Contacts of the strand formed by residues 193 - 197 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 3.9 45.7 + - + +
160A LYS* 3.0 22.7 + - + +
161A VAL* 4.2 9.9 - - + -
162A LEU* 3.0 25.1 + - - +
192A LEU* 1.3 78.3 - - - +
194A LEU* 1.3 62.0 + - - +
195A ILE* 4.0 1.3 - - + -
220A GLU 3.8 12.3 - - - -
221A ARG* 3.6 21.1 - - + -
223A VAL* 5.6 0.7 - - + -
245A SER* 3.4 20.9 - - - -
247A GLU* 3.7 31.6 - - + -
248A ALA* 3.7 22.0 - - + -
251A ARG* 3.6 29.6 - - - +
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 3.7 15.9 - - + +
164A LEU* 4.7 14.1 - - + -
180A PHE* 5.8 1.6 - - + -
183A ALA* 4.4 7.9 - - + -
184A LEU* 4.0 32.5 - - + +
187A ALA* 4.3 15.5 - - + -
192A LEU 3.9 0.2 + - - -
193A TRP* 1.3 73.6 - - - +
195A ILE* 1.3 78.9 + - - +
196A HIS* 4.3 8.5 - - + +
212A PRO* 4.4 13.9 - - + -
221A ARG* 2.7 16.0 + - + +
222A VAL* 3.2 23.9 - - + +
223A VAL* 2.9 26.7 + - - +
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Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 4.0 15.5 - - + -
103A LEU* 3.8 36.3 - - + -
104A LEU* 3.9 20.9 - - + +
107A LEU* 4.5 11.7 - - + -
161A VAL* 3.8 25.6 - - + -
162A LEU 2.9 9.9 + - - +
163A LEU* 3.5 21.4 - - + +
164A LEU 3.0 23.9 + - - +
193A TRP* 5.2 0.2 - - + -
194A LEU* 1.3 80.1 - - - +
196A HIS* 1.3 65.1 + - - +
197A ASP 4.7 0.2 - - - +
223A VAL* 3.4 9.6 - - + +
225A LEU* 4.3 10.8 - - + -
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Residues in contact with HIS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.4 24.7 - - + -
165A ASN 3.9 0.2 - - - -
166A TYR 2.9 39.9 + - - -
180A PHE* 3.3 29.1 - + - -
194A LEU* 4.0 6.0 + - + -
195A ILE* 1.3 76.5 - - - +
197A ASP* 1.3 60.4 + - - +
198A ASN* 3.4 24.7 - - + +
212A PRO* 3.7 22.3 - - + +
222A VAL* 5.3 0.7 - - + -
223A VAL 2.9 10.1 + - - +
224A GLU* 3.0 27.1 + - + +
225A LEU 2.9 25.1 + - - -
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Residues in contact with ASP 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A SER* 4.0 14.0 + - - -
97A GLN* 5.4 1.2 - - - +
100A LEU* 4.5 8.5 - - + +
124A TYR* 2.5 39.2 + - + +
163A LEU* 5.0 3.1 - - + +
164A LEU 3.0 10.9 + - - +
165A ASN* 3.0 28.2 + - - -
195A ILE* 4.1 1.8 - - - +
196A HIS* 1.3 74.7 - - - +
198A ASN* 1.3 62.4 + - - +
199A PRO* 3.3 12.0 - - - +
225A LEU* 3.8 28.0 - - + +
501A EPE 2.8 16.8 + - - -
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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