Contacts of the helix formed by residues 377 - 392 (chain B) in PDB entry 5U03
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 GLY 377 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B SER* 3.3 16.3 + - - -
340B ALA* 4.4 6.3 - - - +
343B GLU* 3.1 20.2 + - - -
375B VAL 3.3 0.6 + - - -
376B ARG* 1.4 77.6 - - - +
378B THR* 1.3 65.1 + - - +
379B GLU 3.1 3.6 - - - -
380B GLY 3.0 2.3 + - - -
381B LYS* 2.7 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 378 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLU* 3.9 0.2 + - - -
374B GLY 4.2 2.3 + - - -
375B VAL* 2.6 38.1 + - + +
376B ARG 3.2 1.4 + - - -
377B GLY* 1.3 76.1 - - - +
379B GLU* 1.3 57.7 + - - +
381B LYS* 3.1 12.9 + - - +
382B ILE* 2.8 39.1 + - + +
400B LEU* 5.6 1.4 - - - +
404B LEU* 3.7 30.3 - - + +
411B ARG* 6.3 0.2 - - - +
420B ASN* 5.9 2.7 - - - +
424B PHE* 4.1 13.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 379 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLU* 3.3 17.0 + - - +
344B PRO* 3.5 33.8 - - - +
345B ILE* 5.0 6.6 - - - +
377B GLY 3.1 0.6 - - - -
378B THR* 1.3 79.8 - - - +
380B GLY* 1.3 58.6 + - - +
382B ILE* 3.0 8.9 + - - +
383B GLN* 2.8 51.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 380 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B SER* 3.4 27.6 - - - -
342B LEU* 3.7 8.2 - - - +
343B GLU* 3.0 21.7 + - - +
377B GLY 3.0 0.6 + - - -
379B GLU* 1.3 75.9 - - - +
381B LYS* 1.3 56.0 + - - +
383B GLN* 3.3 12.0 + - - +
384B ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 381 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B VAL* 4.5 11.0 - - + -
305B GLY* 3.9 14.1 - - - -
306B LYS* 3.7 18.7 - - - +
339B SER* 2.9 34.6 + - - -
369B VAL* 4.5 16.7 - - + +
370B PRO 5.7 2.5 - - - -
372B GLY* 6.1 3.6 - - - -
374B GLY 5.6 1.1 - - - -
376B ARG 2.9 25.1 + - - -
377B GLY* 2.7 13.6 + - - +
378B THR* 3.3 9.2 - - - +
380B GLY* 1.3 78.0 - - - +
382B ILE* 1.3 62.1 + - - +
384B ALA* 3.1 5.0 + - - +
385B ILE* 3.0 26.7 + - - +
400B LEU* 4.5 15.5 - - + -
404B LEU* 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 382 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B THR* 2.8 37.3 + - + +
379B GLU* 3.7 5.8 - - - +
381B LYS* 1.3 71.7 - - - +
383B GLN* 1.3 62.5 + - + +
385B ILE* 3.0 8.3 + - - +
386B ALA* 2.8 28.8 + - + +
404B LEU* 4.1 28.3 - - + +
407B VAL* 4.8 7.2 - - + -
408B GLU* 3.6 28.3 - - + -
411B ARG* 3.5 35.4 - - - +
412B ASN* 5.5 2.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
342B LEU 2.9 25.8 + - - +
343B GLU* 3.8 3.6 - - - -
344B PRO* 3.9 10.7 - - - +
354B TYR* 5.6 1.8 + - - -
358B TRP* 3.9 18.7 - - + -
379B GLU* 2.8 41.6 + - + +
380B GLY* 3.5 14.8 + - - +
382B ILE* 1.3 78.3 - - + +
384B ALA* 1.3 56.1 + - - +
386B ALA* 3.3 5.8 + - - +
387B TRP* 2.8 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B VAL* 4.2 17.3 - - + -
