Contacts of the helix formed by residues 349 - 354 (chain A) in PDB entry 2QQ6
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 HIS 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ARG 3.9 10.9 + - - -
347A MSE 3.5 32.1 - - + +
348A PRO* 1.3 85.7 - - + +
350A TRP* 1.3 67.3 + - - +
351A GLU 3.3 2.0 - - - -
352A ASP* 2.8 37.6 + - - +
353A PHE* 3.8 27.9 + + - -
387A HIS* 3.7 39.2 + + + +
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Residues in contact with TRP 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 5.8 0.7 - - + -
17A VAL* 5.9 2.0 - - + -
319A SER 3.1 20.1 + - - -
320A SER* 3.3 12.6 - - - +
321A PRO* 3.2 52.8 - - + +
324A THR* 3.5 23.6 - - + -
342A TRP* 3.7 24.4 - + + -
344A ALA* 3.6 19.5 - - + +
347A MSE 3.2 38.8 + - - +
348A PRO 3.3 1.2 - - - -
349A HIS* 1.3 80.1 + - - +
351A GLU* 1.3 92.9 + - + +
352A ASP 3.3 0.5 + - - -
353A PHE* 3.4 12.3 + + - +
361A VAL* 4.3 6.3 - - + -
362A ILE* 3.2 38.6 - - + -
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Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A PRO* 4.2 5.6 - - - +
342A TRP* 6.3 0.2 - - + -
348A PRO 4.6 4.3 + - - +
349A HIS 3.3 0.8 - - - -
350A TRP* 1.3 91.2 - - + +
352A ASP* 1.3 60.9 + - - +
353A PHE 3.1 6.3 + - - -
354A VAL* 3.0 25.4 + - - +
356A TYR* 5.4 0.3 - - - +
359A GLY 4.6 1.2 - - - +
360A PRO* 3.4 19.1 - - + +
361A VAL* 2.8 49.1 + - - +
362A ILE* 3.3 15.2 + - - +
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Residues in contact with ASP 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A PRO 4.3 2.6 - - - +
349A HIS* 2.8 41.5 + - + +
351A GLU* 1.3 75.8 - - - +
353A PHE* 1.3 59.5 + - - +
354A VAL 3.2 2.9 + - - +
380A ASP* 3.8 6.4 - - - +
383A ALA* 3.1 29.3 - - + +
387A HIS* 5.0 7.9 + - + +
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Residues in contact with PHE 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE* 3.5 47.1 - - + -
15A ARG 3.6 19.1 - - - -
16A ALA* 4.1 7.9 - - + -
320A SER* 4.3 12.3 - - - +
321A PRO* 3.8 11.4 - - + -
322A VAL* 5.4 1.1 - - + +
347A MSE 5.1 0.9 - - - -
349A HIS* 3.8 28.2 + + - -
350A TRP* 3.4 22.8 + + - +
351A GLU 3.1 1.0 - - - -
352A ASP* 1.3 78.4 - - - +
354A VAL* 1.3 60.3 + - + +
379A LEU* 3.0 32.5 - - + +
380A ASP 3.3 3.7 + - - +
383A ALA* 4.8 2.5 - - - -
384A ALA* 3.8 26.9 - - + -
387A HIS* 3.8 19.1 - + + -
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 5.4 0.9 - - + -
321A PRO* 4.1 20.6 - - + +
322A VAL* 3.9 24.2 - - + -
351A GLU* 3.0 19.1 + - - +
352A ASP* 3.2 3.5 - - - +
353A PHE* 1.3 84.0 - - - +
355A ARG* 1.3 71.9 + - - +
356A TYR* 4.0 6.5 + - + +
361A VAL* 4.9 3.4 - - + -
377A LEU* 3.5 30.5 - - + -
378A GLU 3.3 20.9 - - - +
379A LEU* 3.5 11.0 - - + +
380A ASP* 4.1 3.4 - - - +
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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