Contacts of the strand formed by residues 195 - 200 (chain B) in PDB entry 2Q41
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 TYR 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B LYS* 4.1 22.6 - - + -
124B VAL* 4.1 4.0 - - - -
125B LEU* 3.3 49.8 - - + -
148B ASP* 2.7 31.8 + - - -
186B PHE* 3.1 16.0 - + - -
190B ALA* 4.0 18.6 - - + +
191B ALA 5.5 0.2 - - - -
193B GLY 3.6 0.6 - - - -
194B SER* 1.3 102.7 - - - +
196B ASP* 1.3 63.8 + - - +
197B ALA 4.2 4.3 - - - +
198B VAL* 4.5 2.5 - - + -
224B ALA* 3.0 21.9 + - + +
225B LEU* 3.5 15.5 - - + +
226B ARG* 2.7 33.2 + - - +
229B GLY* 4.8 0.2 - - - -
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Residues in contact with ASP 196 (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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118B ILE* 3.6 7.5 - - + +
119B PRO 5.5 0.3 - - - +
120B ASN 4.9 2.1 - - - +
121B PRO* 4.3 12.9 - - + +
122B LYS* 3.0 21.5 + - - +
123B LYS* 2.9 40.2 + - - +
195B TYR* 1.3 74.7 - - - +
197B ALA* 1.3 60.9 + - + +
225B LEU* 4.1 1.6 - - - -
226B ARG* 2.7 58.0 + - - +
229B GLY* 3.7 0.5 - - - -
230B VAL 3.3 18.7 + - - -
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Residues in contact with ALA 197 (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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114B PRO* 4.9 2.7 - - + -
115B LEU* 3.6 31.0 - - + -
118B ILE* 4.4 2.2 - - + -
123B LYS 3.5 2.2 + - - -
124B VAL* 3.1 13.0 - - + +
125B LEU* 2.6 33.0 + - - +
195B TYR* 3.4 2.2 - - - -
196B ASP* 1.3 84.9 - - - +
198B VAL* 1.3 61.1 + - - +
199B ILE* 5.7 0.7 - - + -
225B LEU* 3.9 1.1 - - - -
230B VAL* 3.2 20.4 - - + +
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Residues in contact with VAL 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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114B PRO* 5.5 1.4 - - - +
125B LEU* 3.0 36.3 - - + +
127B ILE* 4.3 8.1 - - + -
187B LEU* 4.6 6.3 - - + -
195B TYR* 4.5 7.2 - - + -
197B ALA* 1.3 77.9 - - - +
199B ILE* 1.3 66.9 + - - +
200B VAL* 4.1 20.2 - - + -
221B VAL* 4.3 23.6 - - + +
224B ALA* 5.3 0.7 - - + -
225B LEU* 3.6 22.7 - - + -
230B VAL 3.4 4.3 + - - +
231B VAL* 3.5 4.1 - - + +
232B CYS* 3.2 24.8 + - - +
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Residues in contact with ILE 199 (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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110B ILE* 3.9 36.3 - - + +
111B THR* 4.3 13.5 - - + +
114B PRO* 5.0 8.3 - - + -
115B LEU* 4.8 4.7 - - + -
124B VAL* 4.4 8.3 - - + -
125B LEU 2.7 14.6 + - - +
126B VAL* 3.6 19.3 - - + -
127B ILE* 2.8 30.1 + - - +
134B VAL* 3.6 17.9 - - + -
138B VAL* 3.6 31.2 - - + -
197B ALA* 5.4 0.4 - - + -
198B VAL* 1.3 78.1 - - - +
200B VAL* 1.3 62.8 + - - +
201B ASP* 3.6 4.5 + - + +
232B CYS* 3.8 4.3 - - + +
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Residues in contact with VAL 200 (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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110B ILE* 4.5 1.4 - - - +
127B ILE* 4.2 8.5 - - + +
198B VAL* 4.1 15.0 - - + -
199B ILE* 1.3 76.6 - - - +
201B ASP* 1.3 57.6 + - - +
202B SER* 3.3 23.2 + - - +
212B LEU* 4.7 12.6 - - + +
217B PHE* 4.0 33.0 - - + -
218B PHE* 6.1 0.2 - - + -
221B VAL* 4.9 0.9 - - + -
231B VAL* 4.3 9.6 - - + -
232B CYS 2.9 11.5 + - - +
233B THR* 3.3 28.3 - - + +
234B GLN* 3.3 20.3 + - - +
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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