Contacts of the helix formed by residues 380 - 392 (chain A) in PDB entry 6UZA
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 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A VAL* 4.4 15.6 + - + +
333A LEU* 3.8 23.5 - - + +
334A ASP* 3.5 37.4 + - + -
376A LYS 3.4 17.0 + - - +
377A PHE 4.0 2.7 - - - +
378A VAL 3.3 1.4 - - - -
379A ALA* 1.3 78.3 - - - +
381A PRO* 1.3 79.0 - - + +
382A ASN* 3.2 48.0 + - + +
383A CYS* 3.0 5.4 + - - +
384A GLN* 3.0 22.9 + - - +
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Residues in contact with PRO 381 (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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379A ALA 4.1 4.9 - - - +
380A HIS* 1.3 99.3 - - + +
382A ASN* 1.3 62.7 + - - +
384A GLN* 3.9 9.0 - - + +
385A GLN* 3.0 32.5 + - - +
313B GLU* 4.5 25.0 - - + +
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Residues in contact with ASN 382 (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 LEU* 3.3 35.5 + - + +
334A ASP* 4.5 6.3 + - - +
336A CYS* 4.6 8.1 + - - +
342A VAL* 3.6 9.7 - - + +
346A LEU* 3.4 15.1 - - - +
380A HIS* 3.2 24.0 + - + -
381A PRO* 1.3 81.5 - - - +
383A CYS* 1.3 56.6 + - - +
385A GLN* 3.3 27.9 + - - +
386A GLN 4.1 0.3 + - - -
267B PHE* 3.3 29.4 - - - -
271B ARG* 5.2 2.7 + - - +
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Residues in contact with CYS 383 (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 LEU* 4.8 0.6 - - + +
346A LEU* 4.0 15.5 - - + -
366A LEU* 3.7 41.3 - - - -
377A PHE 3.5 22.7 - - - +
378A VAL* 4.0 14.1 - - - +
380A HIS* 3.0 12.3 + - + +
382A ASN* 1.3 77.4 - - - +
384A GLN* 1.3 60.6 + - - +
385A GLN 3.2 1.6 - - - -
386A GLN* 3.2 3.1 + - - +
387A LEU* 3.0 34.9 + - - +
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Residues in contact with GLN 384 (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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378A VAL 2.9 23.1 - - - +
379A ALA* 4.5 4.7 - - - +
380A HIS 3.0 19.6 + - - +
381A PRO* 3.3 8.0 + - + +
383A CYS* 1.3 75.1 - - - +
385A GLN* 1.3 58.4 + - - +
387A LEU* 4.1 9.9 - - - +
388A LEU* 2.9 44.9 + - + +
743A LYS* 3.6 28.9 + - + +
746A ARG* 3.1 33.4 - - - +
747A ALA* 4.6 5.2 - - - +
750A TRP* 4.3 13.7 - - + -
313B GLU* 5.3 5.4 - - - +
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Residues in contact with GLN 385 (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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339A THR* 5.4 4.8 + - - -
342A VAL* 3.7 18.0 - - - +
381A PRO 3.0 20.6 + - - +
382A ASN* 3.3 22.6 + - - +
384A GLN* 1.3 76.9 - - - +
386A GLN* 1.3 68.7 + - - +
388A LEU* 4.3 6.9 - - - +
389A SER* 3.1 23.0 + - - -
399A ARG* 5.0 4.2 + - - +
267B PHE* 4.1 25.0 - - + +
313B GLU* 5.4 9.3 + - + +
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Residues in contact with GLN 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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342A VAL* 4.7 3.3 - - - +
343A GLU* 4.3 13.3 - - - +
346A LEU* 3.4 32.3 - - + +
347A ASN* 3.3 36.9 + - - +
361A PRO* 3.7 20.9 - - + +
363A LEU* 4.1 10.7 - - - +
366A LEU* 4.3 4.4 - - + +
382A ASN 4.3 0.4 - - - +
