Contacts of the strand formed by residues 277 - 281 (chain F) in PDB entry 3KDO
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 ALA 277 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141F PHE* 3.6 27.2 - - + -
146F VAL* 4.6 2.7 - - + -
149F MET* 4.2 5.4 - - + -
250F LYS 2.8 10.7 + - - +
251F HIS* 3.4 32.5 - - + +
252F ALA* 2.9 26.9 + - - +
276F LEU* 1.3 74.2 - - - +
278F ILE* 1.3 60.3 + - - +
311F ASP* 3.5 13.5 - - + +
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Residues in contact with ILE 278 (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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251F HIS* 5.0 0.2 - - - -
252F ALA* 3.4 10.1 - - + +
254F VAL* 4.5 16.2 - - + -
264F LEU* 6.4 0.2 - - + -
267F ILE* 5.8 2.2 - - + -
268F ARG* 3.7 46.2 - - + +
271F ALA* 3.9 22.0 - - + -
272F ALA 5.3 0.4 - - - +
276F LEU 4.0 2.7 - - - +
277F ALA* 1.3 76.9 - - - +
279F HIS* 1.3 66.0 + - - +
280F GLY 3.9 0.2 + - - -
309F GLY 3.9 9.0 - - - +
310F ILE* 3.9 24.7 - - + -
311F ASP* 2.8 24.7 + - - +
312F GLN* 2.9 29.4 + - - +
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Residues in contact with HIS 279 (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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187F TYR* 5.8 0.2 - - - -
189F KCX 3.5 23.2 - - + +
227F PHE* 3.8 32.7 - + + -
251F HIS* 5.0 1.5 - - + -
252F ALA 3.0 8.4 + - - +
253F MET* 3.3 17.8 - - + +
254F VAL 2.9 28.9 + - - +
277F ALA 4.0 1.0 + - - -
278F ILE* 1.3 73.4 - - - +
280F GLY* 1.3 61.5 + - - +
281F HIS 4.7 1.1 - - - -
312F GLN* 3.0 32.4 + - + +
314F HIS* 2.7 40.6 + + - -
365F THR* 3.7 20.0 - - + -
387F VAL* 5.2 0.9 - - + -
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Residues in contact with GLY 280 (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 VAL 3.5 6.1 - - - -
256F VAL* 3.9 10.5 - - - -
278F ILE* 5.1 0.7 - - - -
279F HIS* 1.3 71.2 - - - +
281F HIS* 1.3 59.7 + - - -
310F ILE* 3.6 16.9 - - - +
312F GLN 2.7 17.1 + - - +
313F LEU* 3.6 10.2 - - - +
314F HIS* 3.3 31.1 + - - -
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Residues in contact with HIS 281 (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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111C ASN* 3.0 27.4 - - - -
189F KCX 3.4 27.6 - - - -
192F GLU* 3.2 23.0 + - + +
253F MET* 3.9 10.1 - - + -
254F VAL 2.9 7.4 + - - +
255F ASP* 3.5 19.5 + - - +
256F VAL* 3.0 25.7 + - - +
257F VAL 4.0 0.5 + - - -
279F HIS* 3.8 2.3 + - + -
280F GLY* 1.3 73.0 - - - -
282F ARG* 1.3 60.2 + - - +
283F ALA* 3.0 31.1 + - + +
314F HIS* 4.0 16.2 - + + +
600F CAP 2.8 29.4 + - - -
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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