Contacts of the helix formed by residues 340 - 350 (chain A) in PDB entry 3QPV
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 TYR 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A VAL* 3.7 37.0 + - + +
328A CYS* 4.1 22.9 - - - -
331A LEU* 4.1 13.8 - - + +
336A ILE* 2.7 27.8 + - + +
339A THR* 1.3 101.3 - - + +
341A PRO* 1.4 53.2 - - - +
342A GLU* 3.2 2.5 - - - -
343A GLU* 3.0 29.0 + - + +
344A TYR* 2.8 31.9 + - - +
357A PRO* 5.5 2.0 - - + -
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Residues in contact with PRO 341 (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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337A ARG* 3.1 24.0 - - + +
338A ASP 3.7 7.6 - - - +
339A THR 3.5 8.1 - - - +
340A TYR* 1.4 88.2 - - - +
342A GLU* 1.3 60.2 + - + +
344A TYR* 3.1 6.3 + - + +
345A ALA* 2.8 32.1 + - - +
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Residues in contact with GLU 342 (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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8A ARG* 2.7 45.5 + - - +
340A TYR 3.2 1.1 - - - -
341A PRO* 1.3 86.0 - - + +
343A GLU* 1.3 59.9 + - + +
345A ALA* 3.4 5.2 + - - +
346A LEU* 2.8 38.6 + - + +
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Residues in contact with GLU 343 (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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8A ARG* 4.6 0.7 - - - +
11A LYS* 2.8 34.7 + - - -
336A ILE* 5.4 4.0 - - + -
340A TYR* 3.0 30.7 + - + +
342A GLU* 1.3 80.7 - - + +
344A TYR* 1.3 58.5 + - - +
346A LEU* 3.1 15.9 + - - +
347A ARG* 2.9 31.2 + - - +
354A TYR* 2.6 36.4 + - - +
356A TYR* 6.4 0.2 - - + -
357A PRO* 3.9 16.5 - - + +
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Residues in contact with TYR 344 (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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333A TYR* 3.5 26.9 - + + +
336A ILE* 4.1 14.1 - - + +
337A ARG* 3.4 68.4 + - + +
340A TYR 2.8 16.1 + - - +
341A PRO* 3.5 8.3 - - + +
343A GLU* 1.3 74.1 - - - +
345A ALA* 1.3 63.7 - - + +
347A ARG* 3.3 6.2 + - - +
348A GLU* 3.1 51.3 + - + +
442A ARG* 2.6 32.5 + - - -
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Residues in contact with ALA 345 (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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341A PRO 2.8 16.1 + - - +
342A GLU* 3.8 5.6 - - - +
344A TYR* 1.3 79.5 - - + +
346A LEU* 1.3 63.7 + - + +
348A GLU* 3.3 7.8 + - - +
349A GLN* 3.0 44.6 + - - +
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Residues in contact with LEU 346 (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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8A ARG* 3.4 71.1 - - + +
9A VAL* 3.9 21.8 - - + +
342A GLU* 2.8 32.1 + - + +
343A GLU* 3.1 20.8 + - - +
345A ALA* 1.3 73.6 - - + +
347A ARG* 1.3 63.6 + - - +
349A GLN* 3.2 25.0 + - + +
350A ASP* 3.2 15.2 + - - +
354A TYR* 4.0 14.7 - - + -
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Residues in contact with ARG 347 (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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323A ILE* 4.2 10.3 - - - +
333A TYR* 4.5 6.0 - - - -
343A GLU 2.9 14.3 + - - +
344A TYR* 3.7 6.7 - - - +
345A ALA 3.2 0.2 - - - -
346A LEU* 1.3 76.5 - - - +
348A GLU* 1.3 64.2 + - - +
350A ASP 3.2 0.3 + - - -
351A LYS* 3.1 53.9 + - + +
354A TYR* 3.4 42.1 + - + -
356A TYR* 3.5 40.1 + - - -
362A TYR* 3.6 18.2 - - - -
720A F6P 2.7 47.2 + - - -
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Residues in contact with GLU 348 (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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337A ARG* 5.4 3.3 + - - -
344A TYR* 3.1 44.0 + - + +
345A ALA* 3.7 11.3 - - - +
346A LEU 3.3 0.2 - - - -
347A ARG* 1.3 78.2 - - + +
349A GLN* 1.3 62.4 + - - +
350A ASP 3.4 0.5 + - - -
351A LYS* 5.3 1.3 - - - -
408A TYR* 3.9 16.7 + - - +
442A ARG* 5.7 0.7 + - - -
443A GLU 5.2 1.9 - - - +
444A ARG* 6.2 0.4 - - - -
445A SER* 2.6 50.5 + - - +
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Residues in contact with GLN 349 (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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9A VAL* 5.9 2.2 - - + -
345A ALA* 3.0 42.7 + - - +
346A LEU* 3.2 19.6 + - + +
348A GLU* 1.3 79.3 - - - +
350A ASP* 1.3 63.1 + - + +
351A LYS 4.1 0.2 - - - -
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Residues in contact with ASP 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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9A VAL* 3.9 26.4 - - + +
346A LEU 3.2 7.9 + - - +
347A ARG 3.2 2.4 + - - -
349A GLN* 1.3 81.1 - - + +
351A LYS* 1.3 60.7 + - - +
352A TYR* 3.2 2.3 + - - +
353A TYR* 3.4 31.8 + - - +
354A TYR* 2.8 33.3 + - - +
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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