B ASP* 4.7 6.9 + - - -
157B VAL* 4.3 9.5 - - - +
168B ILE* 2.8 37.6 + - + +
169B GLU* 2.9 35.4 + - - +
171B PHE* 1.3 76.2 - - + +
173B ALA* 1.3 60.8 + - - +
175B LEU* 3.0 11.8 + - + +
176B ARG* 2.8 49.6 + - + +
181B GLY* 5.5 1.7 - - - -
182B LEU* 3.0 41.9 + - + +
183B PRO* 3.8 2.6 - - - +
184B THR* 3.0 40.8 + - - +
263B LEU* 4.6 1.4 - - + +
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Residues in contact with ALA 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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169B GLU 2.8 16.6 + - - +
170B GLU* 3.7 10.1 - - - +
171B PHE 3.3 0.2 - - - -
172B ARG* 1.3 75.1 - - - +
174B GLY* 1.3 63.7 + - - +
176B ARG* 3.2 28.5 + - - +
177B LYS* 3.2 34.2 + - - +
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Residues in contact with GLY 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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170B GLU 3.3 12.0 + - - -
171B PHE 3.3 4.7 + - - -
172B ARG 3.2 0.4 - - - -
173B ALA* 1.3 80.7 - - - +
175B LEU* 1.3 62.4 + - - +
177B LYS* 3.4 24.1 + - - +
178B ASP* 3.9 10.8 + - - +
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Residues in contact with LEU 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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294A ALA* 4.6 1.3 - - + -
299A LEU* 3.5 33.9 - - + -
306A VAL* 5.6 1.1 - - + -
171B PHE* 3.2 33.7 + - + +
172B ARG* 3.0 13.1 + - - +
174B GLY* 1.3 75.9 - - - +
176B ARG* 1.3 58.2 + - - +
178B ASP* 2.9 23.9 + - - +
180B LEU* 3.0 43.2 + - + +
181B GLY* 3.8 26.7 - - - +
182B LEU* 3.9 15.0 - - + +
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Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B GLU* 3.3 25.7 + - - -
172B ARG* 2.8 32.2 + - - +
173B ALA* 3.2 32.7 + - - +
175B LEU* 1.3 73.3 - - - +
177B LYS* 1.3 57.1 + - + +
178B ASP 2.8 6.1 - - - -
179B GLY* 2.7 22.2 + - - -
180B LEU 3.3 17.5 - - - +
181B GLY* 5.2 3.0 - - - -
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Residues in contact with LYS 177 (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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173B ALA* 3.2 30.5 + - - +
174B GLY* 3.7 13.9 - - - +
175B LEU 3.3 0.6 - - - -
176B ARG* 1.3 75.6 - - + +
178B ASP* 1.3 64.4 + - - +
179B GLY 3.5 0.2 - - - -
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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
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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