Contacts of the strand formed by residues 193 - 199 (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 ILE 193 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192G PRO* 1.3 68.6 - - - +
194G VAL* 1.3 60.4 + - - +
195G GLU* 3.7 3.8 + - + +
232G CYS 3.1 8.3 - - - +
233G ALA* 3.4 1.0 - - - -
234G ARG* 2.8 45.2 + - + +
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Residues in contact with VAL 194 (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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184G CYS* 3.5 44.9 - - + +
186G SER* 4.1 25.4 - - - +
192G PRO* 3.6 16.3 + - + +
193G ILE* 1.3 71.7 - - - +
195G GLU* 1.3 58.4 + - - +
196G TRP* 5.4 0.2 - - - +
217G GLU* 3.8 6.9 - - - +
218G GLU 3.6 17.8 + - - -
219G LYS* 3.6 26.6 + - + +
231G CYS* 3.7 3.6 - - - -
232G CYS 3.5 3.4 - - - +
233G ALA* 5.0 0.4 - - - -
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Residues in contact with GLU 195 (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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193G ILE* 3.7 5.4 + - + +
194G VAL* 1.3 73.7 - - - +
196G TRP* 1.3 64.4 + - - +
197G VAL* 3.8 10.6 + - + +
215G LYS* 5.6 3.4 - - + -
216G LYS 4.7 1.3 - - - +
217G GLU* 3.7 24.7 - - + +
231G CYS* 3.6 2.8 - - - -
232G CYS* 2.9 44.6 + - + +
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Residues in contact with TRP 196 (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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173G PHE* 3.4 35.0 - + - -
182G LEU* 3.7 23.1 - - + -
183G VAL 4.1 5.4 - - - -
184G CYS* 3.8 28.5 - - + +
195G GLU* 1.3 72.1 - - - +
197G VAL* 1.3 60.4 + - - +
198G LEU 4.2 0.8 + - - -
214G VAL 4.1 0.5 - - - +
216G LYS* 2.8 44.9 + - + +
218G GLU* 4.8 1.3 - - + -
219G LYS* 3.5 37.7 + - - -
220G VAL 3.9 2.0 - - - -
221G LEU* 3.5 46.4 - - + +
229G ILE* 3.8 30.7 - - + -
230G ARG 4.0 1.8 - - - -
231G CYS* 3.9 15.9 - - + -
244G LEU* 5.3 1.8 - - + -
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Residues in contact with VAL 197 (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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195G GLU* 4.4 13.2 - - + +
196G TRP* 1.3 78.8 - - - +
198G LEU* 1.4 63.3 + - - +
199G CYS* 4.7 4.5 - - + +
213G VAL* 4.7 10.8 - - + -
214G VAL 3.5 16.4 - - - +
215G LYS* 3.9 19.3 - - + -
228G ASP 3.2 5.0 - - - +
229G ILE* 3.6 2.8 - - - -
230G ARG* 2.9 44.0 + - + +
232G CYS* 5.5 9.6 - - + -
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Residues in contact with LEU 198 (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 4.2 1.2 + - - -
197G VAL* 1.4 70.2 - - - +
199G CYS* 1.3 61.4 + - - +
214G VAL* 2.9 41.0 + - + +
221G LEU* 5.8 6.1 - - + -
223G GLU 5.6 6.1 - - - +
225G PHE 5.8 1.8 - - - +
226G GLY 5.2 1.1 - - - +
227G THR* 4.5 8.5 - - - -
228G ASP 3.5 5.6 - - - -
229G ILE* 4.5 16.6 - - + +
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Residues in contact with CYS 199 (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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197G VAL* 4.0 4.7 - - + -
198G LEU* 1.3 75.0 - - - +
213G VAL* 3.8 31.0 - - + +
227G THR* 3.0 16.0 - - - -
228G ASP* 2.9 47.6 + - + +
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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