Contacts of the strand formed by residues 288 - 294 (chain A) in PDB entry 5TSQ
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 THR 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A PHE* 4.3 18.2 - - + +
186A VAL* 3.3 17.0 - - + -
188A MET* 6.5 0.2 - - - -
258A ARG* 3.5 6.6 - - - +
259A VAL 2.7 41.9 + - - +
260A PRO* 3.8 0.7 - - - +
261A VAL* 3.5 23.3 + - + +
286A CYS* 3.4 11.2 - - - -
287A HIS* 1.3 110.4 - - + +
289A GLN* 1.3 61.7 + - - +
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A GLU* 5.3 1.2 + - - -
186A VAL 3.0 8.6 + - - +
187A THR* 2.8 32.3 + - + +
188A MET* 2.8 28.4 + - - +
247A TYR* 2.8 26.9 + - - -
256A THR* 2.8 26.4 + - - +
257A ASN 3.2 18.8 - - - +
258A ARG* 3.8 30.5 + - + +
259A VAL 4.4 0.9 - - - +
288A THR* 1.3 76.1 - - - +
290A VAL* 1.3 63.9 - - - +
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A CYS* 3.5 27.1 - - - -
188A MET* 3.5 28.3 - - + +
190A GLY 5.5 1.1 - - - +
192A ASP* 4.8 1.8 - - - +
256A THR* 3.3 2.8 - - - -
257A ASN* 2.8 34.8 + - - +
259A VAL* 3.6 15.0 - - + -
261A VAL* 3.6 29.6 - - + -
276A THR* 4.2 4.9 - - + -
278A PHE* 4.7 6.3 - - + -
289A GLN* 1.3 78.8 - - - +
291A ALA* 1.3 73.6 + - - +
292A SER* 4.7 0.2 - - - -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A THR* 5.3 1.1 - - + +
188A MET 3.0 18.0 + - - +
189A VAL* 4.1 7.4 - - + -
190A GLY 5.1 1.6 + - - -
192A ASP* 4.3 9.5 - - - +
193A LEU* 3.7 23.1 - - + +
254A MET* 3.5 32.3 - - - -
255A THR 3.3 7.9 - - - +
256A THR* 4.0 6.0 - - + +
289A GLN 4.4 0.2 + - - -
290A VAL* 1.3 84.3 - - - +
292A SER* 1.3 60.7 + - - +
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Residues in contact with SER 292 (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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192A ASP* 3.8 6.8 - - - +
193A LEU* 3.5 9.7 - - - +
196A GLN* 2.8 22.2 + - - -
255A THR* 2.8 21.6 + - - -
257A ASN* 4.0 23.0 + - - -
291A ALA* 1.3 76.1 - - - +
293A LYS* 1.3 62.1 + - - +
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Residues in contact with LYS 293 (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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193A LEU* 3.5 2.7 - - - -
196A GLN* 2.9 27.6 + - - +
254A MET* 3.0 7.3 - - - +
255A THR* 2.9 48.6 + - + +
292A SER* 1.3 76.4 - - - +
294A LEU* 1.3 75.8 + - - +
296A PHE* 6.0 0.8 - - - +
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Residues in contact with LEU 294 (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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193A LEU* 3.5 29.3 - - + +
196A GLN* 2.9 26.8 + - + +
197A ALA* 3.8 39.0 - - + +
243A CYS* 4.6 1.6 - - - -
253A VAL* 3.6 18.4 - - + +
254A MET* 4.5 6.7 - - + -
293A LYS* 1.3 94.5 + - - +
295A ASP* 1.3 64.5 + - - +
296A PHE* 3.2 16.6 + - + +
299A TYR* 4.0 32.8 - - + -
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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