Contacts of the helix formed by residues 373 - 390 (chain A) in PDB entry 1U1H
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 ASP 373 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ALA* 5.5 1.5 + - + -
366A LYS* 5.5 3.2 - - + +
371A GLN 3.4 5.6 + - - +
372A LYS* 1.3 70.1 - - - +
374A GLU* 1.3 63.3 + - - +
375A ALA* 2.9 26.8 + - - +
376A LEU* 2.9 43.8 + - + +
377A PHE* 3.4 18.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A LYS* 3.0 51.1 + - - +
373A ASP* 1.3 71.3 + - - +
375A ALA* 1.3 58.2 + - - +
376A LEU 3.4 0.2 - - - -
377A PHE* 4.2 4.8 - - - +
378A SER* 2.8 36.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ASP* 2.9 13.6 + - - +
374A GLU* 1.3 77.3 - - - +
376A LEU* 1.3 63.3 + - + +
378A SER* 4.1 4.0 - - - -
379A ALA* 3.4 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 4.3 12.9 - - + -
359A VAL* 4.9 17.9 - - + -
363A ALA* 3.9 24.5 - - + -
373A ASP* 2.9 38.3 + - + +
375A ALA* 1.3 78.1 - - + +
377A PHE* 1.3 70.0 + - + +
379A ALA* 3.3 6.9 + - + +
380A ASN* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A PHE* 3.7 44.6 - + + +
304A ALA* 5.0 2.0 - - - -
307A LEU* 3.5 25.1 - - + -
363A ALA* 3.8 23.8 - - + -
364A LEU* 4.2 8.1 - - + -
367A ALA* 3.4 26.2 - - + -
372A LYS* 3.5 31.4 - - + -
373A ASP* 3.4 20.3 + - + +
374A GLU* 4.5 7.0 - - - +
376A LEU* 1.3 81.5 - - + +
378A SER* 1.3 56.5 + - - +
380A ASN* 3.6 1.3 - - - +
381A ALA* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLU* 2.8 28.6 + - - +
375A ALA* 4.1 5.2 - - - -
376A LEU 3.2 0.6 - - - -
377A PHE* 1.3 76.8 - - - +
379A ALA* 1.3 64.7 + - - +
381A ALA* 3.3 5.9 + - - +
382A ALA* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ALA 3.4 15.2 + - - +
376A LEU* 3.3 7.7 + - + +
378A SER* 1.3 79.1 - - - +
380A ASN* 1.3 57.5 + - - +
382A ALA* 3.5 6.7 + - - +
383A ALA* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 4.5 13.9 - - - +
301A ASN 3.1 26.7 + - - +
303A PHE* 3.2 48.5 + - + +
304A ALA 4.8 0.3 + - - -
360A GLU* 4.6 0.6 + - - -
376A LEU 3.0 17.1 + - - +
377A PHE 3.6 4.9 - - - +
379A ALA* 1.3 74.8 - - - +
381A ALA* 1.3 66.0 + - - +
383A ALA* 3.2 7.1 + - - +
384A LEU* 2.9 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A PHE 2.9 18.1 + - - +
378A SER* 3.3 7.4 + - - +
380A ASN* 1.3 77.4 + - - +
382A ALA* 1.3 63.7 + - - +
384A LEU* 3.5 8.9 + - - +
385A ALA* 3.0 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A SER 3.0 17.0 + - - +
379A ALA* 3.6 7.0 - - - +
381A ALA* 1.3 74.7 - - - +
383A ALA* 1.3 59.1 + - - +
385A ALA* 3.2 6.9 + - - +
386A SER* 2.9 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 6.0 0.9 - - + -
349A SER* 3.4 40.6 - - - +
350A TRP* 3.4 9.0 - - + -
379A ALA 3.0 17.7 + - - +
380A ASN* 3.6 9.0 - - - +
382A ALA* 1.3 77.6 - - - +
384A LEU* 1.3 64.2 + - + +
386A SER* 2.9 22.4 + - - -
387A ARG 3.0 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 4.5 13.5 - - + +
301A ASN 4.4 10.3 - - - +
302A ASP* 3.2 37.5 - - + +
303A PHE 4.5 0.2 - - - +
304A ALA* 5.4 1.8 - - + +
350A TRP* 6.5 0.7 - - - -
380A ASN* 2.9 38.5 + - - +
381A ALA* 3.8 6.7 - - - +
383A ALA* 1.3 78.0 - - + +
385A ALA* 1.3 56.8 + - - +
387A ARG* 3.5 19.0 + - - +
388A ARG* 3.0 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA 3.0 18.6 + - - +
382A ALA* 3.4 7.4 - - - +
384A LEU* 1.3 74.9 - - - +
386A SER* 1.3 66.8 + - - +
388A ARG* 3.0 19.1 + - - +
389A SER* 3.0 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLU* 3.8 14.9 + - - +
349A SER* 4.5 3.3 + - - -
350A TRP* 3.0 13.5 + - - -
382A ALA 2.9 17.9 + - - -
383A ALA* 2.9 15.1 + - - -
385A ALA* 1.3 72.9 - - - +
387A ARG* 1.3 59.2 + - - +
389A SER* 3.4 7.7 + - - -
390A SER* 2.8 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A TRP* 4.0 30.3 - - - +
300A ALA 5.2 4.2 + - - -
350A TRP* 3.1 57.1 + - + +
383A ALA 3.0 6.8 + - - +
384A LEU* 3.6 18.7 - - - +
386A SER* 1.3 83.5 + - - +
388A ARG* 1.3 61.2 + - + +
389A SER 3.1 5.0 + - - -
390A SER 3.4 5.5 + - - -
393A VAL* 3.4 25.5 - - + +
529A TYR 5.0 5.3 + - - -
571A ARG* 4.0 8.5 - - - +
572A ASN* 3.1 34.2 + - - +
573A ASP* 3.6 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A ASP* 3.0 34.4 + - - +
384A LEU* 3.0 49.9 + - + +
385A ALA* 3.0 7.7 + - - +
387A ARG* 1.3 78.8 - - + +
389A SER* 1.3 58.7 + - - +
390A SER 5.3 0.4 - - - -
393A VAL* 6.0 0.4 - - - -
394A THR* 5.6 2.3 + - - -
573A ASP* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ALA 3.0 14.7 + - - -
386A SER* 3.4 9.4 + - - -
388A ARG* 1.3 78.9 - - - +
390A SER* 1.3 67.1 + - - +
391A PRO* 3.6 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLU* 4.1 7.6 + - - -
350A TRP* 3.7 20.5 - - - -
386A SER 2.8 17.3 + - - -
387A ARG 3.4 4.7 + - - +
388A ARG 5.3 0.2 - - - -
389A SER* 1.3 79.8 - - - +
391A PRO* 1.3 71.7 - - - +
392A ARG* 3.3 31.2 + - - +
393A VAL* 3.3 13.5 + - - +
394A THR* 3.4 12.6 + - - -
----------------------------------------------------------
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