Contacts of the helix formed by residues 380 - 392 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330D VAL* 4.4 15.3 - - + +
333D LEU* 3.8 23.7 - - + +
334D ASP* 3.5 38.5 + - + -
376D LYS 3.4 17.0 + - - +
377D PHE 4.0 2.7 - - - +
378D VAL 3.3 1.6 - - - -
379D ALA* 1.3 78.3 - - - +
381D PRO* 1.3 80.8 - - + +
382D ASN* 3.2 47.9 + - + -
383D CYS* 3.0 5.6 + - - +
384D GLN* 3.0 22.8 + - - +
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Residues in contact with PRO 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A GLU* 4.5 25.6 - - + +
379D ALA 4.1 4.7 - - - +
380D HIS* 1.3 99.3 - - + +
382D ASN* 1.3 62.4 + - - +
384D GLN* 3.9 9.9 - - + +
385D GLN* 3.0 32.4 + - - +
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Residues in contact with ASN 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PHE* 3.3 30.8 - - + -
271A ARG* 5.2 2.9 + - - +
333D LEU* 3.3 37.1 + - + +
334D ASP* 4.5 6.9 + - - +
336D CYS* 4.6 7.1 + - - +
342D VAL* 3.6 9.0 - - + +
346D LEU* 3.4 14.9 - - - +
380D HIS* 3.2 22.2 + - + -
381D PRO* 1.3 81.2 - - - +
383D CYS* 1.3 56.4 + - - +
385D GLN* 3.3 27.9 + - - +
386D GLN 4.1 0.3 + - - -
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Residues in contact with CYS 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D LEU* 4.8 0.4 - - + -
346D LEU* 4.0 15.2 - - + +
366D LEU* 3.7 40.8 - - - -
377D PHE 3.5 21.1 - - - +
378D VAL* 4.0 15.5 - - - +
380D HIS* 3.0 11.7 + - + +
382D ASN* 1.3 76.9 - - - +
384D GLN* 1.3 60.7 + - - +
385D GLN 3.2 1.6 - - - -
386D GLN* 3.2 2.8 + - - +
387D LEU* 3.0 35.7 + - - +
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Residues in contact with GLN 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A GLU* 5.3 5.6 - - - +
378D VAL 2.9 22.0 - - - +
379D ALA* 4.5 4.7 - - - +
380D HIS 3.0 20.4 + - - +
381D PRO* 3.9 7.9 - - + +
383D CYS* 1.3 75.3 - - - +
385D GLN* 1.3 58.6 + - - +
387D LEU* 4.3 10.4 - - - +
388D LEU* 2.9 45.3 + - + +
743D LYS* 3.6 29.4 + - + +
746D ARG* 3.1 32.9 - - - +
747D ALA* 4.6 4.7 - - - +
750D TRP* 4.3 13.8 - - + -
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Residues in contact with GLN 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PHE* 4.1 26.2 - - + +
313A GLU* 5.4 9.5 + - + +
339D THR* 5.4 4.6 + - - -
342D VAL* 3.7 18.2 - - - +
381D PRO 3.0 20.6 + - - +
382D ASN* 3.3 22.9 + - - +
384D GLN* 1.3 77.4 - - - +
386D GLN* 1.3 68.5 + - - +
388D LEU* 4.3 6.5 - - - +
389D SER* 3.1 23.7 + - - -
399D ARG* 5.0 3.8 + - - +
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Residues in contact with GLN 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342D VAL* 4.7 3.1 - - - +
343D GLU* 4.3 13.7 - - - +
346D LEU* 3.4 31.0 - - + +
347D ASN* 3.3 37.1 + - - +
361D PRO* 3.7 20.6 - - + +
363D LEU* 4.1 10.3 - - - +
366D LEU* 4.3 4.6 - - + +
383D CYS 3.2 8.2 + - - +
384D GLN 3.2 0.6 - - - -
385D GLN* 1.3 90.4 + - - +
