Contacts of the strand formed by residues 193 - 197 (chain B) in PDB entry 2DOU
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 TRP 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 3.8 44.4 + - + +
160B LYS* 3.1 22.7 + - + +
161B VAL* 4.0 9.4 - - + +
162B LEU* 3.0 26.0 + - - +
192B LEU* 1.3 79.3 - - - +
194B LEU* 1.3 60.6 + - - +
195B ILE* 4.0 1.3 - - + -
220B GLU 3.7 11.9 - - - -
221B ARG* 3.5 19.5 - - + -
223B VAL* 5.5 0.9 - - + -
245B SER* 3.6 12.6 - - - -
247B GLU* 3.8 29.8 - - + -
248B ALA* 3.6 36.1 - - + -
251B ARG* 3.6 29.9 - - - +
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Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.5 23.3 - - + +
164B LEU* 5.1 9.4 - - + -
180B PHE* 5.9 1.6 - - + -
183B ALA* 4.3 8.5 - - + +
184B LEU* 4.1 28.9 - - + +
187B ALA* 4.3 11.0 - - + -
192B LEU 3.9 0.2 + - - -
193B TRP* 1.3 74.1 - - - +
195B ILE* 1.3 77.9 + - - +
196B HIS* 3.8 11.8 + - + +
212B PRO* 4.4 15.5 - - + -
221B ARG* 2.6 16.3 + - + +
222B VAL* 3.3 23.5 - - + +
223B VAL 3.1 24.6 + - - +
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Residues in contact with ILE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 4.2 5.4 - - + -
103B LEU* 3.7 40.2 - - + -
104B LEU* 3.9 22.0 - - + -
107B LEU* 4.5 11.9 - - + -
161B VAL* 3.7 27.4 - - + -
162B LEU 2.9 8.4 + - - +
163B LEU* 3.5 20.7 - - + +
164B LEU 3.1 24.6 + - - -
193B TRP 5.1 0.2 - - - -
194B LEU* 1.3 77.2 - - - +
196B HIS* 1.3 63.1 + - - +
223B VAL* 3.4 8.1 - - + +
225B LEU* 3.9 20.4 - - + -
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Residues in contact with HIS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LEU* 3.4 24.9 - - + -
165B ASN* 3.8 0.4 - - - -
166B TYR* 3.0 39.9 + + - -
180B PHE* 3.3 27.0 - + - -
194B LEU* 3.8 7.7 + - + +
195B ILE* 1.3 75.7 - - - +
197B ASP* 1.3 59.7 + - - +
198B ASN* 3.5 19.0 - - + +
210B PRO 4.9 0.2 - - - -
212B PRO* 3.6 23.6 - - + +
222B VAL* 5.3 0.4 - - + -
223B VAL 2.9 10.8 + - - +
224B GLU* 2.7 35.7 + - + +
225B LEU 2.8 24.7 + - - -
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Residues in contact with ASP 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B SER* 4.1 14.7 + - - +
97B GLN* 5.9 1.0 - - - -
100B LEU* 4.7 5.8 - - - +
124B TYR* 2.8 40.3 + - + +
163B LEU* 4.8 5.1 - - + +
164B LEU 3.0 11.9 + - - +
165B ASN* 2.9 29.6 + - + -
166B TYR 4.0 0.2 + - - -
195B ILE* 4.0 1.6 - - - +
196B HIS* 1.3 73.3 + - - +
198B ASN* 1.3 60.1 + - - +
199B PRO* 3.3 20.1 - - + +
225B LEU* 3.4 31.4 - - + +
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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