Contacts of the strand formed by residues 386 - 393 (chain B) in PDB entry 3QGY
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 386 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381B TYR* 3.1 7.0 - - - -
382B TRP* 3.0 52.4 + - + +
385B LYS* 1.3 108.9 + - - +
387B LYS* 1.3 66.1 + - - +
388B VAL* 3.4 6.1 - - + +
422B TYR* 3.4 33.4 + - + +
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Residues in contact with LYS 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B LEU* 3.9 26.5 - - + +
380B GLY 3.4 9.9 - - - +
381B TYR* 3.7 27.7 + - + +
385B LYS 4.0 1.6 + - - -
386B ASP* 1.3 73.3 - - - +
388B VAL* 1.3 65.3 + - - +
422B TYR* 4.6 3.6 - - - -
436B GLU 4.4 0.2 - - - -
437B PHE* 3.4 49.2 + - + +
439B GLU* 3.3 24.6 + - - +
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B LEU* 5.1 0.7 - - + -
379B LEU* 3.4 5.2 - - - +
380B GLY 2.7 59.2 + - - +
381B TYR* 3.4 13.5 - - - +
382B TRP* 3.9 15.3 - - + -
386B ASP* 3.4 12.1 - - + +
387B LYS* 1.3 83.2 - - - +
389B ALA* 1.3 58.8 + - - +
390B ILE* 3.9 17.3 - - + -
422B TYR* 4.0 13.2 - - + -
434B VAL* 3.8 15.7 - - + -
435B PHE 3.5 13.2 - - - +
437B PHE* 3.9 9.9 - - - -
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B L7O 3.3 55.4 - - + +
369B ILE* 4.8 1.3 - - + -
377B VAL* 4.7 4.9 - - + -
378B HIS 3.2 7.2 - - - +
388B VAL* 1.3 72.7 - - - +
390B ILE* 1.3 60.8 + - - +
435B PHE* 2.9 37.7 + - - -
436B GLU 3.9 3.1 + - - +
437B PHE* 4.2 4.3 - - + -
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Residues in contact with ILE 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B LEU* 4.0 23.8 - - + -
364B THR 4.4 1.8 - - - +
365B PHE* 3.7 40.6 - - + -
376B LEU 3.6 0.9 - - - +
377B VAL* 3.2 4.3 - - - -
378B HIS* 2.6 45.1 + - + +
380B GLY* 4.1 15.9 - - - -
388B VAL* 3.9 24.9 - - + -
389B ALA* 1.3 75.1 - - - +
391B LYS* 1.3 61.5 + - - +
392B THR* 3.8 2.2 + - + -
432B CYS* 3.7 30.7 - - + -
433B LEU 3.4 4.9 - - - +
434B VAL* 4.5 8.1 - - + -
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Residues in contact with LYS 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B L7O 3.3 31.3 + - + -
374B PHE 6.2 0.2 - - - -
375B GLY* 5.0 4.7 - - - -
376B LEU 3.2 15.5 - - - +
377B VAL* 4.4 9.9 - - + +
389B ALA 4.0 1.6 + - - -
390B ILE* 1.3 71.3 - - - +
392B THR* 1.3 65.6 + - - +
403B PHE* 3.3 26.8 - - + -
406B GLU* 2.9 35.6 + - - +
432B CYS* 3.1 3.9 - - - -
433B LEU* 2.8 38.6 + - + +
435B PHE* 3.8 16.6 - - + -
500B ASP* 4.6 10.9 + - - -
502B GLY* 5.4 1.6 - - - +
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Residues in contact with THR 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B PHE* 3.9 28.5 - - + -
375B GLY* 3.2 3.8 - - - -
376B LEU* 2.9 49.3 + - - +
378B HIS* 4.2 8.2 - - + +
390B ILE* 3.8 1.7 + - + -
391B LYS* 1.3 75.0 - - - +
393B ILE* 1.3 64.6 + - - +
403B PHE* 3.6 2.0 - - - -
430B PRO* 3.9 25.3 - - + +
431B ILE 3.5 3.8 - - - -
432B CYS* 3.7 17.9 - - + -
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Residues in contact with ILE 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B PHE 3.7 2.9 - - - +
376B LEU* 5.1 0.6 + - - +
392B THR* 1.3 80.9 + - - +
394B LYS* 1.3 72.8 + - - +
395B GLU 3.6 4.1 + - - -
396B GLY* 5.7 2.2 - - - -
398B MET* 3.2 31.6 - - + +
400B GLU* 4.0 21.8 - - + +
403B PHE* 3.2 49.1 - - + -
429B ALA 4.8 2.0 - - - +
430B PRO* 4.2 11.4 - - + +
431B ILE* 3.0 33.6 + - + +
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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