Contacts of the helix formed by residues 380 - 392 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330B VAL* 4.4 16.2 - - + +
333B LEU* 3.8 24.0 - - + +
334B ASP* 3.5 37.8 + - + -
376B LYS 3.4 17.2 + - - +
377B PHE 4.0 2.9 - - - +
378B VAL 3.3 1.8 - - - -
379B ALA* 1.3 77.0 - - - +
381B PRO* 1.3 78.7 - - + +
382B ASN* 3.4 48.4 + - + +
383B CYS* 3.0 5.4 + - - +
384B GLN* 3.0 23.1 + - - +
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Residues in contact with PRO 381 (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 ALA 4.1 5.2 - - - +
380B HIS* 1.3 100.1 - - + +
382B ASN* 1.3 61.6 + - - +
384B GLN* 3.9 8.4 - - + +
385B GLN* 3.0 32.8 + - - +
313C GLU* 4.5 26.0 - - + +
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Residues in contact with ASN 382 (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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333B LEU* 3.3 35.5 + - + +
334B ASP* 4.5 6.5 + - - +
336B CYS* 4.6 7.9 + - - +
342B VAL* 3.6 9.8 - - + +
346B LEU* 3.4 14.9 - - - +
380B HIS* 3.2 23.0 + - + -
381B PRO* 1.3 80.9 - - - +
383B CYS* 1.3 58.1 + - - +
385B GLN* 3.3 27.6 + - - +
386B GLN 4.1 0.3 + - - -
267C PHE* 3.3 28.8 - - + -
271C ARG* 5.2 2.5 + - - +
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Residues in contact with CYS 383 (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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333B LEU* 4.8 0.6 - - + +
346B LEU* 4.0 15.0 - - + +
366B LEU* 3.7 41.5 - - - -
377B PHE 3.5 22.9 - - - +
378B VAL* 4.0 14.6 - - - +
380B HIS* 3.0 11.7 + - + +
382B ASN* 1.3 76.1 - - - +
384B GLN* 1.3 59.6 + - - +
385B GLN 3.2 1.8 - - - -
386B GLN* 3.2 3.7 + - - +
387B LEU* 3.0 34.4 + - - +
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Residues in contact with GLN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B VAL 2.9 22.1 - - - +
379B ALA* 4.5 4.5 - - - +
380B HIS 3.0 19.8 + - - +
381B PRO* 3.9 7.6 - - + +
383B CYS* 1.3 75.7 - - - +
385B GLN* 1.3 57.6 + - - +
387B LEU* 4.1 10.4 - - - +
388B LEU* 2.9 44.9 + - + +
743B LYS* 3.6 27.7 + - + +
746B ARG* 3.1 34.4 - - - +
747B ALA* 4.6 5.2 - - - +
750B TRP* 4.3 14.3 - - + -
313C GLU* 5.3 6.3 - - - +
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Residues in contact with GLN 385 (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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339B THR* 5.4 4.6 + - - -
342B VAL* 3.7 17.6 - - - +
381B PRO 3.0 20.8 + - - +
382B ASN* 3.3 22.7 + - - +
384B GLN* 1.3 76.9 - - - +
386B GLN* 1.3 69.4 + - - +
388B LEU* 4.6 6.6 - - - +
389B SER* 3.1 23.2 + - - -
399B ARG* 5.0 3.6 + - - +
267C PHE* 4.1 25.7 - - + -
313C GLU* 5.4 9.1 + - + +
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Residues in contact with GLN 386 (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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342B VAL* 4.7 2.8 - - - +
343B GLU* 4.3 15.3 - - - +
346B LEU* 3.4 31.0 - - + +
347B ASN* 3.3 36.6 + - - +
361B PRO* 3.7 20.6 - - + +
363B LEU* 4.1 10.1 - - - +
366B LEU* 4.3 4.8 - - + +
383B CYS 3.2 8.2 + - - +
384B GLN 3.2 0.8 - - - -
385B GLN* 1.3 90.4 + - - +
387B LEU* 1.3 67.6 + - + +
389B SER* 3.3 15.2 + - - -
