Contacts of the helix formed by residues 347 - 360 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33E ILE* 4.2 8.8 - - - +
37E GLY* 4.7 9.9 - - - +
111E THR 4.5 3.8 - - - +
113E LEU* 3.7 37.1 - - + +
219E TRP* 3.2 31.5 + - + -
287E ALA 5.5 1.0 + - - -
289E ASP 5.9 0.2 - - - -
290E PRO* 5.5 5.1 - - + +
346E CYS* 1.3 74.5 - - - +
348E PRO* 1.3 66.7 - - - +
349E PHE* 2.8 34.1 + - - -
350E SER* 2.9 19.4 + - - -
351E VAL* 3.1 11.3 + - - +
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Residues in contact with PRO 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E MET* 3.8 35.0 - - + -
215E GLY* 3.8 20.4 - - - +
218E LEU* 3.9 15.0 - - + -
219E TRP* 3.4 28.7 - - + +
222E ARG* 3.6 17.7 - - - +
346E CYS* 3.6 2.4 - - - +
347E ASP* 1.3 89.3 - - - +
349E PHE* 1.3 56.5 + - - +
351E VAL* 3.8 2.0 - - + -
352E THR* 2.7 36.0 + - + +
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Residues in contact with PHE 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ILE* 4.6 8.3 - - + -
98E LEU* 4.7 4.7 - - + -
113E LEU* 3.7 22.7 - - + +
114E ARG* 3.5 34.3 - - + -
117E CYS* 3.2 9.0 - - + +
212E ILE* 3.4 33.7 - - + -
215E GLY* 3.4 30.1 - - - -
216E ASP* 3.3 22.7 - - - -
219E TRP* 3.5 20.0 - + - -
347E ASP* 2.8 23.7 + - - +
348E PRO* 1.3 77.3 - - - +
350E SER* 1.3 57.6 + - - +
352E THR* 3.7 3.1 - - - -
353E GLU* 3.0 30.8 + - - +
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Residues in contact with SER 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E LEU* 3.9 25.4 - - - +
287E ALA* 2.5 36.9 + - - +
347E ASP* 2.9 13.6 + - - -
349E PHE* 1.3 76.7 - - - +
351E VAL* 1.3 65.1 + - - +
353E GLU* 3.5 5.3 + - - +
354E ALA* 3.0 25.5 + - - +
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Residues in contact with VAL 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E MET* 4.4 2.5 - - + -
254E THR* 3.4 35.9 - - + +
287E ALA 4.2 3.1 - - - +
288E TYR* 3.9 35.5 - - + -
342E PRO* 3.9 9.2 - - + -
346E CYS* 3.6 38.1 - - + -
347E ASP 3.1 6.3 + - - +
348E PRO* 4.0 7.6 - - + +
350E SER* 1.3 77.1 - - - +
352E THR* 1.3 64.3 + - - +
354E ALA* 3.3 2.4 + - - +
355E LEU* 3.2 23.6 + - + +
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Residues in contact with THR 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E CYS* 3.3 10.7 - - - -
121E MET* 3.3 21.9 - - - +
131E PHE* 3.7 27.1 - - + -
133E MET* 4.3 8.7 - - - -
214E MET* 3.9 30.3 - - + -
215E GLY 5.1 1.6 + - - +
254E THR* 5.1 1.1 - - + -
348E PRO 2.7 30.6 + - - +
349E PHE* 3.7 1.7 - - - -
351E VAL* 1.3 73.4 - - + +
353E GLU* 1.3 64.8 + - - +
355E LEU* 3.5 1.3 + - - +
356E ILE* 3.2 26.5 + - - +
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Residues in contact with GLU 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E LEU* 4.2 3.5 - - - +
116E THR* 3.2 18.4 - - - +
117E CYS* 3.2 35.3 + - - +
120E ILE* 4.3 11.9 - - + -
121E MET* 4.5 2.5 - - - -
283E TYR* 5.5 0.4 + - - +
349E PHE 3.0 16.6 + - - +
350E SER* 3.9 5.5 - - - +
352E THR* 1.3 77.5 + - - +
354E ALA* 1.3 67.0 - - - +
356E ILE* 3.2 4.9 + - - +
357E ARG* 3.0 57.8 + - - +
