Contacts of the helix formed by residues 347 - 360 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33I ILE* 4.0 9.7 - - - +
37I GLY* 4.4 10.5 - - - +
111I THR 4.6 2.9 - - - +
113I LEU* 3.8 34.5 + - + +
219I TRP* 3.3 24.3 + - + -
289I ASP* 5.6 1.0 - - - +
290I PRO* 5.4 5.4 - - + +
345I ASN 3.9 0.6 + - - -
346I CYS* 1.3 73.8 - - - +
348I PRO* 1.3 61.8 - - - +
349I PHE* 2.9 43.1 + - - +
350I SER* 2.9 26.3 + - - -
351I VAL* 3.1 11.6 + - - +
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Residues in contact with PRO 348 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I MET* 3.9 22.0 - - + -
215I GLY* 3.8 20.0 - - - +
218I LEU* 3.6 30.1 - - + -
219I TRP* 3.3 37.2 - - + +
222I ARG* 3.7 5.4 - - - +
346I CYS 3.4 8.7 - - - +
347I ASP* 1.3 83.1 - - - +
349I PHE* 1.3 50.4 + - - +
351I VAL* 4.3 1.8 - - + +
352I THR* 2.6 43.0 + - + +
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Residues in contact with PHE 349 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I ILE* 4.6 9.0 - - + -
98I LEU* 4.5 4.7 - - + -
113I LEU* 3.8 22.7 - - + +
114I ARG* 3.5 44.4 - - + -
117I CYS* 3.3 9.2 - - + +
212I ILE* 3.9 24.0 - - + -
215I GLY* 3.5 29.2 - - - -
216I ASP* 3.5 20.0 - - - -
219I TRP* 3.4 20.9 - + - -
347I ASP* 2.9 23.6 + - - +
348I PRO* 1.3 76.4 - - - +
350I SER* 1.3 57.0 + - - +
352I THR* 3.5 4.0 - - - -
353I GLU* 3.0 31.6 + - - +
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Residues in contact with SER 350 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I LEU* 4.3 16.1 - - - +
287I ALA* 2.7 36.3 + - - +
347I ASP* 2.9 22.3 + - - -
349I PHE* 1.3 78.1 - - - +
351I VAL* 1.3 65.6 + - - +
353I GLU* 3.4 4.6 + - - +
354I ALA* 3.0 24.1 + - - +
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Residues in contact with VAL 351 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I MET* 4.6 2.5 - - + -
254I THR* 3.5 34.1 - - + +
287I ALA 4.1 3.1 - - - +
288I TYR* 3.5 40.7 - - + +
342I PRO* 3.9 8.7 - - + -
346I CYS* 3.6 36.3 - - + -
347I ASP 3.1 5.9 + - - +
348I PRO* 4.0 6.3 - - + +
350I SER* 1.3 77.4 - - - +
352I THR* 1.3 63.5 + - - +
354I ALA* 3.2 12.1 + - - +
355I LEU* 3.3 15.4 + - + +
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Residues in contact with THR 352 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I CYS* 3.4 18.2 - - - -
121I MET* 3.7 13.5 - - - -
131I PHE* 3.9 27.2 - - + -
133I MET* 4.3 8.3 - - - -
211I GLY 5.5 1.3 + - - -
214I MET* 3.9 31.0 - - + -
215I GLY 5.1 1.7 + - - +
254I THR* 5.2 0.4 - - + -
348I PRO 2.6 28.2 + - - +
349I PHE* 3.4 2.1 + - - -
351I VAL* 1.3 78.9 - - + +
353I GLU* 1.3 62.9 + - - +
354I ALA 3.4 0.2 + - - -
355I LEU* 3.4 3.9 + - - +
356I ILE* 3.3 25.6 + - - +
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Residues in contact with GLU 353 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113I LEU 4.0 4.0 - - - +
116I THR* 3.2 18.4 - - - +
117I CYS* 2.9 34.3 + - - +
120I ILE* 4.0 12.8 - - + -
121I MET* 4.0 8.2 - - - +
349I PHE 3.0 21.0 + - - +
350I SER* 3.8 5.2 - - - +
351I VAL 3.3 0.2 - - - -
352I THR* 1.3 76.8 + - - +
354I ALA* 1.3 63.5 + - - +
356I ILE* 3.3 4.9 + - - +
357I ARG* 3.0 57.8 + - - +
