Contacts of the helix formed by residues 196 - 204 (chain O) 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 THR 196 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54K GLU* 3.3 16.8 - - - +
57K SER* 5.4 0.2 + - - -
174O CYS* 5.9 0.7 - - - -
194O THR* 3.5 20.1 + - + +
195O LEU* 1.3 85.8 - - - +
197O MET* 1.3 54.9 + - - +
198O GLU* 3.2 16.4 + - + +
199O ASP* 2.6 36.9 + - - +
200O LEU* 2.8 31.6 + - - +
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Residues in contact with MET 197 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K GLU* 3.0 29.8 + - - +
57K SER* 4.8 4.9 - - - -
45M ARG* 5.2 11.0 - - - +
196O THR* 1.3 72.1 - - - +
198O GLU* 1.3 56.8 + - - +
200O LEU* 3.4 30.7 - - + +
201O THR* 2.8 35.0 + - - +
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Residues in contact with GLU 198 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173O HIS* 4.8 7.0 - - + +
176O MET* 3.7 17.9 - - - +
177O LYS 3.0 36.8 - - - +
196O THR* 3.3 13.9 + - - +
197O MET* 1.3 79.3 - - - +
199O ASP* 1.3 63.0 + - - +
201O THR* 3.7 6.9 + - - -
202O PRO* 3.2 18.2 - - - +
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Residues in contact with ASP 199 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K PHE* 4.5 0.2 - - - -
170O ALA* 3.0 48.9 + - + +
173O HIS* 3.1 23.6 - - - +
174O CYS* 3.5 9.5 - - - +
194O THR 2.9 25.3 - - - +
195O LEU* 3.9 5.1 - - + -
196O THR* 2.6 30.1 + - - +
198O GLU* 1.3 74.0 - - - +
200O LEU* 1.3 64.5 + - - +
201O THR 3.2 0.2 - - - -
202O PRO* 3.3 17.3 - - - +
203O ALA* 3.8 8.5 + - - +
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Residues in contact with LEU 200 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57K SER* 4.3 17.5 - - - +
60K THR* 6.2 5.6 - - + -
61K LEU* 3.9 35.7 - - + -
64K MET* 5.6 2.7 - - - -
195O LEU* 5.1 4.3 - - + -
196O THR 2.8 16.7 + - - +
197O MET* 3.0 38.3 + - + +
199O ASP* 1.3 77.0 - - - +
201O THR* 1.3 64.1 + - - +
203O ALA* 3.1 19.3 + - + +
204O LEU* 3.2 30.2 + - + +
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Residues in contact with THR 201 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197O MET 2.8 16.4 + - - -
198O GLU* 4.0 5.6 + - - -
200O LEU* 1.3 77.6 - - - +
202O PRO* 1.3 67.7 - - + +
204O LEU* 3.1 34.4 + - + +
205O SER 4.3 0.3 + - - -
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Residues in contact with PRO 202 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169O ASP* 3.0 32.6 - - - +
173O HIS* 3.8 29.8 - - + +
198O GLU 3.2 17.5 - - - +
199O ASP 3.3 10.5 - - - +
201O THR* 1.3 90.5 - - + +
203O ALA* 1.3 58.9 + - - +
204O LEU 3.1 0.9 - - - -
205O SER* 3.2 24.0 + - - -
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Residues in contact with ALA 203 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61K LEU* 5.2 3.6 - - + -
64K MET* 4.8 11.3 - - - +
166O ILE* 4.5 29.9 - - + +
169O ASP* 3.3 12.2 + - + +
170O ALA* 6.4 0.4 - - + -
199O ASP 4.0 8.7 - - - +
200O LEU* 3.1 24.1 + - + +
202O PRO* 1.3 77.6 - - - +
204O LEU* 1.3 57.8 + - - +
205O SER* 3.1 8.5 + - - -
206O GLU* 4.2 8.7 + - - +
207O TYR 5.5 0.2 + - - -
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Residues in contact with LEU 204 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K MET* 5.3 11.7 - - + -
200O LEU* 3.3 29.4 - - + +
201O THR* 3.3 28.7 - - + +
202O PRO 3.1 1.0 - - - -
203O ALA* 1.3 75.2 - - - +
205O SER* 1.3 59.8 + - - +
206O GLU 3.2 3.1 - - - -
208O GLY* 3.0 46.0 + - - +
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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