Contacts of the helix formed by residues 192 - 200 (chain B) in PDB entry 5H8N
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 LEU 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B ILE* 5.1 4.7 - - + -
166B ARG* 3.8 30.3 - - - +
185B TYR* 3.5 42.8 - - + +
186B PHE* 3.8 39.4 - - + +
189B GLN* 2.9 28.5 + - + +
191B GLU* 1.3 80.3 - - + +
193B SER* 1.3 58.0 + - - +
194B THR 3.4 2.7 - - - -
195B MET* 3.1 15.1 + - - +
196B TYR* 3.0 24.6 + - - +
246B PHE* 5.9 0.7 - - + -
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Residues in contact with SER 193 (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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186B PHE 4.8 0.9 - - - -
187B ARG 6.2 0.2 - - - -
189B GLN 3.3 4.3 + - - -
190B VAL* 3.2 25.7 + - - -
191B GLU 3.5 0.8 - - - -
192B LEU* 1.3 75.8 - - - +
194B THR* 1.3 61.5 + - - +
196B TYR* 3.4 9.0 + - - +
197B ARG* 2.7 63.4 + - - +
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Residues in contact with THR 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ARG 3.6 24.2 - - - +
167B ASN* 5.0 0.7 - - - -
168B PRO* 3.6 19.4 - - + +
174B TYR* 4.7 0.2 - - - -
191B GLU 5.2 2.3 + - - -
192B LEU 3.4 0.8 - - - -
193B SER* 1.3 77.2 - - - +
195B MET* 1.3 62.2 + - - +
197B ARG* 3.5 21.8 + - - +
198B HIS* 3.4 19.6 + - - +
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Residues in contact with MET 195 (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 ILE* 3.8 23.1 - - + +
165B LEU* 3.4 40.4 - - + +
166B ARG* 4.1 28.0 - - - +
174B TYR* 3.3 22.8 + - + +
186B PHE* 3.7 30.5 - - + -
192B LEU* 3.1 19.0 + - + +
194B THR* 1.3 75.6 - - - +
196B TYR* 1.3 58.9 + - - +
198B HIS* 3.2 4.7 + - - +
199B MET* 2.9 32.9 + - - +
223B ILE* 3.9 8.3 - - + -
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Residues in contact with TYR 196 (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 ASP* 3.6 24.5 - - - -
186B PHE* 3.5 23.7 - - + +
187B ARG* 2.9 64.5 + - + -
192B LEU 3.0 7.5 + - - +
193B SER* 3.4 10.3 + - - +
195B MET* 1.3 74.1 - - - +
197B ARG* 1.3 63.3 + - + +
199B MET* 3.3 10.2 + - + -
200B GLU* 2.9 67.2 + - + +
203B ASN* 5.3 2.0 - - - -
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Residues in contact with ARG 197 (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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193B SER* 2.7 51.0 + - - +
194B THR* 3.6 20.3 + - - +
195B MET 3.3 0.2 - - - -
196B TYR* 1.3 79.3 - - + +
198B HIS* 1.4 59.8 + - - +
200B GLU* 3.3 32.9 - - - +
201B LYS* 3.4 15.6 - - - +
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Residues in contact with HIS 198 (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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168B PRO* 3.6 24.3 - - + +
169B SER 3.2 28.0 + - - -
170B ASP* 5.0 1.1 - - - -
172B PHE 3.5 10.1 + - - -
173B ILE* 3.5 5.9 - - + -
174B TYR* 3.2 65.1 + + - +
194B THR 3.4 3.0 + - - +
195B MET 3.2 7.9 + - - +
197B ARG* 1.4 77.2 - - - +
199B MET* 1.4 62.1 + - - +
201B LYS* 3.3 25.7 + - - +
202B HIS* 3.2 36.1 + + - -
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Residues in contact with MET 199 (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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174B TYR* 3.7 39.7 - - + +
175B ALA* 3.9 3.6 - - - -
176B THR* 3.8 34.8 - - + +
186B PHE* 3.8 41.3 - - + -
195B MET 2.9 24.0 + - - +
196B TYR* 3.8 7.4 - - + +
198B HIS* 1.4 73.2 - - - +
200B GLU* 1.4 52.2 + - - +
201B LYS 3.2 0.4 - - - -
202B HIS* 2.8 7.1 + - - -
203B ASN* 2.8 46.4 + - - +
223B ILE* 3.8 21.3 - - + -
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Residues in contact with GLU 200 (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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196B TYR* 2.9 49.9 + - + +
197B ARG* 3.3 35.9 - - - +
199B MET* 1.4 69.8 - - - +
201B LYS* 1.3 63.8 + - + +
202B HIS 3.4 0.2 - - - -
203B ASN* 4.0 15.0 + - - +
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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