Contacts of the helix formed by residues 260 - 269 (chain G) in PDB entry 4KYI
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 SER 260 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123G ASP* 4.1 4.9 + - - -
210G ASN* 3.3 20.3 - - - +
212G ARG* 3.8 27.0 - - - +
213G LEU 3.4 13.2 + - - -
215G LEU* 4.0 0.7 - - - +
259G GLN* 1.3 74.4 - - - +
261G ILE* 1.3 65.0 + - - +
262G ALA* 3.5 3.3 + - - +
263G GLN* 3.5 31.0 + - - +
264G VAL* 3.1 25.1 + - - +
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Residues in contact with ILE 261 (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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80G SER* 4.7 0.4 - - - -
126G TYR* 3.6 35.0 - - + +
130G MET* 4.5 9.0 - - - -
213G LEU* 3.0 23.1 + - + +
214G THR 3.3 30.5 - - - +
215G LEU* 4.0 11.4 - - + +
218G LEU* 4.4 23.8 - - + -
236G LEU* 3.7 27.6 - - + -
260G SER* 1.3 72.2 + - - +
262G ALA* 1.3 63.7 + - - +
264G VAL* 3.3 3.8 + - - +
265G VAL* 3.0 28.8 + - + +
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Residues in contact with ALA 262 (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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119G ARG* 3.3 31.1 - - + +
122G LEU* 3.6 19.0 - - + +
123G ASP* 3.3 25.5 + - - +
126G TYR* 3.4 12.2 - - + -
260G SER* 3.5 2.3 + - - +
261G ILE* 1.3 78.8 - - - +
263G GLN* 1.3 57.9 + - - +
266G GLN* 3.0 30.7 + - - +
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Residues in contact with GLN 263 (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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119G ARG* 3.9 20.7 - - + +
198G THR* 4.2 29.6 - - - +
210G ASN* 5.6 1.0 + - - -
212G ARG* 5.9 1.8 - - - -
259G GLN* 4.3 12.0 + - - +
260G SER* 3.5 28.8 + - - +
261G ILE 3.2 1.0 - - - -
262G ALA* 1.3 78.5 - - - +
264G VAL* 1.3 58.5 + - - +
266G GLN* 3.9 2.7 - - - +
267G TRP* 3.1 67.6 + - + +
279G ARG 4.8 3.4 + - - -
280G ASN* 5.7 1.4 - - - +
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Residues in contact with VAL 264 (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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215G LEU* 4.9 3.6 - - + -
238G VAL* 3.5 20.9 - - + +
240G VAL* 4.1 7.4 - - + -
251G TYR* 3.4 37.9 - - + -
259G GLN* 3.5 29.2 - - + -
260G SER 3.1 18.8 - - - +
261G ILE 3.3 3.0 + - - +
262G ALA 3.3 0.2 - - - -
263G GLN* 1.3 79.0 - - + +
265G VAL* 1.3 62.4 + - - +
266G GLN 3.3 0.2 - - - -
267G TRP* 3.7 13.1 - - + +
268G SER* 3.1 27.2 + - - -
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Residues in contact with VAL 265 (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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73G SER 4.8 0.4 - - - +
76G ALA* 3.6 22.0 - - - +
77G MET* 3.6 34.8 - - + +
80G SER* 4.1 4.3 - - - -
118G PHE* 4.6 3.7 - - + -
122G LEU* 3.7 20.6 - - + -
126G TYR* 3.3 19.3 - - - +
236G LEU* 5.1 0.7 - - + -
238G VAL* 4.4 11.7 - - + -
261G ILE* 3.0 21.2 + - + +
264G VAL* 1.3 76.9 - - - +
266G GLN* 1.3 59.8 + - - +
268G SER* 3.4 2.1 + - - -
269G GLY* 2.9 26.7 + - - -
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Residues in contact with GLN 266 (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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114G ARG 3.9 5.9 + - - -
115G GLY* 3.0 44.3 + - - +
116G ASP* 4.9 0.4 - - - +
118G PHE* 3.9 22.4 - - + -
119G ARG* 3.9 16.6 - - + -
122G LEU* 4.2 0.4 - - + +
262G ALA 3.0 20.2 + - - +
263G GLN* 3.9 4.4 - - - +
265G VAL* 1.3 78.8 - - - +
267G TRP* 1.3 91.2 + - - +
269G GLY 3.2 3.1 - - - +
270G ALA* 3.1 33.7 + - - +
275G PHE* 4.9 3.4 - - + -
276G VAL 5.3 4.2 + - - -
278G GLY* 5.3 3.1 - - - -
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Residues in contact with TRP 267 (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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240G VAL* 3.9 2.7 - - + -
251G TYR* 3.5 27.6 - + - -
259G GLN* 4.2 12.1 - - - -
263G GLN* 3.1 49.3 + - + +
264G VAL* 3.7 23.6 - - + +
265G VAL 3.3 0.6 - - - -
266G GLN* 1.3 99.8 + - - +
268G SER* 1.3 60.9 + - - +
270G ALA* 3.1 11.8 + - + +
278G GLY* 4.0 24.5 - - - -
279G ARG 3.5 23.1 + - - -
280G ASN* 3.6 21.5 - - + -
286G ILE* 3.6 36.3 - - + -
287G ALA* 3.0 28.0 - - - +
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Residues in contact with SER 268 (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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72G ALA* 3.3 5.5 - - - +
73G SER* 2.9 31.5 + - - -
76G ALA* 3.7 14.4 - - - -
238G VAL* 4.8 3.4 - - - -
239G VAL 2.8 27.7 + - - -
240G VAL* 3.6 9.3 - - - +
264G VAL 3.1 18.5 + - - -
267G TRP* 1.3 76.3 - - - +
269G GLY* 1.3 55.7 + - - +
270G ALA 3.3 0.4 - - - -
288G ASP* 3.1 26.3 - - - +
289G GLY 3.5 4.7 + - - +
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Residues in contact with GLY 269 (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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73G SER 3.8 14.8 + - - -
74G ALA* 5.7 0.2 - - - -
118G PHE* 4.6 10.4 - - - -
265G VAL 2.9 16.7 + - - -
266G GLN* 3.2 7.2 - - - +
267G TRP 3.1 0.2 - - - -
268G SER* 1.3 77.7 - - - +
270G ALA* 1.3 56.5 + - - -
271G HIS* 3.7 2.4 + - - -
275G PHE* 3.3 22.9 - - - -
288G ASP* 4.1 5.2 - - - -
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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