Contacts of the strand formed by residues 193 - 198 (chain B) in PDB entry 2QPA
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 THR 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLU 4.1 4.9 - - - +
127B LYS* 4.7 13.0 - - + +
128B PRO* 4.7 2.0 - - - -
187B ALA* 4.5 3.8 - - - -
191B ASN 5.7 0.2 - - - +
192B SER* 1.3 81.1 - - - +
194B PHE* 1.3 60.6 + - - +
195B PHE* 3.1 15.8 - - - -
224B ASN* 3.1 19.5 + - - +
225B LYS 6.0 0.4 - - - -
226B PRO* 2.9 17.0 + - + +
227B SER* 3.0 17.5 - - - -
228B ILE* 3.0 27.7 + - - +
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Residues in contact with PHE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 5.8 0.9 - - + -
125B SER* 3.2 4.4 - - - -
126B GLU* 2.8 58.3 + - + +
128B PRO* 3.4 21.3 - - + +
180B SER* 4.0 8.1 - - - -
183B ALA* 3.4 11.2 - - + -
184B LYS* 3.2 39.7 - - + -
187B ALA* 3.3 20.2 - - + -
193B THR* 1.3 69.3 - - - +
195B PHE* 1.3 69.2 + - - +
196B SER* 3.6 29.8 - - - -
228B ILE* 4.4 7.4 - - + -
230B PHE* 3.7 30.5 - + + -
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Residues in contact with PHE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE 5.7 0.2 - - - -
124B LEU 3.5 4.5 - - - -
125B SER* 4.0 22.2 - - - -
126B GLU 5.7 0.2 - - - -
193B THR* 3.1 38.4 - - - -
194B PHE* 1.3 77.4 - - - +
196B SER* 1.3 62.0 + - - +
217B LEU* 3.5 23.5 - - + +
220B MET* 3.6 34.8 - - + -
221B ALA* 3.6 23.6 - - + -
224B ASN* 3.9 15.7 - - + -
227B SER* 3.3 11.0 - - - -
228B ILE 3.3 19.1 + - - +
229B ILE* 3.8 4.5 - - + -
230B PHE 3.0 23.9 + - - +
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Residues in contact with SER 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 3.5 2.9 - - - -
124B LEU* 3.0 53.2 + - - +
180B SER* 5.2 2.3 + - - -
194B PHE* 3.6 24.9 - - - -
195B PHE* 1.3 75.2 - - - +
197B VAL* 1.3 75.8 + - - +
217B LEU* 4.1 1.4 - - - +
230B PHE* 3.5 22.6 - - - -
232B ASP* 5.1 2.6 + - - +
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA* 4.9 8.1 - - + +
123B ILE* 4.7 11.9 - - + +
196B SER* 1.3 84.3 + - - +
198B SER* 1.3 60.9 + - - +
199B SER 3.8 0.5 + - - -
202B LEU* 3.4 38.1 - - + -
217B LEU* 3.4 30.7 - - + -
230B PHE 3.2 13.1 + - - +
231B ILE* 3.7 15.2 - - + +
232B ASP* 3.0 22.6 + - - +
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Residues in contact with SER 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ALA 5.7 0.4 + - - -
197B VAL* 1.3 74.6 - - - +
199B SER* 1.3 56.4 + - - +
200B SER* 2.9 19.3 + - - -
201B ASP* 3.1 24.9 + - - +
202B LEU* 2.9 26.5 - - - +
232B ASP* 4.1 4.5 - - - -
233B GLN* 2.7 30.2 + - - +
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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