Contacts of the strand formed by residues 266 - 270 (chain F) in PDB entry 1K9I
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 ASN 266 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261F THR 3.7 0.5 - - - +
262F PHE* 3.4 5.8 - - - -
263F PHE 2.7 40.4 + - - +
264F GLN* 3.5 17.6 + - - +
265F GLY* 1.3 84.0 - - - +
267F CYS* 1.3 63.7 + - - +
268F TYR* 3.6 21.0 + - + +
299F GLU* 5.7 0.6 - - - -
378F LYS* 3.8 24.9 - - + +
379F LYS 3.8 3.9 - - - +
380F SER* 3.7 19.9 + - - -
381F ALA 4.0 0.9 - - - +
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Residues in contact with CYS 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255F PRO 3.6 0.9 - - - -
256F CYS* 2.0 54.1 - - + -
257F PRO* 4.1 6.1 - - + -
260F TRP* 3.6 19.4 - - + -
261F THR 3.4 4.0 - - - -
266F ASN* 1.3 72.7 - - - +
268F TYR* 1.3 64.3 + - - +
378F LYS* 3.3 7.3 - - - +
379F LYS* 2.8 38.5 + - + +
380F SER 4.5 1.8 - - - -
381F ALA* 3.5 24.7 - - - -
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Residues in contact with TYR 268 (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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260F TRP* 3.4 7.5 - - - -
261F THR* 2.7 49.9 + - - +
263F PHE* 3.6 23.5 - - + -
266F ASN* 3.6 30.0 + - + +
267F CYS* 1.3 76.2 - - - +
269F PHE* 1.3 61.8 + - - +
270F MET* 4.2 17.9 + - + +
292F VAL* 3.8 7.6 - - + -
299F GLU* 2.6 35.1 + - + +
302F PHE* 3.9 20.0 - + + -
303F LEU* 4.0 17.0 - - + -
376F ILE* 4.1 4.9 - - + -
377F CYS 3.3 13.5 - - - +
378F LYS* 3.3 31.0 - - + -
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Residues in contact with PHE 269 (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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258C TRP* 3.4 35.0 - + - -
259C GLU* 3.9 23.1 - - + -
269C PHE* 4.8 16.4 - + - -
272C ASN* 4.0 21.1 - - - +
258F TRP 5.9 0.2 - - - -
259F GLU* 4.9 2.0 - - + -
260F TRP* 3.6 46.2 - + + +
268F TYR* 1.3 75.5 - - - +
270F MET* 1.3 62.4 + - - +
271F SER* 3.5 28.4 + - - -
272F ASN* 5.1 1.6 - - + -
375F TRP* 4.7 1.8 - + - -
376F ILE* 3.2 6.5 - - - -
377F CYS* 3.1 35.0 + - + -
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Residues in contact with MET 270 (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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272C ASN* 3.7 35.6 + - + +
261F THR* 3.4 32.1 - - + +
268F TYR* 4.2 18.8 - - + +
269F PHE* 1.3 79.5 - - - +
271F SER* 1.3 68.2 + - - +
272F ASN* 5.0 2.6 - - - -
302F PHE* 5.1 1.3 - - + -
303F LEU* 5.7 0.4 - - - -
306F GLN* 3.3 41.3 - - + +
312F ARG* 5.3 1.3 + - - +
375F TRP 3.8 4.3 - - - -
376F ILE* 3.9 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