Contacts of the helix formed by residues 261 - 277 (chain G) in PDB entry 3Q84
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 261 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97G LEU* 4.0 19.4 - - - +
100G GLU* 5.3 4.9 + - - -
257G ASN 3.9 12.1 + - - +
258G LEU* 3.0 20.9 + - + +
260G GLU* 1.3 79.2 - - - +
262G SER* 1.3 61.7 + - - +
263G SER* 2.7 24.2 + - - -
264G TYR* 3.0 15.8 + - + +
265G ILE* 2.8 23.5 - - - +
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Residues in contact with SER 262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260G GLU 3.8 2.7 + - - -
261G ASN* 1.3 75.0 + - - +
263G SER* 1.3 64.3 + - - +
265G ILE* 3.5 9.4 + - - +
266G HIS* 3.2 21.7 + - - +
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Residues in contact with SER 263 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G LEU* 4.0 18.8 - - - +
261G ASN* 2.7 15.4 + - - -
262G SER* 1.3 76.6 + - - +
264G TYR* 1.4 61.1 + - - -
266G HIS* 3.1 15.6 + - - +
267G VAL* 3.0 20.5 + - - +
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Residues in contact with TYR 264 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G VAL* 4.2 16.6 - - + -
97G LEU* 3.8 25.3 - - + +
98G HIS* 5.8 0.9 - - - -
258G LEU* 3.8 36.6 - - + +
259G ALA 5.2 0.2 - - - -
261G ASN* 3.0 18.1 + - - +
262G SER 3.2 0.2 - - - -
263G SER* 1.4 70.0 - - - +
265G ILE* 1.3 81.6 + - + +
266G HIS 3.0 1.6 + - - -
267G VAL* 3.1 17.1 + - - +
268G TYR* 3.5 36.4 + + - -
256H LEU 4.0 2.4 + - - -
257H ASN* 4.3 0.2 - - - -
258H LEU* 2.9 39.0 + - + +
259H ALA* 3.6 25.6 - - + -
264H TYR* 4.1 13.0 - + - -
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Residues in contact with ILE 265 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258G LEU 4.1 0.2 - - - +
259G ALA 3.3 24.2 - - - +
260G GLU* 4.8 0.9 - - - -
261G ASN 2.8 28.2 + - - +
262G SER* 3.5 8.7 + - - +
263G SER 3.4 0.2 - - - -
264G TYR* 1.3 90.5 - - + +
266G HIS* 1.3 62.9 + - - +
268G TYR* 3.2 8.1 + - - +
269G ARG* 3.1 31.2 + - + +
257H ASN* 6.2 1.3 - - - +
259H ALA* 3.7 21.8 - - + -
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Residues in contact with HIS 266 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G LYS* 5.8 2.7 - - - -
262G SER 3.2 13.5 + - - +
263G SER* 3.1 15.7 + - - +
264G TYR 3.0 0.8 - - - -
265G ILE* 1.3 78.3 - - - +
267G VAL* 1.3 60.3 + - - +
269G ARG* 3.2 24.8 + - + +
270G GLU* 2.9 52.4 + - + +
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Residues in contact with VAL 267 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G GLU* 3.7 43.1 - - + +
93G LYS* 4.2 26.0 - - + -
94G VAL* 4.2 5.2 - - + -
97G LEU* 4.4 9.2 - - + -
263G SER* 3.0 18.9 + - - +
264G TYR* 3.1 15.7 - - - +
266G HIS* 1.3 81.4 - - - +
268G TYR* 1.3 66.4 + - + +
270G GLU* 3.7 11.6 - - - +
271G LEU* 3.2 25.6 + - - +
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Residues in contact with TYR 268 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G GLU* 2.4 47.3 + - + -
94G VAL* 3.3 11.4 - - + +
264G TYR* 3.5 42.2 + + - -
265G ILE 3.2 7.6 + - - +
267G VAL* 1.3 86.6 - - + +
269G ARG* 1.3 58.3 + - - +
271G LEU* 3.8 4.2 - - + +
272G GLU* 3.1 28.9 + - - +
49H ARG* 4.9 1.0 + - - -
253H LYS* 3.6 20.9 + - + -
256H LEU* 3.8 29.3 + - + +
257H ASN* 3.1 49.1 - - + +
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Residues in contact with ARG 269 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G ILE* 3.1 28.4 + - + +
266G HIS* 3.2 27.7 + - + +
268G TYR* 1.3 71.3 - - - +
