Contacts of the strand formed by residues 293 - 299 (chain B) in PDB entry 4WGK
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 ASP 293 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285B LYS* 4.3 3.1 + - - -
286B MET 4.2 1.1 - - - -
287B VAL* 3.9 9.6 - - - +
291B GLY 4.4 3.8 - - - +
292B ASP* 1.3 74.1 - - - +
294B LEU* 1.3 64.9 + - - +
330B LYS* 3.4 24.4 - - + +
340B PRO* 5.7 2.9 - - - +
341B PHE* 3.6 23.4 + - + +
412B TYR* 2.8 36.8 + - - +
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Residues in contact with LEU 294 (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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104B ILE* 4.2 32.3 - - + +
106B VAL* 3.5 26.2 - - + +
239B LYS* 3.9 37.0 - - + +
241B GLY* 5.3 0.2 - - - -
286B MET* 2.9 18.3 + - + +
287B VAL* 3.6 22.4 - - - +
288B ASP* 3.6 26.9 - - + +
292B ASP* 5.1 0.7 - - + -
293B ASP* 1.3 80.1 - - - +
295B GLY* 1.3 56.8 + - - +
340B PRO 3.9 1.0 - - - +
341B PHE* 3.5 9.2 - - - -
342B VAL 3.3 16.5 + - - -
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Residues in contact with GLY 295 (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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106B VAL* 4.6 5.6 - - - -
142B PHE* 4.6 0.2 - - - -
286B MET* 3.0 37.2 + - - +
294B LEU* 1.3 83.3 - - - +
296B LEU* 1.3 63.4 + - - +
341B PHE* 3.5 12.0 - - - -
342B VAL* 3.1 13.5 - - - -
412B TYR* 3.7 4.9 - - - -
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Residues in contact with LEU 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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142B PHE* 3.5 7.8 - - - -
283B VAL* 4.4 7.6 - - + -
284B LEU 3.1 12.6 - - - +
286B MET* 3.6 2.7 - - - +
295B GLY* 1.3 75.2 - - - +
297B ILE* 1.3 77.8 + - - +
298B SER* 4.1 11.7 - - - +
326B LEU* 4.0 38.1 - - + -
330B LYS* 5.6 1.3 - - - +
341B PHE* 3.7 18.6 - - + -
342B VAL 3.0 6.5 + - - -
343B ALA* 3.6 9.8 - - + -
344B ALA 3.0 27.3 + - - +
408B ALA* 5.0 3.4 - - + +
412B TYR* 3.5 35.0 - - + -
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Residues in contact with ILE 297 (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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142B PHE* 3.8 31.2 - - + -
144B MET* 5.8 3.1 - - + -
155B PHE* 3.8 38.1 - - + -
282B ILE 3.5 1.2 - - - +
283B VAL* 3.3 4.2 - - - +
284B LEU* 2.7 47.8 + - + +
286B MET* 3.8 13.2 - - + -
296B LEU* 1.3 80.8 - - - +
298B SER* 1.3 64.2 + - - +
299B TRP* 3.6 37.1 - - + -
344B ALA* 3.3 8.1 - - + +
346B ALA* 4.0 7.2 - - + -
529B LEU* 6.1 0.4 - - + -
534B ILE* 5.9 0.4 - - + -
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Residues in contact with SER 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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281B MET* 3.3 21.0 - - - +
282B ILE 3.5 4.3 - - - -
283B VAL* 4.4 7.9 - - - -
296B LEU* 4.1 10.5 - - - -
297B ILE* 1.3 75.3 - - - +
299B TRP* 1.3 57.2 + - - +
300B PHE 3.8 0.7 + - - -
344B ALA 2.9 8.9 + - - -
345B PHE* 3.3 44.2 - - - -
346B ALA 2.7 29.6 + - - +
408B ALA* 4.7 1.1 - - - -
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Residues in contact with TRP 299 (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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155B PHE* 3.9 12.7 - + - -
280B GLU 4.1 1.8 - - - +
281B MET* 3.5 4.2 - - - +
282B ILE* 3.0 54.4 + - + +
284B LEU* 4.1 17.9 - - + -
297B ILE* 3.6 38.4 - - + -
298B SER* 1.3 70.7 - - - +
300B PHE* 1.3 64.4 + - - +
346B ALA* 3.4 22.8 - - + +
347B SER 3.7 6.7 - - - -
348B SER* 4.8 6.3 - - - +
532B LEU* 4.5 11.0 - - + -
534B ILE* 3.6 37.0 - - + -
568B VAL* 3.8 28.4 - - + +
569B ILE 3.6 21.1 - - - -
570B SER* 3.9 16.6 - - - -
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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