Contacts of the helix formed by residues 197 - 207 (chain B) in PDB entry 3QLC
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 CYS 197 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171B CYS* 3.3 13.4 - - + +
174B CYS* 4.0 3.6 - - - -
176B GLN* 5.7 3.4 - - + +
178B VAL* 3.9 14.8 - - + -
185B SER 4.0 9.0 - - - +
187B TYR* 4.4 0.7 - - - -
196B ILE* 1.3 78.2 - - - +
198B LYS* 1.3 66.4 + - - +
199B ASN* 3.2 13.8 + - + +
200B CYS* 3.2 20.5 + - - -
201B PHE* 3.0 20.8 + - - +
661B ZN 2.2 35.9 - - - -
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Residues in contact with LYS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ASP* 3.3 34.4 + - - +
185B SER* 3.9 8.8 + - - -
187B TYR* 3.4 42.2 + - + +
197B CYS* 1.3 72.1 - - - +
199B ASN* 1.3 61.0 + - - +
201B PHE* 3.4 1.0 + - - +
202B LYS* 2.9 60.5 + - + +
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Residues in contact with ASN 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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197B CYS* 3.2 12.5 - - - +
198B LYS* 1.3 83.1 - - - +
200B CYS* 1.3 59.5 + - - +
202B LYS* 3.6 5.2 + - - +
203B TYR* 2.9 30.1 + - - +
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Residues in contact with CYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B CYS* 4.2 2.0 - - - -
173B ALA* 3.8 23.1 - - + -
174B CYS* 3.5 18.4 - - - -
196B ILE* 4.4 6.5 - - + -
197B CYS* 3.2 8.2 - - - +
199B ASN* 1.3 74.5 - - - +
201B PHE* 1.3 61.8 + - - +
203B TYR* 3.3 8.6 + - - +
204B TYR* 2.8 31.2 + - - +
223B CYS* 6.0 3.8 - - - +
661B ZN 2.3 36.3 - - - -
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Residues in contact with PHE 201 (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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187B TYR* 3.6 42.4 - + + -
188B ARG 3.8 23.8 - - - -
190B PRO* 4.4 16.8 - - + -
196B ILE* 3.8 17.3 - - + +
197B CYS 3.0 17.6 + - - +
198B LYS 3.6 2.7 - - - +
200B CYS* 1.3 75.5 - - - +
202B LYS* 1.3 84.6 + - + +
204B TYR* 3.1 6.6 + - - +
205B MET* 2.9 44.1 + - + +
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Residues in contact with LYS 202 (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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187B TYR* 4.2 9.1 + - - -
198B LYS* 2.9 55.5 + - + +
199B ASN* 3.7 6.5 - - - +
201B PHE* 1.3 92.5 - - + +
203B TYR* 1.3 58.8 + - - +
205B MET* 3.2 6.5 + - - +
206B SER* 2.9 28.7 + - - -
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Residues in contact with TYR 203 (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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199B ASN 2.9 18.1 + - - +
200B CYS* 3.7 8.7 - - + +
201B PHE 3.2 0.2 - - - -
202B LYS* 1.3 76.6 - - - +
204B TYR* 1.3 65.1 + - - +
206B SER* 3.1 33.3 + - - -
207B ASP* 3.9 4.1 + - + +
223B CYS 4.0 11.0 - - - -
224B ALA* 3.6 29.9 + - + +
225B GLU* 3.8 28.0 + - + +
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Residues in contact with TYR 204 (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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189B HIS* 3.5 18.6 - + + -
190B PRO* 3.8 35.1 - - + +
191B SER* 3.6 10.2 + - - -
196B ILE* 5.4 2.5 - - + -
200B CYS 2.8 17.6 + - - +
201B PHE* 3.4 11.7 - - - +
203B TYR* 1.3 73.2 - - - +
205B MET* 1.3 71.0 + - + +
207B ASP 3.5 13.5 - - - +
209B ILE* 4.6 8.1 - - + +
221B ARG* 2.8 58.8 + - - -
222B TRP 4.7 2.7 - - - -
223B CYS 5.4 0.4 - - - -
224B ALA* 3.9 24.7 - - + +
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Residues in contact with MET 205 (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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190B PRO* 4.6 11.7 - - - -
201B PHE* 2.9 43.3 + - + +
202B LYS* 3.2 8.9 + - - +
204B TYR* 1.3 90.9 - - + +
206B SER* 1.3 66.9 + - - +
207B ASP 3.3 4.5 + - - +
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Residues in contact with SER 206 (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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202B LYS 2.9 13.8 + - - -
203B TYR* 3.1 30.5 + - - -
205B MET* 1.3 78.4 - - - +
207B ASP* 1.3 71.2 + - - +
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Residues in contact with ASP 207 (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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203B TYR* 3.9 5.0 + - + +
204B TYR 3.5 14.9 - - - +
205B MET* 3.9 4.0 - - - +
206B SER* 1.3 90.3 + - - +
208B ASP* 1.3 85.3 + - - +
209B ILE* 5.8 0.7 - - - +
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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