387D LEU* 1.3 67.7 + - + +
388D LEU 3.3 0.2 - - - -
389D SER* 3.3 14.0 + - - -
390D ILE* 3.5 17.1 + - + +
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Residues in contact with LEU 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D LEU* 4.4 9.0 - - + -
366D LEU* 3.8 15.9 - - + -
378D VAL* 4.6 2.7 - - + -
383D CYS* 3.0 35.1 + - - +
384D GLN* 4.1 6.7 - - - +
386D GLN* 1.3 76.5 - - + +
388D LEU* 1.3 60.7 + - - +
390D ILE* 3.2 6.5 + - + +
391D TRP* 3.0 27.5 + - - +
747D ALA* 4.2 20.9 - - + -
750D TRP* 3.8 23.5 - - + -
751D PHE* 3.7 36.3 - - + -
754D PHE* 3.9 16.9 - - + -
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Residues in contact with LEU 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A GLU* 5.8 4.3 - - - +
384D GLN* 2.9 30.4 + - + +
385D GLN* 4.6 3.4 - - - +
387D LEU* 1.3 76.2 - - - +
389D SER* 1.3 56.6 + - - +
391D TRP* 4.1 6.1 - - + -
392D TYR* 2.9 60.8 + - + +
399D ARG* 3.4 25.3 + - - +
746D ARG* 5.6 4.5 - - - +
750D TRP* 3.6 31.6 - - + -
1004D Y01 5.0 2.9 - - - +
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Residues in contact with SER 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385D GLN 3.1 15.3 + - - -
386D GLN* 3.3 12.0 + - - -
387D LEU 3.2 0.8 - - - -
388D LEU* 1.3 77.6 - - - +
390D ILE* 1.3 59.5 + - - +
392D TYR 4.1 5.3 - - - +
393D GLU* 3.9 16.8 - - - +
399D ARG* 4.6 9.6 + - - +
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Residues in contact with ILE 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D ARG* 3.7 46.7 - - + +
361D PRO* 4.3 20.4 - - + -
363D LEU* 3.8 35.7 - - + -
386D GLN* 3.5 18.6 - - + +
387D LEU* 3.2 8.7 + - + +
388D LEU 3.2 0.2 - - - -
389D SER* 1.3 79.7 - - - +
391D TRP* 1.3 67.5 + - - +
392D TYR 3.5 0.2 - - - -
393D GLU* 3.5 13.1 - - + +
439D PRO* 3.4 16.1 - - - +
754D PHE* 3.9 21.3 - - + -
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Residues in contact with TRP 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D LEU 3.0 17.5 + - - +
388D LEU* 3.8 12.3 - - + +
390D ILE* 1.3 80.0 - - - +
392D TYR* 1.3 82.4 + + - +
393D GLU 3.2 5.0 + - - -
395D LEU* 5.4 0.5 - - - +
439D PRO* 3.6 29.6 - - + +
440D PHE* 3.4 52.8 + + + +
443D PHE* 3.7 32.3 - + + -
616D ALA* 5.4 0.4 - - + -
749D LEU* 4.4 5.6 - - + -
750D TRP* 3.6 40.8 - + + -
753D TYR* 3.9 22.4 - + + -
754D PHE* 4.0 11.4 - + + -
1004D Y01 3.0 31.2 + - - -
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Residues in contact with TYR 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D LEU* 2.9 42.7 + - + +
389D SER* 4.1 7.9 - - - +
391D TRP* 1.3 83.1 - + - +
393D GLU* 1.3 63.6 + - - +
394D ASN 3.7 1.1 - - - -
395D LEU* 3.8 27.5 + - + +
398D LEU 4.3 8.1 - - - -
399D ARG* 3.6 47.5 + - + +
406D LYS* 3.4 18.5 + - - -
440D PHE* 3.7 38.4 - + - -
1004D Y01 2.4 29.8 + - - +
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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