Contacts of the helix formed by residues 347 - 360 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33F ILE* 4.5 6.4 - - - +
37F GLY 4.7 10.6 - - - +
111F THR 4.7 4.2 - - - +
113F LEU* 3.6 34.7 + - + +
219F TRP* 3.0 34.3 + - + -
287F ALA 5.4 0.6 + - - -
289F ASP* 5.6 0.6 - - - +
290F PRO* 5.4 4.8 - - + +
345F ASN 4.0 0.2 + - - -
346F CYS* 1.3 73.3 - - - +
348F PRO* 1.3 58.9 - - - +
349F PHE* 2.8 36.3 + - - -
350F SER* 2.7 31.3 + - - -
351F VAL* 3.1 10.6 + - - +
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Residues in contact with PRO 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F MET* 3.8 24.9 - - + -
215F GLY* 3.8 18.8 - - - +
218F LEU* 3.6 27.8 - - + -
219F TRP* 3.4 27.8 - - + +
222F ARG* 3.6 9.4 - - - +
346F CYS* 3.5 9.8 - - - +
347F ASP* 1.3 87.8 - - - +
349F PHE* 1.3 50.8 + - - +
351F VAL* 3.8 2.5 - - + -
352F THR* 2.5 42.8 + - + +
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Residues in contact with PHE 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ILE* 4.6 9.9 - - + -
98F LEU* 4.5 4.9 - - + -
113F LEU* 3.9 20.9 - - + +
114F ARG* 3.5 48.2 - - + -
117F CYS* 3.3 9.9 - - + +
212F ILE* 3.8 24.7 - - + -
215F GLY* 3.4 31.4 - - - -
216F ASP* 3.6 17.3 - - - -
219F TRP* 3.2 20.4 - + - -
347F ASP* 2.8 24.9 + - - +
348F PRO* 1.3 76.9 - - - +
350F SER* 1.3 58.2 + - - +
352F THR* 3.6 4.3 - - - -
353F GLU* 3.1 28.7 + - - +
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Residues in contact with SER 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F LEU* 4.2 24.4 - - - +
287F ALA* 2.7 36.3 + - - +
347F ASP* 2.7 16.0 + - - -
349F PHE* 1.3 79.8 - - - +
351F VAL* 1.3 61.4 + - - -
353F GLU* 3.8 4.6 - - - +
354F ALA* 3.2 24.3 + - - +
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Residues in contact with VAL 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F MET* 4.5 2.2 - - + -
254F THR* 3.3 35.9 - - + +
287F ALA 4.1 2.7 - - - +
288F TYR* 3.8 35.0 - - + -
342F PRO* 3.9 7.0 - - + -
346F CYS* 3.5 38.6 - - + -
347F ASP 3.1 5.8 + - - +
348F PRO* 4.0 7.6 - - + +
350F SER* 1.3 73.4 - - - +
352F THR* 1.3 67.0 + - - +
353F GLU 3.3 0.2 + - - -
354F ALA* 3.4 4.2 + - - +
355F LEU* 3.2 25.5 + - + +
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Residues in contact with THR 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F CYS* 3.7 2.3 - - - -
121F MET* 3.5 21.4 - - - +
131F PHE* 3.6 38.6 - - + -
133F MET* 4.4 7.6 - - - -
211F GLY 5.5 0.2 - - - -
214F MET* 3.9 21.8 - - + -
215F GLY 5.2 1.1 + - - +
254F THR* 5.0 0.9 - - + -
348F PRO* 2.5 30.6 + - + +
349F PHE* 3.6 9.0 + - - -
351F VAL* 1.3 74.5 - - - +
353F GLU* 1.3 62.1 + - - +
355F LEU* 3.4 3.8 + - - +
356F ILE* 3.2 26.9 + - - +
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Residues in contact with GLU 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F LEU* 3.8 6.4 - - - +
116F THR* 3.1 27.5 - - - +
117F CYS* 3.2 35.1 + - - +
120F ILE* 4.1 13.2 - - + -
121F MET* 4.3 3.8 - - - -
283F TYR* 5.6 0.2 + - - -
349F PHE 3.1 16.8 + - - +
350F SER* 3.8 5.2 - - - +
351F VAL 3.2 0.8 - - - -
352F THR* 1.3 77.9 + - - +
354F ALA* 1.3 65.8 + - - +
356F ILE* 3.1 7.4 + - - +
