Contacts of the strand formed by residues 193 - 199 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192F PRO* 1.3 70.4 - - - +
194F VAL* 1.3 65.4 + - - +
195F GLU* 3.8 5.7 - - + +
217F GLU* 4.8 14.1 - - + -
232F CYS 3.1 8.1 - - - +
233F ALA* 3.3 1.7 - - - -
234F ARG* 2.8 55.4 + - + +
235F ASN* 5.6 0.2 - - - -
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Residues in contact with VAL 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F CYS* 3.6 44.9 - - + +
186F SER* 4.2 25.4 - - - +
192F PRO* 3.6 16.9 + - + +
193F ILE* 1.3 76.6 - - - +
195F GLU* 1.4 58.0 + - - +
217F GLU* 3.8 5.2 - - - +
218F GLU 3.7 6.2 + - - -
219F LYS* 3.7 37.0 + - + +
231F CYS* 3.7 3.4 - - - -
232F CYS 3.6 3.1 - - - +
233F ALA* 5.0 1.1 - - + -
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Residues in contact with GLU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F ILE* 3.8 8.0 + - + +
194F VAL* 1.4 73.2 - - - +
196F TRP* 1.3 64.9 + - - +
197F VAL* 3.8 9.1 + - + +
215F LYS* 5.6 3.6 - - + -
216F LYS 4.7 1.3 - - - +
217F GLU* 3.7 24.5 - - + +
231F CYS* 3.6 2.8 - - - -
232F CYS* 2.9 45.6 + - + +
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Residues in contact with TRP 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F PHE* 3.3 35.9 - + - -
182F LEU* 3.7 20.2 - - + -
183F VAL 4.1 7.9 - - - -
184F CYS* 3.7 29.8 - - + +
195F GLU* 1.3 71.8 - - - +
197F VAL* 1.3 60.6 + - - +
198F LEU 4.2 0.8 + - - -
214F VAL 4.1 0.5 - - - +
216F LYS* 2.8 44.1 + - + +
218F GLU* 4.8 1.6 - - + -
219F LYS* 3.5 33.2 + - - -
220F VAL 4.0 1.6 - - - -
221F LEU* 3.5 60.6 - - + +
229F ILE* 3.8 23.6 - - + -
230F ARG 4.0 1.3 - - - -
231F CYS* 3.9 15.5 - - + -
244F LEU* 5.3 2.5 - - + -
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Residues in contact with VAL 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F GLU* 4.4 12.6 - - + +
196F TRP* 1.3 77.5 - - - +
198F LEU* 1.3 63.6 + - - +
199F CYS* 4.7 3.8 - - + +
213F VAL* 4.6 11.0 - - + -
214F VAL 3.4 19.3 - - - +
215F LYS* 3.8 20.6 - - + -
228F ASP 3.1 5.5 - - - +
229F ILE* 3.5 2.6 - - - -
230F ARG* 2.9 46.8 + - + +
232F CYS* 5.4 10.3 - - + -
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Residues in contact with LEU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F TRP 4.2 1.0 + - - -
197F VAL* 1.3 71.0 - - - +
199F CYS* 1.3 61.0 + - - +
213F VAL 3.9 0.2 - - - -
214F VAL* 2.9 36.3 + - + +
221F LEU* 5.7 6.3 - - + -
223F GLU 5.5 6.7 - - - +
225F PHE 5.8 1.8 - - - +
226F GLY 5.2 1.1 - - - +
227F THR* 4.5 9.4 - - - -
228F ASP 3.6 5.4 - - - -
229F ILE* 4.4 16.6 - - + +
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Residues in contact with CYS 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F VAL* 3.9 4.7 - - + -
198F LEU* 1.3 73.2 - - - +
213F VAL* 3.8 31.4 - - + +
227F THR* 3.1 16.3 - - - -
228F ASP* 2.9 47.3 + - + +
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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