Contacts of the helix formed by residues 347 - 360 (chain G) in PDB entry 2QC8
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 ASP 347 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33G ILE* 4.6 5.2 - - - +
37G GLY* 4.5 10.7 - - - +
111G THR 4.7 4.2 - - - +
113G LEU* 3.5 36.4 + - + +
219G TRP* 3.2 31.8 + - + -
287G ALA 5.3 1.8 + - - -
289G ASP* 5.5 1.4 - - - +
290G PRO* 5.4 5.2 - - + +
345G ASN 3.8 0.2 + - - -
346G CYS* 1.3 73.1 - - - +
348G PRO* 1.3 61.9 - - - +
349G PHE* 2.9 23.5 + - - -
350G SER* 2.8 26.2 + - - -
351G VAL* 3.1 10.6 + - - +
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Residues in contact with PRO 348 (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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133G MET* 3.8 32.8 - - + -
215G GLY* 3.8 19.3 - - - +
218G LEU* 3.8 17.0 - - + -
219G TRP* 3.4 28.7 - - + +
222G ARG* 3.6 10.8 - - - +
346G CYS* 3.5 9.8 - - - +
347G ASP* 1.3 85.9 - - - +
349G PHE* 1.3 57.0 + - - +
350G SER 3.2 0.2 - - - -
351G VAL* 3.8 2.9 - - + +
352G THR* 2.7 36.8 + - + +
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Residues in contact with PHE 349 (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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33G ILE* 4.6 9.2 - - + -
98G LEU* 4.5 4.3 - - + -
113G LEU* 3.8 21.5 - - + +
114G ARG* 3.4 43.3 - - + -
117G CYS* 3.3 7.4 - - + +
212G ILE* 3.9 23.3 - - + -
215G GLY* 3.6 26.0 - - - -
216G ASP* 3.4 25.4 - - - -
219G TRP* 3.4 21.1 - + - -
347G ASP* 2.9 23.3 + - - +
348G PRO* 1.3 77.6 - - - +
350G SER* 1.3 61.1 + - - +
352G THR* 3.8 3.4 - - - -
353G GLU* 3.1 27.8 + - - +
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Residues in contact with SER 350 (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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113G LEU* 4.0 25.0 - - - +
287G ALA* 2.8 34.7 + - - +
347G ASP* 2.8 14.9 + - - -
349G PHE* 1.3 79.0 - - - +
351G VAL* 1.3 63.3 + - - -
353G GLU* 3.9 5.2 - - - +
354G ALA* 3.1 24.1 + - - +
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Residues in contact with VAL 351 (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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133G MET* 4.7 2.5 - - + -
254G THR* 3.4 27.6 - - + +
287G ALA 4.2 2.9 - - - +
288G TYR* 3.7 36.2 - - + -
342G PRO* 4.0 7.4 - - + -
346G CYS* 3.8 36.8 - - + -
347G ASP 3.1 5.7 + - - +
348G PRO* 4.1 7.4 - - + +
350G SER* 1.3 73.3 - - - +
352G THR* 1.3 68.3 + - - +
354G ALA* 3.3 10.6 + - - +
355G LEU* 3.3 25.6 + - + +
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Residues in contact with THR 352 (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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117G CYS* 3.5 6.8 - - - -
121G MET* 3.5 23.3 - - - +
131G PHE* 3.7 36.6 - - + -
133G MET* 4.2 9.0 - - - -
211G GLY 5.2 0.7 + - - -
212G ILE* 6.1 0.2 - - - -
214G MET* 3.8 22.2 - - + +
215G GLY 5.2 2.0 + - - +
254G THR* 5.1 0.2 - - + -
348G PRO 2.7 26.2 + - - +
349G PHE* 3.5 5.4 + - - -
351G VAL* 1.3 78.9 - - + +
353G GLU* 1.3 64.9 + - - +
355G LEU* 3.2 13.7 + - - +
356G ILE* 3.2 16.1 + - - +
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Residues in contact with GLU 353 (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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113G LEU* 4.1 4.0 - - - +
116G THR* 3.1 27.6 - - - +
117G CYS* 3.2 19.6 + - - +
120G ILE* 4.0 15.5 - - + -
121G MET* 4.0 7.4 - - - +
283G TYR* 5.4 0.6 + - - +
349G PHE 3.1 20.7 + - - +
350G SER* 3.9 5.0 - - - +
352G THR* 1.3 76.9 + - - +
