Contacts of the strand formed by residues 294 - 300 (chain B) in PDB entry 3THW
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 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ASP* 2.9 40.8 + - - +
237B ALA* 3.2 17.1 - - + -
238B VAL* 2.8 26.5 + - - +
292B GLY 3.7 1.8 + - - -
293B TYR* 1.3 73.9 - - - +
295B VAL* 1.3 64.4 + - - +
324B LEU* 4.6 22.0 - - + -
325B TYR 3.6 4.5 - - - +
326B THR* 3.8 18.8 - - + -
445B ARG* 3.2 31.3 - - - +
447B GLU* 3.0 22.3 + - - -
500B TYR* 4.3 9.6 + - - -
503B GLU* 4.5 9.5 + - - -
504B PHE* 5.0 4.2 - - + -
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 3.4 13.5 - - + +
240B CYS* 4.3 17.3 - - - -
285B VAL* 4.0 28.0 - - + +
288B LEU* 3.8 35.0 - - + -
289B VAL* 4.2 11.2 - - + -
293B TYR* 4.3 4.7 - - + +
294B LYS* 1.3 79.6 - - - +
296B GLY* 1.3 70.3 + - - +
297B VAL* 4.6 3.6 - - + -
324B LEU* 3.2 6.4 - - - -
325B TYR* 2.7 43.3 + - + +
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Residues in contact with GLY 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ALA* 4.2 1.6 - - - +
238B VAL 2.7 14.4 + - - +
239B LEU* 3.5 7.3 - - - +
240B CYS* 2.9 28.4 + - - +
295B VAL* 1.3 74.5 - - - +
297B VAL* 1.3 63.3 + - - -
298B VAL 3.8 0.2 + - - -
321B LEU* 3.5 8.5 - - - -
323B ALA 3.5 8.1 - - - -
324B LEU* 3.5 16.2 - - - +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B CYS* 3.8 4.7 - - + -
247B TYR* 4.1 24.5 - - + +
281B LEU* 4.3 13.7 - - + -
285B VAL* 4.5 17.9 - - + -
295B VAL* 4.6 3.6 - - + -
296B GLY* 1.3 75.7 - - - +
298B VAL* 1.3 60.1 + - - +
299B LYS* 4.1 22.7 - - + -
321B LEU* 3.4 2.6 - - - +
322B THR* 3.0 33.6 + - - +
323B ALA* 3.0 13.6 + - + +
325B TYR* 3.8 29.8 - - + -
334B ASP* 4.6 4.7 - - + +
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B MET* 3.5 35.2 - - + -
239B LEU* 4.6 20.0 - - + -
240B CYS 2.7 18.7 + - - +
241B VAL* 4.0 19.5 - - + -
242B GLU* 2.8 29.1 + - - +
247B TYR* 3.9 2.4 - - - -
297B VAL* 1.3 72.9 - - - +
299B LYS* 1.3 61.1 + - - +
319B ARG* 3.7 9.4 - - + -
320B LYS 3.3 22.9 - - - +
321B LEU* 4.2 19.3 - - + -
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Residues in contact with LYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B GLU* 3.4 10.8 - - - +
247B TYR* 4.0 20.9 - - - +
297B VAL* 3.8 6.2 + - + -
298B VAL* 1.3 78.3 - - - +
300B GLN* 1.3 69.7 + - - +
301B THR* 4.4 1.5 - - - +
319B ARG* 3.3 7.0 - - - +
320B LYS 3.0 30.9 + - - +
322B THR* 3.7 33.5 + - + +
334B ASP* 2.8 41.0 + - - -
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Residues in contact with GLN 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B GLU* 2.6 53.4 + - - +
244B GLY* 3.3 24.3 + - - +
299B LYS* 1.3 79.5 - - - +
301B THR* 1.3 63.0 + - - +
302B GLU 4.3 10.4 + - - +
317B PHE* 4.1 26.3 - - + -
318B SER 3.6 6.7 - - - +
319B ARG* 3.3 20.9 + - + +
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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