Contacts of the strand formed by residues 228 - 234 (chain G) in PDB entry 3QS7
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 ASP 228 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197G VAL 3.2 7.3 - - - +
199G CYS* 2.9 42.7 + - + +
227G THR* 1.3 75.5 - - - +
229G ILE* 1.3 61.2 + - - +
230G ARG* 3.8 1.9 + - - +
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Residues in contact with ILE 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G TRP* 3.8 17.3 - - + -
197G VAL 3.6 6.5 - - - +
198G LEU* 4.5 12.1 - - + +
221G LEU* 3.8 28.3 - - + -
223G GLU 5.9 0.4 - - - +
224G LEU* 3.9 21.8 - - - +
226G GLY* 3.3 30.3 - - - +
227G THR 4.2 4.0 - - - +
228G ASP* 1.3 68.4 - - - +
230G ARG* 1.3 63.8 + - - +
243G ARG* 3.8 1.9 - - - +
244G LEU* 2.9 57.1 + - + +
246G THR* 5.4 6.5 - - - -
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Residues in contact with ARG 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196G TRP* 4.3 4.0 - - - -
197G VAL* 2.9 39.7 + - + +
228G ASP 5.0 2.5 - - - +
229G ILE* 1.3 75.8 - - - +
231G CYS* 1.3 62.6 + - - +
232G CYS* 4.1 8.0 + - - -
241G CYS* 5.5 3.1 - - + -
242G THR 3.8 5.6 - - - +
243G ARG* 3.7 21.5 - - + +
244G LEU 4.3 0.9 - - - +
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Residues in contact with CYS 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G PRO* 3.7 4.8 - - + +
173G PHE* 3.7 17.7 - - + -
184G CYS* 2.0 50.9 - - - -
194G VAL* 3.7 14.1 - - - -
195G GLU 3.6 10.8 - - - -
196G TRP* 3.9 15.8 - - + -
230G ARG* 1.3 72.8 - - - +
232G CYS* 1.3 64.9 + - - +
241G CYS* 3.4 4.9 - - - +
242G THR 2.9 33.8 + - - +
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Residues in contact with CYS 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G PRO* 4.5 1.8 - - - -
193G ILE 3.1 4.5 - - - +
194G VAL* 3.5 2.2 - - - -
195G GLU* 2.9 44.1 + - + +
197G VAL* 5.5 8.5 - - + -
230G ARG* 4.8 9.0 - - - -
231G CYS* 1.3 76.6 - - - +
233G ALA* 1.3 59.5 + - - +
234G ARG* 5.5 1.6 - - + -
239G ARG* 5.6 2.7 - - + -
240G GLU 3.8 0.2 - - - -
241G CYS* 2.0 48.7 - - - -
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Residues in contact with ALA 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168G LEU* 4.2 12.8 - - + +
169G ARG 5.2 2.2 - - - +
171G PRO* 4.1 5.3 - - + +
186G SER* 3.6 30.5 - - - -
187G GLU 5.9 0.2 - - - +
192G PRO* 4.1 13.9 - - + -
193G ILE 3.4 5.4 - - - -
194G VAL* 4.8 0.7 - - - +
232G CYS* 1.3 72.2 - - - +
234G ARG* 1.3 58.8 + - - +
238G GLY 3.6 1.0 - - - +
239G ARG* 3.1 6.0 - - - +
240G GLU* 2.9 38.9 + - + +
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Residues in contact with ARG 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192G PRO* 3.4 4.5 - - - +
193G ILE* 2.8 46.8 + - + +
232G CYS* 5.4 2.2 - - + +
233G ALA* 1.3 74.1 - - - +
235G ASN* 1.4 59.2 - - - +
238G GLY 3.2 7.4 - - - +
239G ARG* 4.3 11.7 - - + -
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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