Contacts of the strand formed by residues 263 - 266 (chain F) in PDB entry 3KQG
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 263 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257F LYS* 3.4 1.8 - - - -
258F ALA 3.1 37.0 + - - +
259F GLY* 5.9 1.1 - - - -
261F GLU* 3.9 28.5 - - - +
262F GLY* 1.3 77.9 - - - +
264F TRP* 1.3 67.4 + - - +
265F SER* 3.5 2.6 + - - -
274F LYS* 5.1 11.8 - - - +
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Residues in contact with TRP 264 (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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255F LEU* 4.0 11.4 - - + -
256F THR* 3.7 20.9 - - - -
257F LYS* 3.9 25.0 - - + +
262F GLY 4.8 4.9 - - - -
263F ASP* 1.3 76.2 - - - +
265F SER* 1.3 59.4 + - - +
272F PHE* 3.4 45.4 - + + +
274F LYS* 5.4 12.7 - - - +
281F TRP* 3.6 28.7 - + - -
286F PRO* 3.3 22.1 - - + +
293F GLU 3.9 1.1 - - - -
294F HIS* 3.7 26.7 - - - -
295F CYS* 3.7 31.0 - - - -
296F GLY 3.9 3.6 - - - -
308F ASP* 3.7 17.7 - - + -
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Residues in contact with SER 265 (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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254F GLY 3.4 2.1 - - - +
255F LEU* 3.6 6.6 - - - +
256F THR* 2.9 45.0 + - - +
258F ALA* 3.9 19.6 - - - +
263F ASP* 4.3 3.6 - - - -
264F TRP* 1.3 76.7 - - - +
266F TRP* 1.3 69.4 + - - +
267F VAL* 4.1 0.3 + - - -
272F PHE* 4.0 11.0 - - - -
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Residues in contact with TRP 266 (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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231F THR 3.6 7.6 - - - -
232F SER* 3.4 27.4 - - - -
233F VAL* 3.3 45.7 + - + -
253F ILE* 4.0 5.2 - - + -
254F GLY* 3.4 20.2 - - - -
255F LEU* 3.6 26.9 - - + -
265F SER* 1.3 81.7 + - - +
267F VAL* 1.3 64.5 + - - +
268F ASP* 3.4 18.6 - - - +
269F ASP* 3.1 17.2 + - - +
270F THR* 3.1 37.7 + - + +
271F PRO 4.4 0.8 + - - -
272F PHE* 3.4 33.4 - + - +
273F ASN 4.9 1.2 - - - +
276F GLN* 5.9 0.2 + - - -
277F SER* 4.8 1.7 + - - -
306F TRP* 3.6 25.4 - + - -
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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