Contacts of the strand formed by residues 230 - 235 (chain I) in PDB entry 1QDU
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 PHE 230 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164I TYR* 3.6 16.2 - - + -
166I LEU* 3.8 36.3 - - + -
218I TYR* 4.1 12.3 - + + -
224I HIS* 4.1 14.6 - + - +
229I CYS* 1.3 78.0 - - - +
231I ILE* 1.3 73.6 + - - +
232I CYS* 4.0 18.6 - - + -
265I PHE* 3.3 48.9 - + - -
273I LEU* 3.9 24.9 - - + -
277I PRO 3.2 6.5 + - - +
278I LYS* 3.6 5.2 - - + -
279I VAL 2.9 25.6 + - - +
280I PHE* 4.3 9.9 - + - -
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Residues in contact with ILE 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164I TYR 2.9 9.2 + - - +
165I CYS* 3.0 13.2 - - - -
166I LEU* 2.7 25.5 + - - +
193I PHE* 3.4 31.6 - - + -
198I PHE* 3.6 30.5 - - + -
229I CYS* 3.8 6.1 - - - -
230I PHE* 1.3 84.9 - - - +
232I CYS* 1.3 64.3 + - - +
233I CYS* 3.8 22.4 - - - -
279I VAL* 3.3 13.7 - - + +
281I PHE* 3.9 19.5 - - + -
400J PHE* 4.2 12.3 - - + -
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Residues in contact with CYS 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166I LEU* 3.8 13.0 - - + -
168I ILE* 4.9 2.5 - - - -
215I LEU* 4.0 21.1 - - - -
230I PHE* 4.0 16.6 - - + -
231I ILE* 1.3 76.7 - - - +
233I CYS* 1.3 62.6 + - - +
234I ILE* 4.1 20.3 + - - +
279I VAL 2.8 9.6 + - - +
280I PHE* 3.2 36.0 - - + +
281I PHE 3.0 22.5 + - - -
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Residues in contact with CYS 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I CYS* 4.2 9.6 - - - -
166I LEU 2.8 21.2 + - - +
167I ILE* 4.1 9.6 + - + -
168I ILE* 2.8 29.4 + - - +
189I LEU* 4.4 20.0 - - + -
193I PHE* 4.8 2.0 - - - -
231I ILE* 3.8 20.0 - - - -
232I CYS* 1.3 77.6 - - - +
234I ILE* 1.3 66.4 + - - +
235I LEU* 4.3 10.8 - - + -
281I PHE* 3.8 24.2 - - + +
350J ILE* 6.2 0.2 - - + -
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Residues in contact with ILE 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168I ILE* 3.4 28.5 - - + +
211I ILE* 4.9 4.7 - - + -
215I LEU* 5.4 0.7 - - + -
232I CYS* 4.1 20.9 - - - -
233I CYS* 1.3 80.3 - - - +
235I LEU* 1.3 70.3 + - - +
236I SER* 4.6 3.1 - - - -
243I ILE* 3.9 29.6 - - + -
261I LEU* 3.6 33.4 - - + -
280I PHE* 5.4 1.3 - - + -
281I PHE 3.1 7.7 + - - +
282I ILE* 4.4 22.2 - - + -
283I GLN 2.7 32.2 + - - +
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Residues in contact with LEU 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167I ILE* 4.7 3.6 - - + -
168I ILE 3.0 13.5 + - - +
169I ASN* 4.2 11.9 - - + +
170I ASN 2.9 28.8 + - - -
179I ARG* 3.6 9.1 + - - +
182I THR* 3.5 22.7 - - + -
185I ASP* 3.6 28.7 - - + -
186I ALA* 4.0 11.2 - - - +
189I LEU* 4.0 19.3 - - + -
233I CYS* 4.5 5.8 - - + -
234I ILE* 1.3 88.8 - - - +
236I SER* 1.3 62.1 + - - +
281I PHE 4.6 0.7 - - - +
283I GLN* 3.5 19.5 - - + +
350J ILE* 4.2 8.5 - - + -
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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
------------------------------------------------------------
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