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Residues in contact with ALA 354 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283I TYR* 4.1 17.9 - - + +
284I HIS* 3.6 23.3 - - + +
287I ALA* 4.0 18.4 - - + -
288I TYR* 4.6 1.3 - - + -
350I SER 3.0 17.7 + - - +
351I VAL 3.2 5.8 + - - +
353I GLU* 1.3 75.8 - - - +
355I LEU* 1.3 58.7 + - - +
357I ARG* 3.2 4.3 + - - +
358I THR* 2.9 33.8 + - - -
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Residues in contact with LEU 355 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I PHE* 4.0 16.6 - - + -
254I THR* 3.7 32.1 - - + -
256I PHE* 4.2 28.3 - - + -
277I LEU* 3.9 30.3 - - + -
284I HIS* 4.0 2.9 - - + -
288I TYR* 3.8 18.2 - - - +
337I PHE* 4.7 4.9 - - + -
339I ASP* 3.9 9.4 - - + +
351I VAL* 3.3 17.3 + - + +
352I THR 3.9 5.8 - - - +
353I GLU 3.3 0.2 - - - -
354I ALA* 1.3 77.1 - - - +
356I ILE* 1.3 59.5 + - - +
359I CYS* 2.8 39.0 + - - +
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Residues in contact with ILE 356 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I ILE* 3.4 28.3 - - + -
121I MET* 3.5 19.3 - - + -
124I VAL* 3.6 28.9 - - + -
129I PRO* 3.7 26.0 - - + -
131I PHE* 3.8 9.9 - - + -
256I PHE* 3.9 5.4 - - + -
352I THR 3.3 14.4 + - - +
353I GLU 3.7 2.5 - - - +
354I ALA 3.3 0.4 - - - -
355I LEU* 1.3 77.0 - - - +
357I ARG* 1.3 57.7 + - - +
360I LEU* 2.9 52.1 + - + -
361I LEU* 2.9 11.6 + - + -
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Residues in contact with ARG 357 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I THR* 3.5 18.8 - - - +
120I ILE* 3.7 28.0 - - + +
280I ARG* 4.7 2.9 - - - +
283I TYR* 3.3 23.1 + - - +
353I GLU* 3.0 49.2 + - + +
354I ALA* 3.7 7.0 - - - +
356I ILE* 1.3 76.5 - - - +
358I THR* 1.3 56.7 + - - +
361I LEU* 3.5 10.2 - - + +
362I ASN 3.1 10.9 + - - -
363I GLU* 3.1 67.1 + - + +
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Residues in contact with THR 358 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276I LYS* 3.6 47.4 - - + +
277I LEU* 3.8 17.0 - - + +
280I ARG* 3.1 32.1 + - + +
283I TYR* 4.3 0.9 - - - -
284I HIS* 2.7 28.6 + - - +
354I ALA 2.9 13.8 + - - -
355I LEU 4.2 0.4 - - - -
357I ARG* 1.3 75.0 - - - +
359I CYS* 1.3 61.8 + - - +
362I ASN* 3.8 10.9 - - - -
363I GLU 4.4 3.7 + - - +
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Residues in contact with CYS 359 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256I PHE* 4.1 22.4 - - + -
261I MET* 5.4 0.9 - - + -
273I ALA* 3.8 27.9 - - + -
276I LYS* 3.3 30.0 + - - +
277I LEU* 3.7 37.5 - - - -
337I PHE* 4.5 0.4 - - - -
355I LEU* 2.8 25.9 + - - +
358I THR* 1.3 76.6 - - - +
360I LEU* 1.3 66.6 + - + +
362I ASN* 4.3 0.4 - - - -
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Residues in contact with LEU 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I VAL* 4.1 28.3 - - + -
127I GLN* 3.5 28.1 + - + +
129I PRO* 4.6 3.6 - - + -
256I PHE* 4.1 5.8 - - + -
258I THR* 3.5 35.0 - - + -
261I MET* 5.1 4.7 - - + -
356I ILE* 2.9 48.5 + - + +
359I CYS* 1.3 83.5 - - + +
361I LEU* 1.3 62.7 + - - +
362I ASN* 3.3 15.4 + - - -
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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