Contacts of the strand formed by residues 420 - 426 (chain F) in PDB entry 2W8B
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 GLN 420 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171F VAL* 3.4 0.9 - - - -
172F GLN* 2.8 68.4 + - + +
397F MET 4.4 4.4 + - - +
398F GLY* 3.4 20.6 - - - -
399F SER* 2.9 37.8 + - - +
419F GLY* 1.3 74.8 - - - -
421F VAL* 1.3 63.4 + - - +
422F LYS* 4.7 8.2 + - - +
156G LEU* 4.9 14.3 - - - +
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Residues in contact with VAL 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F VAL* 5.0 3.6 - - + -
169F TYR* 4.7 6.1 - - + -
170F VAL 3.5 7.6 - - - +
171F VAL* 3.9 22.7 - - + -
399F SER* 2.9 29.9 + - - -
400F VAL* 3.2 11.9 + - - -
401F LEU* 3.2 41.7 - - + +
414F LEU 4.8 5.2 - - - +
416F ALA* 3.7 30.5 - - + -
419F GLY 3.6 3.5 + - - +
420F GLN* 1.3 81.5 - - - +
422F LYS* 1.3 62.0 + - - +
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Residues in contact with LYS 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F TYR* 3.4 5.0 - - - +
170F VAL* 2.9 37.3 + - + +
172F GLN* 3.0 39.2 + - - -
180F TYR* 5.7 2.2 - - - -
202F LEU 5.9 0.2 - - - -
378F GLU* 4.9 7.2 - - - +
392F SER* 3.9 17.3 - - - +
399F SER* 4.0 16.8 + - - +
401F LEU* 3.9 5.3 - - - +
420F GLN* 4.7 10.1 + - - +
421F VAL* 1.3 78.4 - - - +
423F PHE* 1.3 90.4 + - + +
424F PRO* 3.2 4.8 - - - -
150G LYS 5.9 0.6 + - - -
151G GLU* 3.9 22.1 + - - +
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Residues in contact with PHE 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ALA 3.6 2.4 - - - +
169F TYR* 3.6 1.9 - - - -
170F VAL* 3.7 17.9 - - + -
202F LEU 3.6 21.3 - - - -
203F MET* 3.9 8.5 - - + -
204F SER* 3.3 32.1 - - - -
205F PRO* 3.2 23.9 - - + +
378F GLU* 5.5 1.7 + - - -
379F THR* 4.3 19.8 + - + -
422F LYS* 1.3 103.4 - - + +
424F PRO* 1.3 72.2 - - - +
115G PRO* 3.5 29.2 - - + -
116G GLU* 5.7 0.2 - - + -
151G GLU* 3.4 38.4 - - - -
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Residues in contact with PRO 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168F ALA 3.0 10.3 - - - +
169F TYR* 4.2 0.7 - - + -
205F PRO* 5.2 0.5 - - - +
379F THR* 3.5 21.7 - - - +
381F SER* 4.0 9.7 - - - -
390F ILE* 3.8 24.2 - - + -
391F TYR* 3.7 34.8 - - - +
392F SER* 4.0 3.4 - - - -
401F LEU* 3.7 20.4 - - + -
422F LYS 3.2 6.7 - - - +
423F PHE* 1.3 94.3 - - - +
425F ALA* 1.3 61.0 + - - +
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Residues in contact with ALA 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F ILE* 3.3 3.5 - - - +
168F ALA* 2.8 34.1 + - + +
205F PRO* 3.3 34.3 - - + +
206F ALA* 4.7 1.6 - - - +
207F TRP* 3.0 23.2 + - + +
381F SER* 3.6 8.3 - - - +
390F ILE* 4.7 2.9 - - - -
424F PRO* 1.3 76.5 - - - +
426F TRP* 1.3 60.1 + - - +
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Residues in contact with TRP 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F ALA* 4.8 3.5 + - + -
165F THR* 3.0 22.3 + - - -
166F ARG 3.7 9.4 - - - -
167F ILE* 4.3 10.3 - - + -
187F TYR* 4.2 27.8 - + + +
207F TRP* 3.4 9.4 - - - +
381F SER* 2.8 14.6 + - - +
382F LEU 3.4 18.9 - - - +
383F ALA* 3.5 30.1 - - + -
384F PRO* 3.8 8.9 - - + +
388F MET* 3.5 27.8 - - + -
389F VAL 4.0 0.2 - - - -
390F ILE* 3.5 38.3 - - + +
403F LEU* 3.6 19.7 - - + -
425F ALA* 1.3 71.8 - - - +
427F SER* 1.3 84.5 + - - +
428F PRO* 4.5 0.2 - - - +
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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