Contacts of the helix formed by residues 185 - 190 (chain B) in PDB entry 6MZL
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 SER 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B GLY 5.7 0.9 - - - -
158B GLY 5.2 3.5 - - - +
180B CYS 4.6 3.0 + - - -
181B GLY* 3.3 16.7 - - - -
182B TYR* 3.1 30.2 + - - -
183B GLN 3.2 2.7 + - - -
184B ASN* 1.3 76.2 - - - +
186B THR* 1.3 61.2 + - - +
187B ARG 3.1 1.8 - - - -
188B PHE* 3.0 36.6 + - - +
189B TRP* 3.2 11.1 + - - +
319B TYR* 4.6 3.5 + - - -
965B TRP* 5.9 0.9 - - - -
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Residues in contact with THR 186 (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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183B GLN 4.5 0.9 + - - -
184B ASN 3.5 0.6 - - - -
185B SER* 1.3 76.3 + - - +
187B ARG* 1.3 56.5 + - - +
189B TRP* 3.1 10.5 + - + +
190B PHE* 2.8 71.6 + - + +
192B CYS* 4.4 3.8 - - + -
195B SER* 4.2 13.9 - - - -
244B ALA* 3.3 36.1 + - + +
245B SER* 3.4 14.6 + - - -
247B ILE 4.8 5.4 + - - -
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Residues in contact with ARG 187 (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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66B ASN* 3.2 40.8 - - - +
67B SER* 3.2 37.0 - - - +
68B LYS* 3.4 2.1 + - - +
90B THR* 5.5 0.2 + - - -
114B VAL* 5.0 2.0 - - - +
117B VAL* 3.4 23.2 - - - +
118B ASP* 2.4 34.5 + - - +
119B PRO* 4.0 0.2 - - - +
184B ASN* 4.5 25.8 - - + +
186B THR* 1.3 78.1 - - - +
188B PHE* 1.3 74.8 + - + +
189B TRP 3.1 1.7 + - - -
190B PHE 3.8 4.3 + - - -
192B CYS* 5.4 1.7 - - + +
193B VAL 4.4 14.0 + - - +
194B ASP* 2.7 20.4 + - - +
195B SER* 5.0 6.8 - - - -
439B HIS* 5.6 3.0 - - - -
965B TRP* 4.2 20.8 - - - -
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Residues in contact with PHE 188 (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 LYS* 3.7 55.1 - - + +
69B GLN* 5.2 7.3 - - + +
90B THR* 5.6 0.9 - - + -
152B LEU* 4.2 7.8 - - - +
155B PRO* 6.0 0.7 - - - +
157B GLY 3.9 14.1 - - - +
158B GLY* 3.8 27.5 - - - +
159B LEU* 5.2 1.2 - - - +
184B ASN 4.3 3.8 - - - -
185B SER* 3.0 26.4 + - - +
187B ARG* 1.3 85.7 - - + +
189B TRP* 1.3 58.7 + - - +
962B SER 5.0 6.7 - - - -
963B HIS 4.3 11.4 - - - -
964B ASP* 5.1 1.6 - - - -
965B TRP* 3.2 55.4 - + - -
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Residues in contact with TRP 189 (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 VAL* 5.6 11.0 - - + -
35B ILE* 6.2 3.5 - - + +
45B VAL* 5.9 1.8 - - - +
70B CYS* 4.7 0.9 - - - -
150B PHE* 5.0 0.5 - - - -
152B LEU* 3.3 39.7 - - + +
158B GLY 5.1 1.3 - - - +
159B LEU* 3.4 34.2 - - + +
179B SER* 4.8 8.5 - - - -
185B SER 3.2 9.4 + - - +
186B THR* 3.1 10.8 + - + +
187B ARG 4.1 0.9 - - - -
188B PHE* 1.3 80.2 - - - +
190B PHE* 1.3 93.4 + + + +
206B PHE* 5.7 6.7 - + - -
216B SER* 6.0 0.2 - - - -
247B ILE* 3.1 46.0 - - + -
248B SER* 3.7 12.6 - - - -
249B LEU* 4.4 23.3 - - + -
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Residues in contact with PHE 190 (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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31B GLN* 3.2 34.8 - - - -
33B VAL* 4.8 20.0 - - + -
49B VAL* 4.6 9.4 - - + -
70B CYS* 4.8 0.7 - - - -
150B PHE* 4.2 15.9 - + + -
152B LEU* 5.7 0.2 - - + -
186B THR* 2.8 35.0 + - + +
187B ARG 4.2 3.1 - - - -
189B TRP* 1.3 121.5 - + + +
191B PRO* 1.3 78.6 - - + +
192B CYS* 3.4 20.6 + - - -
202B TRP* 4.9 3.6 - + - -
204B LEU* 6.2 0.9 - - + -
247B ILE* 4.4 20.2 - - + -
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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