390B ILE* 3.5 17.7 + - + +
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Residues in contact with LEU 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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363B LEU* 4.4 9.0 - - + -
366B LEU* 3.8 15.9 - - + -
378B VAL* 4.6 2.9 - - + -
383B CYS* 3.0 35.8 + - - +
384B GLN* 4.1 7.6 - - - +
386B GLN* 1.3 76.7 - - + +
388B LEU* 1.3 60.6 + - - +
390B ILE* 3.2 7.5 + - + +
391B TRP* 3.0 27.2 + - - +
747B ALA* 4.2 20.6 - - + -
750B TRP* 3.8 23.1 - - + -
751B PHE* 3.7 36.6 - - + -
754B PHE* 3.9 15.7 - - + -
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Residues in contact with LEU 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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384B GLN* 2.9 28.5 + - + +
385B GLN* 4.6 3.4 - - - +
386B GLN 3.3 0.2 - - - -
387B LEU* 1.3 77.3 - - - +
389B SER* 1.3 57.3 + - - +
391B TRP* 3.7 6.7 - - + -
392B TYR* 2.9 61.6 + - + +
399B ARG* 3.4 25.4 + - - +
746B ARG* 5.6 4.7 - - - +
750B TRP* 3.6 32.5 - - + -
1005B Y01 5.0 3.4 - - - +
313C GLU* 5.8 4.3 - - - +
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Residues in contact with SER 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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385B GLN 3.1 15.0 + - - -
386B GLN* 3.3 11.6 + - - -
387B LEU 3.2 0.8 - - - -
388B LEU* 1.3 80.3 - - - +
390B ILE* 1.3 60.3 + - - +
392B TYR 4.1 4.6 - - - +
393B GLU* 3.9 16.8 - - - +
399B ARG* 4.6 9.6 + - - +
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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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360B ARG* 3.7 47.6 - - + +
361B PRO* 4.3 19.3 - - + -
363B LEU* 3.8 34.5 - - + -
386B GLN* 3.5 19.1 - - + +
387B LEU* 3.2 8.4 + - + +
388B LEU 3.2 0.2 - - - -
389B SER* 1.3 78.0 - - - +
391B TRP* 1.3 66.7 + - - +
392B TYR 3.5 0.2 - - - -
393B GLU* 3.5 12.5 - - - +
439B PRO* 3.4 16.8 - - - +
754B PHE* 3.9 21.8 - - + -
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Residues in contact with TRP 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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387B LEU 3.0 17.1 + - - +
388B LEU* 3.8 12.1 - - + +
390B ILE* 1.3 79.9 - - - +
392B TYR* 1.3 81.8 + + - +
393B GLU 3.2 5.0 + - - -
395B LEU* 5.4 0.2 - - - +
438B GLY* 5.4 0.2 - - - -
439B PRO* 3.6 30.4 - - + +
440B PHE* 3.4 52.3 + + + +
443B PHE* 3.7 33.0 - + + -
616B ALA* 5.4 0.2 - - + -
749B LEU* 4.4 5.4 - - + -
750B TRP* 3.6 40.6 - + + -
753B TYR* 3.9 22.9 - + + -
754B PHE* 4.0 11.4 - + + -
1005B Y01 3.0 31.6 + - - -
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Residues in contact with TYR 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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388B LEU* 2.9 43.2 + - + +
389B SER* 4.1 7.6 - - - +
391B TRP* 1.3 82.7 - + - +
393B GLU* 1.3 62.4 + - - +
394B ASN 3.7 1.3 - - - -
395B LEU* 3.8 27.8 + - + +
398B LEU 4.3 7.9 - - - -
399B ARG* 3.6 45.5 - - + +
406B LYS* 3.4 18.8 + - - -
440B PHE* 3.7 39.9 - + + -
1005B Y01 2.4 30.2 + - - +
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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