354G ALA* 1.3 64.0 + - - +
356G ILE* 3.1 7.5 + - - +
357G ARG* 2.8 61.0 + - - +
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Residues in contact with ALA 354 (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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283G TYR* 4.1 18.8 - - + +
284G HIS* 3.6 18.6 - - + +
287G ALA* 3.8 22.0 - - + -
288G TYR* 4.5 1.6 - - + -
350G SER 3.1 18.3 + - - +
351G VAL 3.3 5.3 + - - +
353G GLU* 1.3 76.4 - - - +
355G LEU* 1.3 63.5 + - - +
357G ARG* 3.3 4.5 + - - +
358G THR* 3.0 28.6 + - - -
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Residues in contact with LEU 355 (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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131G PHE* 3.6 28.7 - - + -
254G THR* 3.7 25.1 - - + +
256G PHE* 4.5 21.5 - - + -
277G LEU* 4.1 23.1 - - + -
284G HIS* 3.9 4.2 - - - -
288G TYR* 3.6 19.3 - - - +
337G PHE* 4.9 2.5 - - + -
339G ASP* 4.0 14.4 - - + +
351G VAL* 3.3 21.1 + - + +
352G THR* 3.2 4.8 + - - +
354G ALA* 1.3 74.4 - - - +
356G ILE* 1.3 60.7 + - - +
359G CYS* 2.8 39.6 + - - +
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Residues in contact with ILE 356 (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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120G ILE* 3.5 20.9 - - + -
121G MET* 3.6 20.4 - - + -
124G VAL* 3.4 32.3 - - + -
129G PRO* 3.6 28.9 - - + -
131G PHE* 3.7 10.8 - - + -
256G PHE* 4.1 4.5 - - + -
352G THR 3.2 13.2 + - - +
353G GLU 3.1 7.2 + - - +
355G LEU* 1.3 76.5 - - - +
357G ARG* 1.3 56.9 + - - +
360G LEU* 3.0 44.2 + - + -
361G LEU* 3.0 12.9 + - + +
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Residues in contact with ARG 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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116G THR* 3.4 17.0 - - - +
120G ILE* 3.6 21.5 - - + +
280G ARG* 4.4 5.4 - - - +
283G TYR* 3.7 21.3 + - - -
353G GLU* 2.8 48.3 + - + +
354G ALA* 3.6 7.9 - - - +
356G ILE* 1.3 78.4 - - - +
358G THR* 1.3 59.4 + - - +
361G LEU* 3.6 15.7 - - + +
362G ASN 3.1 10.9 + - - -
363G GLU* 3.0 63.4 + - - +
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Residues in contact with THR 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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276G LYS* 3.5 48.2 - - + +
277G LEU* 3.8 15.5 - - + -
280G ARG* 3.0 36.5 + - + +
284G HIS* 2.6 27.6 + - - +
354G ALA 3.0 9.1 + - - -
355G LEU 4.2 0.2 - - - -
357G ARG* 1.3 77.5 - - - +
359G CYS* 1.3 61.7 + - - +
362G ASN* 3.7 10.8 - - - -
363G GLU 4.2 4.1 + - - +
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Residues in contact with CYS 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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256G PHE* 4.2 21.8 - - + -
261G MET* 6.1 0.2 - - - +
273G ALA* 3.8 28.8 - - + +
276G LYS* 3.5 27.0 + - - +
277G LEU* 3.8 36.1 - - - -
337G PHE* 4.7 1.3 - - - -
355G LEU* 2.8 25.6 + - - +
358G THR* 1.3 77.0 - - - +
360G LEU* 1.3 67.6 + - + +
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Residues in contact with LEU 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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124G VAL* 3.6 32.3 - - + -
127G GLN* 3.4 27.2 + - + +
129G PRO* 4.5 3.8 - - + -
256G PHE* 4.3 3.4 - - + -
258G THR* 3.4 31.4 - - + -
261G MET* 5.4 2.7 - - + -
356G ILE* 3.0 42.1 + - + +
359G CYS* 1.3 91.8 - - + +
361G LEU* 1.3 60.4 + - - +
362G ASN* 3.2 21.7 + - - -
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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