Contacts of the helix formed by residues 385 - 393 (chain A) in PDB entry 3QNQ
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 PRO 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A ILE* 3.2 26.7 - - + +
330A PHE* 3.8 27.6 - - + -
383A THR 3.5 6.7 - - - +
384A THR* 1.3 99.5 - - + +
386A ILE* 1.3 66.4 + - - +
387A LEU 3.6 0.9 - - - -
388A PHE* 3.9 16.9 + - + +
389A SER* 3.1 17.2 + - - -
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Residues in contact with ILE 386 (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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291A LEU 5.3 0.7 - - - +
295A MET* 3.2 48.9 - - + +
302A LEU* 4.4 24.9 - - + -
329A ILE* 4.1 4.0 + - - +
331A ASN* 4.8 2.4 - - - +
384A THR 4.4 0.9 - - - -
385A PRO* 1.3 73.7 - - - +
387A LEU* 1.3 83.3 + - + +
389A SER* 3.2 8.9 - - - -
404A GLN* 2.5 44.1 + - + +
405A LEU* 6.4 0.4 - - + -
408A PHE* 4.2 20.2 - - + -
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Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A PRO* 3.6 0.6 - - - +
386A ILE* 1.3 91.2 - - + +
388A PHE* 1.3 76.7 + - + +
389A SER 3.0 2.0 + - - -
390A GLY 3.3 10.0 + - - -
391A TYR 3.4 7.4 + - - -
401A VAL* 3.5 27.0 - - + +
404A GLN* 3.2 16.7 + - + +
405A LEU* 3.7 34.1 - - + -
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Residues in contact with PHE 388 (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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384A THR* 4.8 6.3 - - + -
385A PRO* 4.3 18.6 - - + +
386A ILE 3.6 0.2 - - - -
387A LEU* 1.3 84.2 - - + +
389A SER* 1.3 62.3 + - - +
391A TYR* 3.3 12.0 + + - +
392A LEU* 3.0 44.7 + - + +
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Residues in contact with SER 389 (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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291A LEU* 2.9 45.5 + - - +
380A VAL* 4.9 2.3 - - - +
384A THR* 3.8 19.2 + - - +
385A PRO 3.1 20.8 + - - -
386A ILE* 3.2 9.9 - - - -
388A PHE* 1.3 77.5 - - - +
390A GLY* 1.3 54.1 + - - +
392A LEU* 4.3 1.7 - - - +
393A GLY* 2.7 35.5 + - - -
404A GLN* 3.7 1.1 - - - -
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Residues in contact with GLY 390 (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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292A TRP* 3.5 21.4 - - - -
387A LEU 3.3 2.4 + - - -
389A SER* 1.3 71.3 - - - +
391A TYR* 1.3 62.2 + - - +
394A SER* 2.9 27.2 + - - -
400A GLY* 3.6 7.6 - - - -
401A VAL 4.0 7.0 - - - -
404A GLN* 2.7 31.3 + - - -
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Residues in contact with TYR 391 (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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48A LEU* 3.7 12.6 - - + +
49A PRO* 5.0 0.5 - - - +
50A ILE* 3.5 34.9 + - + +
387A LEU 3.4 5.8 + - - +
388A PHE* 3.3 15.5 + + - +
389A SER 3.1 0.6 - - - -
390A GLY* 1.3 80.6 - - - +
392A LEU* 1.3 93.0 + - + +
394A SER* 3.0 10.7 + - - -
396A GLY* 2.9 53.8 + - - -
397A LYS 3.8 8.4 - - - +
398A ILE* 5.0 9.0 - - + -
401A VAL* 3.5 21.6 - - + +
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Residues in contact with LEU 392 (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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44A ILE* 4.4 38.1 - - + +
48A LEU* 5.1 11.0 - - + -
376A SER* 3.8 6.2 + - - -
378A ALA* 4.7 1.7 - - - +
380A VAL* 5.0 14.6 - - + -
384A THR* 4.8 12.1 - - + -
388A PHE* 3.0 33.3 + - + +
389A SER* 4.3 1.8 - - - +
391A TYR* 1.3 98.9 - - + +
393A GLY* 1.3 58.3 + - - +
394A SER 3.1 0.4 - - - -
395A GLY* 3.1 17.1 + - - -
396A GLY 4.3 4.0 - - - +
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Residues in contact with GLY 393 (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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287A GLN* 5.6 0.6 - - - +
291A LEU* 3.8 20.8 - - - +
292A TRP* 3.8 7.0 - - - -
375A PRO* 3.2 13.5 - - - +
376A SER* 3.0 21.4 + - - -
377A GLY 4.5 0.5 + - - -
378A ALA 5.2 3.1 - - - +
380A VAL* 4.3 6.2 - - - +
389A SER 2.7 22.9 + - - -
391A TYR 3.1 0.4 - - - -
392A LEU* 1.3 73.1 - - - +
394A SER* 1.3 58.8 + - - +
395A GLY 3.4 0.4 - - - -
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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