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Residues in contact with ALA 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E TYR* 4.0 20.2 - - + +
284E HIS* 3.6 19.5 - - + +
287E ALA* 3.9 21.1 - - + -
288E TYR* 4.5 1.1 - - + -
350E SER 3.0 18.3 + - - +
351E VAL 3.7 4.0 - - - +
353E GLU* 1.3 77.2 - - - +
355E LEU* 1.3 58.0 + - - +
357E ARG* 3.2 4.0 + - - +
358E THR* 2.9 34.3 + - - -
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Residues in contact with LEU 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E PHE* 3.9 18.2 - - + -
254E THR* 3.6 35.9 - - + +
256E PHE* 4.2 16.0 - - + -
277E LEU* 4.0 26.5 - - + -
284E HIS* 3.8 3.3 - - - -
288E TYR* 3.6 19.5 - - - +
337E PHE* 4.6 10.5 - - + -
339E ASP* 3.8 10.5 - - + +
351E VAL* 3.2 17.7 + - + +
352E THR 3.8 7.0 - - - +
353E GLU 3.2 0.2 - - - -
354E ALA* 1.3 79.5 - - - +
356E ILE* 1.3 57.9 + - - +
359E CYS* 2.9 37.5 + - - +
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Residues in contact with ILE 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E ILE* 3.4 27.6 - - + -
121E MET* 3.8 20.6 - - + -
124E VAL* 3.5 28.7 - - + -
129E PRO* 3.7 23.6 - - + -
131E PHE* 4.0 2.9 - - + -
256E PHE* 3.8 14.4 - - + -
352E THR 3.2 12.9 + - - +
353E GLU 3.2 4.4 + - - +
355E LEU* 1.3 73.2 - - - +
357E ARG* 1.3 63.2 + - - +
360E LEU* 2.7 52.4 + - + +
361E LEU* 3.0 10.4 + - + -
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Residues in contact with ARG 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E THR* 3.6 16.6 - - - +
120E ILE* 3.7 28.0 - - + +
280E ARG* 4.5 4.7 - - - +
283E TYR* 3.6 18.8 + - - -
353E GLU* 3.0 50.5 + - - +
354E ALA* 3.8 3.4 - - - +
356E ILE* 1.3 76.4 - - - +
358E THR* 1.3 56.4 + - - +
361E LEU* 3.5 9.8 - - + +
362E ASN 3.1 25.1 + - - -
363E GLU* 2.6 62.5 + - - +
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Residues in contact with THR 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276E LYS* 3.7 42.2 - - + +
277E LEU* 3.8 18.8 - - + +
280E ARG* 2.7 40.8 + - + +
283E TYR* 4.3 0.2 - - - -
284E HIS* 2.8 29.0 + - - +
354E ALA 2.9 9.3 + - - -
357E ARG* 1.3 77.8 - - - +
359E CYS* 1.3 61.9 + - - +
362E ASN* 4.1 8.8 + - - -
363E GLU 4.6 3.1 - - - +
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Residues in contact with CYS 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E PHE* 4.1 21.1 - - + -
261E MET* 5.5 0.9 - - + -
273E ALA* 4.0 25.0 - - + +
276E LYS* 3.4 26.9 + - - +
277E LEU* 3.8 39.3 - - - -
337E PHE* 4.4 1.8 - - - -
355E LEU* 2.9 24.9 + - - +
358E THR* 1.3 79.2 - - - +
360E LEU* 1.3 64.4 + - + +
362E ASN* 4.6 0.4 - - - -
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Residues in contact with LEU 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E VAL* 3.8 30.1 - - + -
127E GLN* 3.2 30.2 + - + +
129E PRO* 4.5 4.7 - - + -
256E PHE* 4.5 5.4 - - + -
258E THR* 3.4 31.2 - - + -
261E MET* 5.1 4.0 - - + -
356E ILE* 2.7 46.9 + - + +
359E CYS* 1.3 82.2 - - + +
361E LEU* 1.3 64.8 + - - +
362E ASN* 3.4 13.1 + - - -
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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