Contacts of the helix formed by residues 176 - 185 (chain B) in PDB entry 3MZH
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 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B ARG* 5.2 5.8 - - - +
175B LEU* 1.3 79.2 - - - +
177B GLN* 1.3 63.2 + - - +
178B GLU* 2.5 32.9 + - + +
179B GLU* 2.9 31.7 + - - +
180B ILE* 3.4 9.1 + - - +
209B LYS* 3.9 20.8 - - - +
4D A 3.7 27.4 - - - +
5D C 3.8 7.9 - - - -
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Residues in contact with GLN 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 HIS* 6.2 1.3 - - + -
175B LEU 5.4 1.1 - - - +
176B THR* 1.3 70.3 - - - +
178B GLU* 1.3 66.5 + - - +
179B GLU 3.1 0.2 + - - -
180B ILE* 3.1 12.5 + - + +
181B ALA* 2.8 24.3 + - - +
188B ARG* 4.1 17.8 + - - +
191B VAL* 4.5 4.4 - - + +
192B ASN* 3.4 24.3 + - - +
195B LEU* 3.2 34.6 - - + +
206B LEU* 4.4 10.1 - - - +
5D C 2.8 37.4 + - - +
6D G 3.0 25.0 + - - -
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Residues in contact with GLU 178 (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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176B THR* 2.5 28.3 - - + +
177B GLN* 1.3 71.8 - - - +
179B GLU* 1.3 61.7 + - + +
181B ALA* 3.2 5.6 - - - +
182B GLN* 3.1 30.2 + - - +
188B ARG* 3.1 43.5 + - + +
4D A 4.1 22.2 + - - +
5D C 2.6 29.2 + - - -
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Residues in contact with GLU 179 (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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33B ARG* 5.5 3.5 + - - -
56B LYS* 2.9 35.1 + - - +
68B LEU* 3.8 11.8 - - + +
96B ILE* 4.4 5.8 - - - +
174B ASP 4.2 2.6 - - - +
175B LEU* 3.2 29.6 - - + +
176B THR* 2.9 42.1 + - - +
177B GLN 3.0 0.6 - - - -
178B GLU* 1.3 78.8 - - + +
180B ILE* 1.3 55.3 + - - +
182B GLN* 3.1 13.6 - - - +
183B LEU* 2.7 36.2 + - - +
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Residues in contact with ILE 180 (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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150B VAL* 4.8 10.5 - - + -
153B GLN* 5.2 9.9 - - + -
154B LEU* 5.2 13.5 - - + -
157B LEU* 5.5 4.9 - - + -
173B HIS* 4.4 26.7 - - + +
175B LEU* 4.1 17.9 - - + -
176B THR 3.4 10.1 + - - +
177B GLN* 3.1 15.1 + - + +
179B GLU* 1.3 73.4 - - - +
181B ALA* 1.3 72.4 + - - +
183B LEU* 2.9 10.1 + - + +
184B VAL* 2.8 30.7 + - + +
191B VAL* 4.0 15.7 - - + -
195B LEU* 4.9 15.3 - - + -
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Residues in contact with ALA 181 (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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177B GLN 2.8 12.4 + - - +
178B GLU* 3.2 11.4 - - - +
180B ILE* 1.3 74.7 - - - +
182B GLN* 1.3 51.4 + - - +
184B VAL* 2.6 25.3 + - - -
185B GLY 2.6 14.7 + - - -
186B ALA 2.9 24.9 + - - +
187B SER 3.6 20.0 - - - +
188B ARG* 3.7 6.3 - - - +
191B VAL* 3.5 15.6 - - + +
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Residues in contact with GLN 182 (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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56B LYS* 4.6 3.1 + - - -
66B GLU* 3.4 43.7 + - - +
67B ASN* 3.5 6.9 - - - +
68B LEU* 3.1 48.0 + - + +
178B GLU* 3.1 15.8 + - - +
179B GLU* 3.1 26.1 - - - +
181B ALA* 1.3 75.7 - - - +
183B LEU* 1.3 58.1 + - - +
184B VAL 3.0 1.3 + - - -
185B GLY* 3.6 5.9 + - - +
186B ALA 3.8 2.9 + - - -
621B CMP 3.4 12.1 - - - -
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Residues in contact with LEU 183 (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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68B LEU* 3.1 42.6 - - + +
69B LEU 4.2 1.8 - - - +
70B THR* 4.0 22.4 - - - +
71B ILE* 4.2 19.1 - - + -
153B GLN* 3.1 43.2 - - + +
157B LEU* 4.7 1.3 - - + -
175B LEU* 4.4 12.3 - - + -
179B GLU 2.7 22.0 + - - +
180B ILE* 2.9 9.8 + - + +
182B GLN* 1.3 73.7 - - - +
184B VAL* 1.3 57.3 + - - +
621B CMP 2.9 28.9 + - + +
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Residues in contact with VAL 184 (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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141B LEU* 4.0 1.4 - - - +
146B VAL* 4.2 9.4 - - + -
149B ARG* 3.0 35.8 + - + +
150B VAL* 4.0 34.3 - - + +
153B GLN* 4.3 10.8 - - + +
180B ILE* 2.8 13.8 + - + +
181B ALA 2.6 16.2 + - - +
183B LEU* 1.3 74.0 - - - +
185B GLY* 1.3 55.0 + - - +
186B ALA* 3.8 21.3 - - + -
191B VAL* 4.6 1.6 - - + -
621B CMP 3.1 30.1 + - - +
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Residues in contact with GLY 185 (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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142A ILE* 3.7 37.6 - - - +
67B ASN* 5.6 0.2 - - - -
141B LEU* 4.7 3.2 - - - +
149B ARG* 3.7 8.6 + - - -
181B ALA 2.6 10.3 + - - -
182B GLN* 3.6 7.0 + - - -
184B VAL* 1.3 76.8 - - - +
186B ALA* 1.3 56.9 + - - +
621B CMP 3.4 3.6 + - - -
16C G 4.0 6.9 + - - -
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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
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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