Contacts of the strand formed by residues 190 - 195 (chain F) in PDB entry 2QC8
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 190 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179F HIS* 4.0 28.5 - - + +
180F TYR* 3.8 33.9 - - + -
183F CYS* 3.9 20.6 - - + -
184F LEU* 3.0 32.5 - - + +
188F VAL* 2.9 9.0 + - - +
189F LYS* 1.3 71.9 - - - +
191F ALA* 1.3 53.5 + - - +
192F GLY 4.0 9.9 - - - +
193F THR* 4.5 1.3 - - + -
204F PHE* 4.0 17.5 - - + -
205F GLN 3.4 13.7 - - - +
206F ILE* 4.0 7.2 - - + -
46J THR* 2.7 28.9 + - - +
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Residues in contact with ALA 191 (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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189F LYS 3.3 2.0 + - - -
190F ILE* 1.3 68.8 - - - +
192F GLY* 1.3 54.4 + - - +
205F GLN* 2.8 21.6 + - + +
207F GLY 3.6 14.4 - - - +
501F ADP 3.5 35.0 - - - +
45J ARG* 3.3 7.4 - - - +
46J THR* 2.9 32.1 + - - +
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Residues in contact with GLY 192 (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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180F TYR* 3.4 12.0 + - - -
190F ILE* 3.6 4.6 - - - +
191F ALA* 1.3 78.9 - - - +
193F THR* 1.3 69.9 + - - +
204F PHE* 3.3 2.1 - - - +
205F GLN* 2.8 37.5 + - - -
44J THR 3.0 13.0 - - - -
45J ARG* 4.9 0.4 - - - -
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Residues in contact with THR 193 (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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176F VAL* 3.9 23.8 - - + +
179F HIS* 5.8 1.3 - - - +
180F TYR* 3.2 37.1 - - + -
190F ILE* 4.5 3.4 - - + -
192F GLY* 1.3 79.2 - - - +
194F ASN* 1.3 66.2 + - - +
203F GLU 3.3 15.5 - - - +
204F PHE* 3.9 10.3 - - + -
205F GLN* 3.4 3.3 + - - +
706F CL 3.2 15.4 - - - +
43J LYS* 3.6 1.9 - - - +
44J THR* 3.0 30.9 + - - +
90J ARG* 4.4 1.2 + - - -
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Residues in contact with ASN 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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162F TYR* 4.1 8.9 - - - -
163F CYS* 4.0 7.4 - - - -
193F THR* 1.3 76.5 - - - +
195F ALA* 1.3 81.1 + - - +
196F GLU* 3.6 10.7 + - - +
202F TRP* 3.6 7.0 - - - -
203F GLU* 2.9 53.0 + - - +
205F GLN* 3.1 27.2 + - - -
403F MN 4.2 2.8 + - - -
601F P3S 5.5 0.4 + - - -
706F CL 4.2 7.2 - - - -
42J CYS 5.3 0.4 - - - -
43J LYS* 3.7 25.4 + - + +
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Residues in contact with ALA 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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161F TYR 3.6 17.9 - - - +
162F TYR* 3.7 2.4 - - - -
163F CYS* 2.9 28.0 + - - +
164F GLY* 3.8 10.8 - - - +
169F ARG 6.1 0.2 - - - +
170F ALA* 5.8 2.5 - - + -
173F ARG* 5.6 0.2 - - - +
194F ASN* 1.3 82.2 + - - +
196F GLU* 1.3 60.5 + - - +
201F GLN 4.6 0.9 - - - +
202F TRP* 3.3 42.2 - - + -
42J CYS 5.3 0.6 + - - -
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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