342B LEU* 3.9 18.2 - - + -
358B TRP* 4.3 2.2 - - - -
361B LEU* 4.2 15.5 - - + -
367B VAL* 5.5 3.4 - - + +
369B VAL* 4.9 4.7 - - + -
380B GLY 2.9 13.3 + - - +
381B LYS 3.4 8.7 - - - +
383B GLN* 1.3 76.6 - - - +
385B ILE* 1.3 58.2 + - - +
387B TRP* 3.2 9.6 + - - +
388B ALA* 2.8 30.5 + - - +
395B PHE* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 385 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B VAL* 4.2 12.6 - - + -
381B LYS 3.0 20.7 + - - +
382B ILE* 3.0 12.4 + - - +
384B ALA* 1.3 76.4 - - - +
386B ALA* 1.3 57.7 + - - +
388B ALA* 3.1 5.3 + - - +
389B ARG* 2.8 27.4 + - - +
395B PHE* 3.8 22.9 - - + -
401B GLY 3.9 8.1 - - - +
404B LEU* 3.8 18.4 - - + +
405B ALA* 3.7 32.3 - - + +
408B GLU* 3.9 14.4 - - + +
520B PHE* 3.8 26.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B ILE* 2.8 17.2 + - + +
383B GLN* 3.8 6.3 - - - +
385B ILE* 1.3 74.1 - - - +
387B TRP* 1.3 57.8 + - - +
389B ARG* 3.2 2.9 + - - +
390B ASN* 2.8 44.5 + - - +
408B GLU* 3.3 32.5 - - + +
412B ASN* 4.1 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B TRP* 3.8 26.9 - + + -
361B LEU* 3.5 45.1 - - + -
362B CYS* 3.6 34.2 - - + +
364B ALA 5.1 1.6 - - - -
367B VAL* 4.0 13.9 - - + -
383B GLN 2.8 17.4 + - - +
384B ALA 3.3 5.6 - - - +
385B ILE 3.1 0.2 - - - -
386B ALA* 1.3 76.3 - - - +
388B ALA* 1.3 73.0 + - + +
390B ASN* 3.1 6.7 + - - +
391B GLN* 2.9 62.4 + - + +
393B LYS* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B VAL* 3.9 27.8 - - + -
384B ALA 2.8 16.6 + - - +
385B ILE 3.6 3.8 - - - +
387B TRP* 1.3 88.0 - - + +
389B ARG* 1.3 58.6 + - - +
392B LYS* 2.7 25.6 + - - -
393B LYS* 2.9 25.6 + - + +
395B PHE* 4.2 9.9 - - + -
517B HIS* 3.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ILE 2.8 16.1 + - - +
386B ALA* 3.6 3.5 - - - +
388B ALA* 1.3 77.4 - - - +
390B ASN* 1.3 80.1 + - - +
392B LYS* 3.4 26.3 + - - +
408B GLU* 2.8 40.6 + - - +
409B PHE* 4.9 11.2 - - - +
412B ASN* 3.6 19.8 + - - +
413B VAL* 3.9 23.3 - - - +
514B LEU* 3.6 33.2 - - + -
517B HIS* 3.7 9.1 - - + -
520B PHE* 3.7 14.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B ALA* 2.8 30.1 + - - +
387B TRP* 3.8 4.6 - - - +
389B ARG* 1.3 99.8 + - - +
391B GLN* 1.3 70.4 + - - +
392B LYS* 3.2 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B TRP* 2.9 48.4 + - + +
390B ASN* 1.3 85.2 + - - +
392B LYS* 1.3 72.1 + - - +
393B LYS* 3.6 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ALA 2.7 9.7 + - - -
389B ARG* 3.4 15.3 + - - +
390B ASN* 3.2 10.4 - - - +
391B GLN* 1.3 81.6 - - - +
393B LYS* 1.3 61.1 + - - +
394B PRO* 4.1 3.3 - - - +
514B LEU* 5.5 3.0 - - - +
515B GLU 5.2 0.6 + - - -
516B ASP* 2.9 25.5 + - - +
517B HIS* 3.4 24.4 - - + +
518B PRO* 3.8 32.1 - - + +
----------------------------------------------------------
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