270G GLU* 1.3 66.7 + - - +
271G LEU 3.2 0.2 + - - -
272G GLU* 3.4 6.4 + - - +
273G GLN* 3.0 33.0 + - - +
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Residues in contact with GLU 270 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G THR* 4.5 9.7 - - - +
93G LYS* 2.9 36.5 + - - +
266G HIS* 2.9 34.8 + - + +
267G VAL* 3.7 9.5 - - - +
269G ARG* 1.3 75.7 - - - +
271G LEU* 1.3 59.3 + - - +
273G GLN* 3.3 20.0 + - - +
274G ALA* 3.0 27.7 + - + +
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Residues in contact with LEU 271 (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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86G ALA* 3.3 46.9 - - + +
87G ILE* 3.6 17.3 - - + +
90G GLU* 3.8 27.8 - - + -
267G VAL 3.2 15.5 + - - +
268G TYR* 3.8 9.9 - - + +
269G ARG 3.1 1.2 - - - -
270G GLU* 1.3 77.2 - - - +
272G GLU* 1.3 61.1 + - - +
274G ALA* 3.2 6.5 + - - +
275G ILE* 2.9 41.8 + - + +
253H LYS* 3.8 25.1 - - + -
256H LEU* 5.3 1.3 - - + -
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Residues in contact with GLU 272 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268G TYR 3.1 17.2 + - - +
269G ARG* 3.9 6.1 - - - +
271G LEU* 1.3 76.8 - - - +
273G GLN* 1.3 57.8 + - - +
275G ILE* 4.0 6.0 - - - +
276G ARG* 3.0 66.5 + - + +
250H LEU* 4.4 8.5 - - + -
253H LYS* 2.8 41.5 + - + +
254H ARG* 4.9 7.4 + - - -
260H GLU* 5.0 0.5 - - - +
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Residues in contact with GLN 273 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G ARG* 3.0 22.9 + - - +
270G GLU* 4.1 18.7 + - - +
271G LEU 3.2 0.2 - - - -
272G GLU* 1.3 74.0 - - - +
274G ALA* 1.3 58.4 + - - +
276G ARG* 3.7 5.1 - - - +
277G GLY* 2.8 33.1 + - - -
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Residues in contact with ALA 274 (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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82G ARG* 5.1 2.7 - - - +
83G ALA* 4.2 8.8 - - - +
86G ALA* 3.8 25.4 - - + -
270G GLU* 3.0 14.6 + - + +
271G LEU* 3.2 9.6 - - - +
273G GLN* 1.3 79.9 - - - +
275G ILE* 1.3 62.2 + - - +
277G GLY* 3.3 8.0 + - - -
278G ALA* 3.7 6.2 + - - +
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Residues in contact with ILE 275 (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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83G ALA* 3.8 28.3 - - + +
87G ILE* 4.9 4.3 - - + -
271G LEU* 2.9 45.9 + - + +
272G GLU 4.0 0.7 - - - +
274G ALA* 1.3 72.2 - - - +
276G ARG* 1.3 63.1 + - - +
278G ALA* 3.1 20.8 + - - +
246H LYS* 3.4 19.7 - - + +
249H LEU* 3.6 34.8 - - + +
250H LEU* 3.3 34.5 - - + -
253H LYS* 4.0 11.7 - - + -
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Residues in contact with ARG 276 (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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272G GLU* 3.0 55.1 + - + +
273G GLN* 3.9 5.4 - - - +
275G ILE* 1.3 75.4 - - - +
277G GLY* 1.3 59.3 + - - +
278G ALA 3.1 1.0 - - - +
246H LYS* 3.0 28.9 + - - +
250H LEU* 4.3 29.4 - - + +
254H ARG* 4.8 10.9 - - - +
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Residues in contact with GLY 277 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G SER* 4.8 3.6 - - - -
82G ARG* 5.6 1.4 + - - -
273G GLN 2.8 16.8 + - - -
274G ALA* 3.8 4.7 - - - -
275G ILE 3.2 0.8 - - - -
276G ARG* 1.3 75.7 - - - +
278G ALA* 1.3 60.1 + - - +
279G ASP* 3.7 6.9 + - - +
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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