Contacts of the strand formed by residues 186 - 192 (chain A) in PDB entry 1EFX
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 LYS 186 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A HIS* 3.2 36.0 + - - +
185A PRO* 1.3 70.9 - - - +
187A THR* 1.3 63.0 + - - +
188A HIS* 4.3 2.9 - - - -
206A LEU* 3.2 40.3 + - + +
207A GLY 6.2 0.2 - - - +
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Residues in contact with THR 187 (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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185A PRO* 3.2 18.6 + - + +
186A LYS* 1.3 76.1 - - - +
188A HIS* 1.3 69.8 + - - +
203A CYS* 5.4 0.4 - - - -
204A TRP 3.0 14.8 - - - +
205A ALA* 4.0 11.2 - - + -
261A VAL* 3.9 24.9 - - + -
270A LEU* 3.6 22.9 - - + +
272A LEU* 4.2 16.9 - - - +
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Residues in contact with HIS 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LYS 4.3 7.2 - - - -
187A THR* 1.3 83.4 - - - +
189A VAL* 1.3 66.5 + - - +
190A THR* 3.8 15.8 - - + +
202A ARG 3.4 0.2 - - - +
203A CYS* 3.4 3.6 - - - -
204A TRP* 2.7 76.6 + + + +
206A LEU* 4.2 8.0 - - + +
272A LEU* 4.0 9.1 - - - +
14B PRO* 4.7 17.1 - - + +
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Residues in contact with VAL 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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188A HIS* 1.3 85.0 + - - +
190A THR* 1.3 68.0 + - - +
201A LEU* 3.7 31.6 - - + -
202A ARG 2.9 13.0 - - - +
203A CYS* 4.0 12.1 - - + -
217A TRP* 4.4 6.5 - - + -
272A LEU* 3.8 23.1 - - + +
273A ARG 4.1 13.1 + - - +
274A TRP* 3.8 37.9 + - + -
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Residues in contact with THR 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 HIS* 3.8 14.1 - - + +
189A VAL* 1.3 77.9 - - - +
191A HIS* 1.3 59.8 + - - +
192A HIS* 2.7 34.4 + - + -
200A THR 3.3 2.6 - - - +
201A LEU* 3.2 7.6 - - - -
202A ARG* 3.0 28.8 + - - +
204A TRP* 3.1 35.9 + - + +
98B ASP* 6.2 0.7 - - - -
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Residues in contact with HIS 191 (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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189A VAL 4.1 1.0 + - - -
190A THR* 1.3 72.2 - - - +
192A HIS* 1.3 66.0 + - - +
193A PRO* 3.7 21.0 - - + +
199A ALA* 3.1 34.3 - - + +
200A THR 3.7 3.3 + - - -
201A LEU* 4.8 6.1 - - + +
251A SER* 5.7 0.8 + - - -
254A GLU* 3.7 18.4 + - + +
274A TRP* 3.2 66.1 - + + +
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Residues in contact with HIS 192 (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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190A THR* 2.7 42.8 + - + +
191A HIS* 1.3 77.1 + - - +
193A PRO* 1.3 67.6 - - - +
194A VAL* 3.0 5.2 + - + +
199A ALA* 4.3 0.7 - - - -
200A THR* 2.8 46.0 + - + +
202A ARG* 4.4 10.7 + - - +
98B ASP* 3.0 51.8 + - + -
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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