Contacts of the helix formed by residues 380 - 391 (chain B) in PDB entry 5WWT
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 ASN 380 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B THR* 2.5 25.8 + - - -
374B THR* 3.1 25.5 + - - +
375B ILE 3.9 1.0 - - - -
376B THR 3.3 12.0 + - - +
377B LEU 3.1 2.6 + - - -
379B GLU* 1.3 82.5 - - - +
381B GLU* 1.3 79.6 + - - +
382B GLU 3.2 0.7 - - - -
383B GLN* 2.9 17.0 + - - +
384B VAL* 3.0 12.5 + - - +
423B ARG* 3.0 21.6 - - - +
458B PHE 5.3 0.2 + - - -
459B PHE* 3.3 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 3.3 17.1 + - + +
380B ASN* 1.3 80.4 - - - +
382B GLU* 1.3 56.6 + - - +
384B VAL* 3.0 12.7 + - - +
385B ALA 2.9 24.8 + - - -
407B GLY* 3.5 4.9 - - - -
408B MET 2.8 40.3 + - - +
411B ALA* 3.5 22.3 - - + +
413B LEU* 4.0 3.6 - - + +
418B LEU* 4.4 4.5 - - + -
421B LEU* 4.0 18.6 - - + -
423B ARG* 2.7 39.0 + - - -
459B PHE* 3.5 9.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLN* 3.4 15.2 + - - +
352B ARG* 4.9 5.0 + - - +
377B LEU* 3.1 25.2 + - + +
378B ALA* 3.3 30.0 + - - +
381B GLU* 1.3 78.0 - - - +
383B GLN* 1.3 59.5 + - - +
385B ALA* 3.4 3.8 + - + +
386B TRP* 2.9 29.7 + - - +
410B GLY 5.4 3.5 - - - +
411B ALA* 3.7 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 383 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLN* 3.2 30.5 + - - +
351B GLN* 2.8 28.7 + - - +
352B ARG* 2.9 35.6 + - - +
355B PHE* 5.2 5.3 - - + -
370B TYR* 3.7 16.4 - - + +
378B ALA 3.2 19.3 + - - +
379B GLU 3.4 18.8 - - - +
380B ASN 2.9 8.1 + - - +
382B GLU* 1.3 74.0 - - - +
384B VAL* 1.3 59.5 + - - +
386B TRP* 3.5 8.2 - - + -
387B ALA* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B TYR* 5.1 3.1 - - + -
380B ASN 3.0 12.5 + - - +
381B GLU* 3.0 10.4 + - - +
383B GLN* 1.3 75.0 - - - +
385B ALA* 1.3 59.5 + - - +
387B ALA* 3.3 2.4 + - - +
388B LEU* 2.9 42.4 + - + +
396B LEU* 4.2 12.1 - - + -
413B LEU* 4.1 15.9 - - + -
421B LEU* 4.2 4.9 - - + -
459B PHE* 3.6 28.0 - - + -
461B ALA* 3.9 15.3 - - + -
463B PHE* 3.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B GLU 2.9 10.2 + - - +
382B GLU* 3.7 7.9 - - + +
384B VAL* 1.3 76.8 - - - +
386B TRP* 1.3 62.4 + - - +
388B LEU* 3.2 5.8 + - - +
389B THR* 2.9 29.8 + - - +
411B ALA* 3.9 18.8 - - + +
413B LEU* 3.7 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ARG* 3.4 80.9 - - + +
355B PHE* 3.8 29.4 - + + -
356B THR* 3.9 3.1 - - - -
382B GLU 2.9 17.5 + - - +
383B GLN* 3.5 15.5 - - + +
385B ALA* 1.3 76.0 - - - +
387B ALA* 1.3 74.2 + - - +
389B THR* 3.3 6.4 + - - -
390B LYS* 2.9 63.2 + - + +
391B PHE* 3.8 15.9 - + - -
2D A 4.3 7.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PHE* 3.5 37.0 - - + -
383B GLN 2.9 20.3 + - - +
384B VAL 3.6 4.7 - - - +
386B TRP* 1.3 84.6 - - + +
388B LEU* 1.3 59.4 + - - +
391B PHE* 2.9 40.6 + - - +
394B LEU* 4.7 3.1 - - + +
463B PHE* 4.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B VAL* 2.9 34.2 + - + +
385B ALA* 3.7 5.2 - - - +
387B ALA* 1.3 76.5 - - - +
389B THR* 1.3 61.9 + - - +
391B PHE 3.4 12.3 - - - +
392B PRO* 4.2 5.9 - - - +
394B LEU* 4.0 17.7 - - + +
395B GLN* 4.2 1.6 - - + -
396B LEU* 4.0 28.3 - - + +
413B LEU* 4.6 5.2 - - + -
417B GLN* 3.4 31.0 - - - +
463B PHE* 3.9 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ALA* 2.9 19.9 + - - +
386B TRP* 3.6 6.7 - - + -
388B LEU* 1.3 79.5 - - - +
390B LYS* 1.3 67.5 + - - +
391B PHE 3.5 0.3 + - - -
392B PRO* 4.3 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B THR* 4.4 9.2 - - - -
386B TRP* 2.9 55.8 + - + +
389B THR* 1.3 77.0 - - + +
391B PHE* 1.3 87.3 + - + +
392B PRO* 3.3 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PHE* 4.0 10.5 - + - -
356B THR* 3.4 39.9 - - + -
359B VAL* 3.8 28.9 - - + -
360B GLN* 6.0 2.2 - - + -
386B TRP* 3.8 23.8 - + - -
387B ALA* 2.9 28.4 + - - +
388B LEU 3.4 8.8 - - - +
390B LYS* 1.3 100.0 - - + +
392B PRO* 1.3 64.7 - - - +
393B CYS* 3.3 9.9 + - - -
394B LEU* 3.6 30.9 + - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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