Contacts of the strand formed by residues 200 - 204 (chain G) in PDB entry 2ABJ
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 VAL 200 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198G ASN 4.1 4.7 - - - +
199G PRO* 1.3 79.1 - - - +
201G SER* 1.3 62.0 + - - +
202G LEU* 3.9 20.9 - - + -
241G GLN* 3.6 26.9 - - + -
242G GLN* 5.0 5.2 - - + -
259G MET* 5.6 0.9 - - + -
328G SER* 5.3 1.1 - - - +
336G CYS* 3.7 26.7 - - - -
337G PRO 3.0 19.5 + - - +
338G VAL* 3.6 11.9 - - + +
339G SER* 3.0 25.7 + - - -
340G ASP 3.7 0.9 + - - -
3401G CBC 4.0 15.5 - - + -
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Residues in contact with SER 201 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G VAL* 1.3 73.8 - - - +
202G LEU* 1.3 62.2 + - - +
239G GLY 4.3 4.5 - - - -
240G CYS* 3.5 20.9 - - - +
241G GLN* 2.6 43.2 + - - +
242G GLN 3.4 6.8 + - - -
339G SER* 4.3 1.4 + - - -
340G ASP* 3.5 30.2 + - - +
342G LEU* 5.1 3.7 - - - +
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Residues in contact with LEU 202 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200G VAL* 3.9 19.5 - - + -
201G SER* 1.3 74.6 - - - +
203G TRP* 1.3 56.5 + - - +
204G ALA 3.9 0.4 + - - -
240G CYS* 3.7 5.6 - - - -
242G GLN* 3.3 32.1 - - + +
243G VAL 4.7 0.9 - - - +
244G LEU* 4.0 26.5 - - + -
256G VAL* 3.7 33.9 - - + -
259G MET* 6.1 0.2 - - + -
326G MET* 4.7 2.7 - - - -
338G VAL* 3.8 31.0 - - + -
340G ASP 2.9 9.9 + - - +
341G ILE* 3.3 12.1 - - + +
342G LEU 2.8 31.5 + - - -
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Residues in contact with TRP 203 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G LEU* 1.3 72.0 - - - +
204G ALA* 1.3 63.4 + - - +
205G ASN* 3.6 32.3 + - + -
208G TYR* 4.8 1.6 - + - -
231G ALA 5.2 2.5 - - - -
234G GLU* 2.6 45.5 - - + -
235G ASP* 2.7 31.8 + - - +
238G ASN* 3.4 36.1 + - + +
240G CYS* 3.5 15.1 - - - -
242G GLN 3.0 7.1 + - - -
243G VAL* 3.6 10.4 - - + +
244G LEU* 3.0 21.2 + - - +
342G LEU* 3.4 34.0 - - + +
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Residues in contact with ALA 204 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G LEU 3.9 0.2 + - - -
203G TRP* 1.3 75.7 - - - +
205G ASN* 1.3 59.8 + - - +
206G PRO* 3.9 3.9 - - - +
244G LEU* 4.0 18.8 - - + -
246G LEU* 4.1 10.8 - - + -
311G MET* 5.0 0.4 - - + -
341G ILE* 3.9 17.9 - - + -
342G LEU 2.8 23.5 + - - +
343G TYR* 3.5 30.9 - - + -
344G LYS 4.6 2.1 + - - -
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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