Contacts of the helix formed by residues 371 - 383 (chain D) in PDB entry 1C2O
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 SER 371 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D ARG* 3.6 2.9 - - - +
369D GLN 3.4 4.4 + - - -
370D ALA* 1.3 76.8 - - - +
372D ASP* 1.3 60.2 + - - +
373D LEU* 3.5 2.9 + - - +
374D ALA* 3.2 15.4 + - - +
375D ALA* 2.9 25.6 + - - +
540D LEU* 3.6 7.1 - - - +
543D THR* 2.9 42.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 372 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D ARG* 2.9 34.5 + - - +
371D SER* 1.3 70.9 - - - +
373D LEU* 1.3 69.5 + - - +
375D ALA* 2.8 5.2 + - - +
376D GLU* 2.7 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 373 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 6.0 0.9 - - + -
535A PHE* 3.8 29.5 - - + -
538A LYS* 5.0 15.3 - - + +
539A LEU* 4.2 16.4 - - + -
542A ALA* 4.5 16.8 - - + -
543A THR* 6.2 0.4 - - + -
371D SER* 3.5 6.8 + - - +
372D ASP* 1.3 78.6 - - - +
374D ALA* 1.4 58.9 + - - +
376D GLU* 2.9 18.7 + - - +
377D ALA* 2.8 27.5 + - - +
539D LEU* 4.1 18.6 - - + -
543D THR* 4.1 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370D ALA* 4.0 5.4 - - + -
371D SER* 3.2 11.4 + - - +
372D ASP 3.1 0.6 - - - -
373D LEU* 1.4 77.9 - - - +
375D ALA* 1.3 63.4 + - - +
377D ALA* 3.1 4.7 + - - +
378D VAL* 2.9 26.4 + - - +
536D LEU* 3.8 15.2 - - + +
539D LEU* 3.7 17.4 - - + +
540D LEU* 3.2 35.7 - - + -
543D THR* 4.9 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D VAL* 4.2 8.5 - - + +
364D ARG* 3.4 37.5 - - - +
370D ALA* 4.0 7.7 - - + +
371D SER 2.9 14.2 + - - +
372D ASP* 2.8 9.5 + - - +
374D ALA* 1.3 75.6 - - - +
376D GLU* 1.3 64.2 + - - +
378D VAL* 2.9 10.8 + - - +
379D VAL* 2.8 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 376 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A PHE* 4.6 18.8 - - + -
538A LYS* 4.7 22.3 + - + +
372D ASP* 2.7 20.8 + - - +
373D LEU* 3.0 22.3 + - - +
375D ALA* 1.3 72.4 - - - +
377D ALA* 1.3 65.2 + - - +
379D VAL* 2.8 9.3 + - + +
380D LEU* 2.7 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 377 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A PHE* 4.6 15.1 - - + -
373D LEU 2.8 9.5 + - - +
374D ALA 3.2 8.7 - - - +
376D GLU* 1.3 74.0 - - - +
378D VAL* 1.3 58.5 + - - +
380D LEU* 3.1 10.2 + - - +
381D HIS* 2.9 29.8 + - - +
531D PHE* 3.8 22.5 - - + -
535D PHE* 4.7 3.6 - - + -
536D LEU* 4.4 0.9 - - + -
539D LEU* 3.7 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 378 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D VAL* 4.1 13.5 - - + -
367D VAL* 4.7 9.4 - - + -
374D ALA* 2.9 18.2 + - + +
375D ALA* 3.4 7.6 - - - +
377D ALA* 1.3 75.7 - - - +
379D VAL* 1.3 63.9 + - - +
381D HIS 3.2 1.2 + - - -
382D TYR* 2.9 36.0 + - + +
401D VAL* 3.8 32.3 - - + -
531D PHE* 3.8 16.2 - - + -
532D TRP* 4.0 23.6 - - + -
536D LEU* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 379 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356D ARG* 3.4 17.0 - - - +
359D PHE* 3.8 11.2 - - + -
360D LEU* 3.7 27.1 - - + +
363D VAL* 4.2 21.3 - - + -
364D ARG* 6.4 0.2 - - - -
375D ALA* 2.8 27.0 + - + +
376D GLU* 2.8 8.9 + - + +
378D VAL* 1.3 73.5 - - - +
380D LEU* 1.3 55.4 + - - +
383D THR* 2.6 54.6 + - - +
385D TRP* 5.1 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A HIS* 5.5 6.7 - - + +
527A GLN* 4.8 4.6 - - + +
530A ALA* 4.7 2.0 - - + -
531A PHE* 4.2 31.4 - - + +
535A PHE* 4.1 36.8 - - + -
376D GLU 2.7 16.2 + - - +
377D ALA* 3.2 12.6 - - - +
379D VAL* 1.3 74.1 - - - +
381D HIS* 1.3 70.0 + - + +
382D TYR 3.4 0.2 + - - -
383D THR 3.6 3.8 + - - +
385D TRP* 3.2 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 381 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 5.6 5.4 - - + +
377D ALA 2.9 13.1 + - - +
378D VAL 3.2 4.2 + - - +
380D LEU* 1.3 88.0 - - + +
382D TYR* 1.3 87.1 + + + +
383D THR 4.4 2.8 - - - +
527D GLN* 4.8 7.4 - - + -
528D THR* 3.2 39.5 + - - -
531D PHE* 4.0 31.7 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 382 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D PHE* 4.2 13.2 - - + -
378D VAL* 2.9 28.0 + - + +
381D HIS* 1.3 92.4 - + + +
383D THR* 1.3 65.3 + - - +
393D HIS* 3.3 21.8 + - - -
397D ALA* 3.9 17.9 - - + +
400D ALA* 3.6 17.3 - - + -
401D VAL* 3.6 32.3 - - + -
404D ASP* 2.6 29.3 + - - +
528D THR* 3.2 8.8 - - + +
531D PHE* 4.4 1.3 - + - -
532D TRP* 2.6 45.7 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 383 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLN* 4.2 4.5 + - - +
356D ARG* 2.8 43.4 + - - +
359D PHE* 4.5 4.9 - - - -
379D VAL* 2.6 33.3 + - - +
380D LEU 3.8 2.4 - - - +
381D HIS 3.5 2.5 - - - +
382D TYR* 1.3 75.7 - - - +
384D ASP* 1.3 68.6 + - - +
385D TRP* 3.5 47.7 + - + -
388D PRO* 4.0 5.2 - - + -
393D HIS* 4.5 0.9 - - - -
394D LEU* 6.1 2.5 - - - -
----------------------------------------------------------
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