357F ARG* 3.0 46.9 + - - +
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Residues in contact with ALA 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283F TYR* 4.1 16.6 - - + -
284F HIS* 3.7 22.4 - - + +
287F ALA* 4.1 19.5 - - + -
288F TYR* 4.5 1.6 - - + -
350F SER 3.2 15.0 + - - +
351F VAL 3.7 4.5 - - - +
353F GLU* 1.3 78.3 - - - +
355F LEU* 1.3 63.2 + - - +
357F ARG* 3.2 5.5 + - - +
358F THR* 3.0 30.0 + - - -
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Residues in contact with LEU 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F PHE* 3.8 20.2 - - + -
254F THR* 3.6 33.7 - - + +
256F PHE* 4.3 23.1 - - + -
277F LEU* 4.0 22.9 - - + -
284F HIS* 4.1 5.2 - - + -
288F TYR* 3.8 18.8 - - - +
337F PHE* 4.7 4.5 - - + -
339F ASP* 4.0 9.4 - - + +
351F VAL* 3.2 17.1 + - + +
352F THR 3.6 7.0 - - - +
353F GLU 3.2 0.4 - - - -
354F ALA* 1.3 79.5 - - - +
356F ILE* 1.3 58.4 + - - +
359F CYS* 3.0 40.2 + - - +
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Residues in contact with ILE 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F ILE* 3.4 24.7 - - + -
121F MET* 3.8 18.8 - - + -
124F VAL* 3.8 25.4 - - + -
129F PRO* 3.8 25.8 - - + -
131F PHE* 4.0 8.5 - - + -
256F PHE* 4.1 6.1 - - + -
352F THR 3.2 14.5 + - - +
353F GLU 3.1 9.0 + - - +
355F LEU* 1.3 76.6 - - - +
357F ARG* 1.3 58.0 + - - +
360F LEU* 3.1 32.4 + - + -
361F LEU* 3.0 26.9 + - + +
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Residues in contact with ARG 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F THR* 3.4 17.8 - - - +
120F ILE* 3.5 27.8 - - + +
280F ARG* 4.3 5.6 - - - +
283F TYR* 3.7 21.1 + - - -
353F GLU* 3.0 49.4 + - - +
354F ALA* 3.2 5.6 + - - +
356F ILE* 1.3 77.7 - - - +
358F THR* 1.3 57.9 + - - +
361F LEU* 3.6 9.6 - - + +
362F ASN 3.1 11.3 + - - -
363F GLU* 2.9 69.4 + - - +
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Residues in contact with THR 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276F LYS* 3.2 44.5 - - + +
277F LEU* 3.9 16.6 - - + -
280F ARG* 3.1 34.5 + - + +
284F HIS* 2.7 27.8 + - - +
354F ALA 3.0 7.5 + - - -
357F ARG* 1.3 80.0 - - - +
359F CYS* 1.3 60.4 + - - +
362F ASN* 3.7 13.5 - - - -
363F GLU 4.3 4.0 + - - +
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Residues in contact with CYS 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256F PHE* 4.2 18.6 - - + -
261F MET* 5.4 1.0 - - + +
273F ALA* 4.0 25.5 - - + +
276F LYS* 3.8 26.4 + - - +
277F LEU* 3.7 41.1 - - - -
337F PHE* 4.7 0.2 - - - -
355F LEU* 3.0 21.2 + - - +
358F THR* 1.3 79.6 - - - +
360F LEU* 1.3 65.7 + - + +
362F ASN 4.6 0.7 - - - -
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Residues in contact with LEU 360 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F VAL* 3.6 33.7 - - + -
127F GLN* 3.7 28.7 + - + +
129F PRO* 4.7 2.9 - - + -
256F PHE* 4.6 6.7 - - + -
258F THR* 3.5 33.0 - - + -
261F MET* 5.2 2.9 - - + -
356F ILE* 3.1 41.6 + - + +
359F CYS* 1.3 86.0 - - + +
361F LEU* 1.3 65.9 + - - +
362F ASN* 3.2 13.6 + - - -
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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