383A CYS* 3.2 8.1 + - - +
384A GLN 3.2 0.2 - - - -
385A GLN* 1.3 90.2 + - - +
387A LEU* 1.3 68.9 + - + +
389A SER* 3.3 14.1 + - - -
390A ILE* 3.5 17.5 + - + +
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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
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363A LEU* 4.4 8.3 - - + -
366A LEU* 3.8 16.8 - - + -
378A VAL* 4.6 2.9 - - + -
383A CYS* 3.0 34.9 + - - +
384A GLN* 3.3 6.7 + - - +
386A GLN* 1.3 75.9 - - + +
388A LEU* 1.3 60.2 + - - +
390A ILE* 3.2 6.6 + - + +
391A TRP* 3.0 27.2 + - - +
747A ALA* 4.2 20.6 - - + -
750A TRP* 3.8 23.7 - - + -
751A PHE* 3.7 36.8 - - + -
754A PHE* 3.9 17.0 - - + -
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Residues in contact with LEU 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 GLN* 2.9 29.5 + - + +
385A GLN* 4.6 3.4 - - - +
387A LEU* 1.3 77.2 - - - +
389A SER* 1.3 57.8 + - - +
391A TRP* 4.1 5.4 - - + -
392A TYR* 2.9 61.9 + - + +
399A ARG* 3.4 26.7 + - - +
746A ARG* 5.6 4.3 - - - +
750A TRP* 3.6 32.1 - - + -
1004A Y01 5.0 2.9 - - - +
313B GLU* 5.8 3.4 - - - +
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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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385A GLN 3.1 15.2 + - - -
386A GLN* 3.3 11.3 + - - -
387A LEU 3.2 1.0 - - - -
388A LEU* 1.3 78.7 - - - +
390A ILE* 1.3 61.2 + - - +
392A TYR 4.1 4.9 - - - +
393A GLU* 3.9 16.8 - - - +
399A ARG* 4.6 9.3 + - - +
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Residues in contact with ILE 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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360A ARG* 3.7 47.1 - - + +
361A PRO* 4.3 20.0 - - + -
363A LEU* 3.8 35.7 - - + -
386A GLN* 3.5 17.5 - - + +
387A LEU* 3.2 8.9 + - + +
388A LEU 3.2 0.4 - - - -
389A SER* 1.3 78.8 - - - +
391A TRP* 1.3 66.9 + - - +
392A TYR 3.5 0.2 - - - -
393A GLU* 3.5 13.0 - - - +
439A PRO* 3.4 16.6 - - - +
754A PHE* 3.9 20.6 - - + -
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Residues in contact with TRP 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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387A LEU 3.0 16.7 + - - +
388A LEU* 3.8 12.8 - - + +
390A ILE* 1.3 78.6 - - - +
392A TYR* 1.3 82.0 + + - +
393A GLU 3.2 4.7 + - - -
395A LEU* 5.4 0.3 - - - +
439A PRO* 3.6 29.3 - - + +
440A PHE* 3.4 53.2 + + + +
443A PHE* 3.7 32.1 - + + -
616A ALA* 5.4 0.4 - - + -
749A LEU* 4.4 5.6 - - + -
750A TRP* 3.6 41.1 - + + -
753A TYR* 3.9 23.3 - + + -
754A PHE* 4.0 11.4 - + + -
1004A Y01 3.0 31.0 + - - -
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Residues in contact with TYR 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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388A LEU* 2.9 43.9 + - + +
389A SER* 4.1 7.9 - - - +
391A TRP* 1.3 83.7 - + - +
393A GLU* 1.3 64.0 + - - +
394A ASN 3.7 1.3 - - - -
395A LEU* 3.8 28.4 + - + +
398A LEU 4.3 8.1 - - - -
399A ARG* 3.6 45.5 + - + +
406A LYS* 3.4 18.8 + - - -
440A PHE* 3.7 38.8 - + - -
1004A Y01 2.4 30.7 + - - +
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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