Contacts of the strand formed by residues 356 - 360 (chain G) 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 CYS 356 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277G TRP* 3.2 38.6 - - + -
315G TRP* 3.5 26.9 - - + -
318G LEU 3.9 2.5 - - - -
319G SER* 4.3 0.4 - - - -
321G LEU* 4.2 1.8 - - - -
327G TRP* 3.9 4.7 - - - -
354G GLU 3.6 0.4 - - - -
355G ASP* 1.3 80.5 - - - +
357G ALA* 1.3 61.1 + - - +
365G ASN 3.8 0.2 - - - +
366G ASP* 3.2 2.8 - - - -
367G ASP 2.7 32.5 + - - +
369G CYS* 2.0 46.2 - - - -
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Residues in contact with ALA 357 (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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315G TRP* 3.3 7.9 - - - -
316G MET* 3.2 34.6 + - + +
318G LEU* 3.0 45.9 + - + +
327G TRP* 3.8 9.2 - - + -
343G TRP* 4.3 9.2 - - + -
356G CYS* 1.3 73.3 - - - +
358G GLU* 1.3 60.4 + - - +
364G TRP* 5.4 1.1 - - + -
365G ASN 3.5 6.7 - - - +
366G ASP* 4.5 0.4 - - - +
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Residues in contact with GLU 358 (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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313G PHE* 3.2 23.8 - - - +
314G THR 2.9 19.7 - - - +
315G TRP* 3.8 11.0 - - + -
316G MET* 3.8 7.4 - - - -
357G ALA* 1.3 76.6 - - - +
359G PHE* 1.3 62.6 + - - +
360G SER* 3.7 9.2 + - - -
364G TRP* 3.3 5.2 - - - +
365G ASN* 2.9 65.1 + - + +
367G ASP* 4.2 3.1 - - + +
373G LYS* 2.8 39.9 + - - +
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Residues in contact with PHE 359 (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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292G VAL* 4.4 9.6 - - + -
294G ILE* 3.8 12.8 - - + -
300G GLN* 3.7 19.5 - - - -
303G LEU* 3.6 31.4 - - + -
304G GLN* 3.4 30.3 - - - +
307G SER* 3.4 28.3 - - - +
312G ARG 3.9 2.4 - - - +
313G PHE* 3.5 8.5 - - - -
314G THR* 2.6 45.4 + - + +
315G TRP 4.5 1.8 - - - -
316G MET* 3.4 37.9 - - + -
358G GLU* 1.3 73.6 - - - +
360G SER* 1.3 57.7 + - - +
361G GLY 4.2 0.4 - - - -
363G GLY 3.6 3.4 - - - -
364G TRP* 4.1 0.2 - + - -
376G ILE* 4.7 6.7 - - + -
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Residues in contact with SER 360 (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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312G ARG 5.6 0.2 - - - -
313G PHE* 3.2 24.1 - - - -
344G ASN* 2.9 35.7 + - - -
358G GLU* 3.4 18.8 + - - -
359G PHE* 1.3 75.4 - - - +
361G GLY* 1.3 65.7 + - - +
362G ASN 3.1 0.5 + - - -
363G GLY 2.7 17.5 + - - +
365G ASN* 3.8 13.8 + - - +
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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