Contacts of the helix formed by residues 276 - 286 (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 ASN 276 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275G ARG* 1.3 75.7 - - - +
277G TRP* 1.3 62.4 + - - +
278G HIS* 3.3 8.6 + - - +
279G ASP* 2.7 53.7 + - - +
280G SER* 2.8 23.4 + - - -
315G TRP* 3.4 1.1 - - - -
369G CYS 3.3 13.2 - - - +
370G ASN* 3.7 18.8 + - - +
371G LEU 3.4 9.9 - - - -
372G ALA* 3.7 4.1 - - + +
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Residues in contact with TRP 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G ASN* 1.3 73.7 - - - +
278G HIS* 1.3 81.6 + + - +
280G SER* 3.3 4.9 + - - -
281G ILE* 3.1 49.6 + - + +
291G LEU* 3.6 12.8 - - + +
315G TRP* 3.3 27.7 - + + +
316G MET 3.1 21.2 + - - -
317G GLY* 4.4 0.7 - - - -
318G LEU 4.1 8.3 + - - -
319G SER* 3.6 26.5 - - - -
321G LEU* 3.4 23.6 - - + -
330G VAL* 3.6 26.9 - - + -
356G CYS* 3.2 37.6 - - + -
357G ALA 4.9 0.2 + - - -
369G CYS* 3.1 14.6 + - + +
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Residues in contact with HIS 278 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G ASN* 3.3 7.6 + - - +
277G TRP* 1.3 102.9 - + - +
279G ASP* 1.3 67.5 + - - +
281G ILE* 2.9 14.9 + - + +
282G THR* 2.9 28.2 + - + +
321G LEU* 3.9 20.1 - - + +
369G CYS* 4.7 12.5 + - + +
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Residues in contact with ASP 279 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G ARG* 3.7 32.2 + - + +
276G ASN* 2.7 42.2 + - - +
278G HIS* 1.3 72.2 - - - +
280G SER* 1.3 55.8 + - - +
282G THR* 2.9 12.7 + - - +
283G ALA* 2.7 37.4 + - - +
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Residues in contact with SER 280 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G ARG* 3.7 2.2 + - - +
276G ASN 2.8 19.8 + - - -
277G TRP 3.5 8.7 - - - -
278G HIS 3.2 0.2 - - - -
279G ASP* 1.3 76.4 - - - +
281G ILE* 1.3 64.4 + - - +
283G ALA* 3.2 7.9 + - - +
284G CYS* 2.9 28.1 + - - -
291G LEU* 4.1 12.1 - - - -
315G TRP* 3.3 16.1 - - - -
375G TRP* 3.6 40.3 + - - -
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Residues in contact with ILE 281 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G TRP* 3.1 52.9 + - + +
278G HIS* 2.9 15.8 + - + +
280G SER* 1.3 76.6 - - - +
282G THR* 1.3 67.3 + - + +
284G CYS* 3.1 15.1 + - - +
285G LYS* 3.4 39.4 + - - +
291G LEU* 3.7 26.8 + - + +
330G VAL* 4.2 11.4 - - + -
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Residues in contact with THR 282 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G HIS* 2.9 18.4 + - + +
279G ASP* 2.9 23.5 + - - +
281G ILE* 1.3 76.0 - - + +
283G ALA* 1.3 60.9 + - - +
285G LYS* 3.3 23.3 + - + +
286G GLU* 3.4 23.2 + - - +
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Residues in contact with ALA 283 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G ARG* 4.3 10.3 - - - +
279G ASP 2.7 22.8 + - - +
280G SER* 3.4 6.7 - - - +
282G THR* 1.3 75.1 + - - +
284G CYS* 1.3 61.3 + - - +
285G LYS 3.4 0.2 + - - -
286G GLU* 3.5 27.9 + - - +
287G VAL* 4.3 6.1 + - - +
375G TRP* 3.9 26.5 - - + -
377G CYS* 5.0 0.8 - - - -
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Residues in contact with CYS 284 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G SER 2.9 16.7 + - - -
281G ILE 3.1 8.0 + - - +
283G ALA* 1.3 75.9 - - - +
285G LYS* 1.3 63.9 + - - +
287G VAL* 3.1 13.4 - - - +
289G ALA* 3.0 19.8 + - - -
290G GLN* 3.8 8.5 - - - +
291G LEU* 3.6 29.8 - - - +
375G TRP* 3.8 8.5 - - - -
377G CYS* 2.0 54.7 - - - -
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Residues in contact with LYS 285 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281G ILE* 3.4 33.8 + - - +
282G THR* 3.3 15.2 + - + +
283G ALA 3.3 0.6 - - - -
284G CYS* 1.3 72.5 - - - +
286G GLU* 1.3 54.3 + - + +
287G VAL 2.6 7.0 + - - -
288G GLY* 2.5 26.6 + - - +
289G ALA 3.8 13.2 - - - +
290G GLN* 5.9 0.9 - - - -
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Residues in contact with GLU 286 (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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282G THR* 3.4 22.5 + - - +
283G ALA* 3.5 20.0 - - - +
284G CYS 3.3 0.8 - - - -
285G LYS* 1.3 74.7 - - - +
287G VAL* 1.3 64.6 + - + +
288G GLY 3.6 0.2 - - - -
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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