Contacts of the strand formed by residues 187 - 190 (chain A) in PDB entry 4KMR
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 VAL 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A THR* 4.6 5.6 - - + -
179A LEU* 3.8 35.4 - - + -
180A LEU* 4.1 27.4 - - + -
184A ARG 4.4 5.4 - - - +
185A ARG 3.8 1.4 + - - -
186A ARG* 1.3 76.5 - - - +
188A MSE 1.3 65.6 + - - +
208A TYR* 2.7 46.6 + - + -
212A LEU* 4.6 10.0 - - + +
223A LEU* 3.8 9.7 - - - +
251A ALA* 3.6 17.3 - - + +
253A PHE* 4.5 3.6 - - + -
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Residues in contact with MSE 188 (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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186A ARG 3.6 1.6 + - - -
187A VAL* 1.3 74.7 - - - +
189A LEU* 1.3 67.0 + - - +
190A LEU* 4.2 9.0 - - + +
208A TYR* 4.6 0.2 - - - -
222A ASP 3.9 4.9 - - - +
223A LEU* 3.2 20.8 - - + +
225A VAL* 3.8 23.8 - - + -
239A MSE 4.0 22.2 - - - +
242A VAL* 3.8 20.6 - - + -
247A VAL* 3.8 20.4 - - + -
249A MSE 3.6 24.9 - - + -
251A ALA 2.9 16.5 + - - +
252A VAL* 3.5 8.7 - - + -
253A PHE* 2.8 35.5 + - - +
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Residues in contact with LEU 189 (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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187A VAL 3.8 1.6 + - - -
188A MSE 1.3 74.1 - - - +
190A LEU* 1.3 58.7 + - - +
191A GLY 3.7 1.6 + - - -
192A ALA* 4.0 26.8 + - + -
204A ARG 5.2 1.6 - - - +
205A TYR* 4.0 24.5 - - + +
208A TYR* 3.9 42.6 - - + -
223A LEU 2.8 9.7 + - - +
224A VAL* 3.7 5.6 - - + -
225A VAL* 2.9 27.5 + - - +
253A PHE* 3.5 20.2 - - + -
255A MSE 3.3 35.0 - - + -
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Residues in contact with LEU 190 (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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188A MSE 3.8 9.4 - - + -
189A LEU* 1.3 70.4 - - - +
191A GLY* 1.3 57.3 + - - +
225A VAL* 3.8 29.4 - - + -
227A VAL* 3.8 16.4 - - + -
235A GLY* 4.3 11.7 - - - +
238A ALA* 4.0 9.9 - - + -
239A MSE 4.5 8.5 - - - +
242A VAL* 6.0 0.2 - - + -
252A VAL* 4.0 20.4 - - + -
253A PHE 3.0 10.9 + - - +
254A ALA* 3.5 10.5 - - + -
255A MSE 3.0 30.7 + - - +
259A LEU* 3.7 16.4 - - + +
263A ALA* 3.9 28.3 - - + -
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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