Contacts of the helix formed by residues 391 - 405 (chain A) in PDB entry 2IBI
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 PRO 391 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A HIS 4.1 4.9 - - - +
390A LEU* 1.4 88.5 - - + +
392A ASP* 1.3 61.3 + - - +
393A ASP* 3.2 20.2 - - - +
394A GLU* 2.8 30.6 + - + +
395A LYS 3.0 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU 3.4 3.5 + - - +
391A PRO* 1.3 69.9 - - - +
393A ASP* 1.3 59.4 + - - +
395A LYS* 3.6 17.5 - - + -
396A GLY 2.8 20.1 + - - -
420A LYS* 3.2 26.9 + - - -
431A CYS* 5.1 3.3 - - - +
433A THR* 3.4 37.8 + - - +
435A PHE* 2.9 19.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A PRO* 4.2 16.0 - - - +
392A ASP* 1.3 78.0 + - - +
394A GLU* 1.3 69.5 + - - +
396A GLY* 3.6 1.0 + - - -
397A ARG* 3.2 47.3 + - - +
420A LYS* 5.2 3.4 + - - +
492A GLN* 4.1 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.8 21.8 - - + -
391A PRO* 2.8 27.0 + - + +
393A ASP* 1.3 82.9 + - - +
395A LYS* 1.3 56.5 + - - +
397A ARG* 2.8 49.3 + - - +
398A GLN* 3.0 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A LEU* 4.0 41.7 - - + +
388A ASP* 5.2 6.2 + - - -
390A LEU* 4.3 8.4 - - + +
391A PRO 3.0 9.9 + - - +
392A ASP* 3.5 21.8 - - + +
394A GLU* 1.3 73.5 - - - +
396A GLY* 1.3 63.2 + - - +
398A GLN* 3.6 8.1 - - - +
399A MET* 2.8 45.6 + - - +
433A THR* 2.8 36.3 + - - +
434A VAL* 5.0 0.4 - - - +
435A PHE* 3.4 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A ASP 2.8 22.2 + - - -
393A ASP* 3.9 3.6 - - - -
394A GLU 3.4 0.4 - - - -
395A LYS* 1.3 73.0 - - - +
397A ARG* 1.3 51.2 + - - +
399A MET* 3.2 0.5 + - - +
400A TRP* 2.8 31.6 + - - +
418A GLN* 3.1 16.7 + - - -
435A PHE* 3.7 28.0 - - - -
492A GLN* 4.9 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ASP* 3.2 41.3 + - - +
394A GLU* 2.8 44.4 + - - +
395A LYS 3.2 0.6 - - - -
396A GLY* 1.3 71.4 - - - +
398A GLN* 1.3 61.0 - - - +
400A TRP* 3.4 8.5 + - + +
401A ARG* 2.9 31.3 + - - +
493A ARG* 4.4 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU* 5.7 2.6 + - - -
387A LEU* 3.7 29.5 - - + +
390A LEU* 4.5 12.2 - - + +
394A GLU* 3.0 31.3 + - + +
395A LYS* 3.3 6.7 + - - +
397A ARG* 1.3 73.9 - - - +
399A MET* 1.3 63.3 + - + +
401A ARG* 2.9 43.3 + - - +
402A LYS* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU 5.3 2.2 - - - +
387A LEU* 3.0 40.2 - - + -
395A LYS* 2.8 32.4 + - - +
396A GLY 3.5 4.3 - - - +
398A GLN* 1.3 72.7 - - - +
400A TRP* 1.3 58.1 + - - +
402A LYS* 3.1 31.2 + - - +
403A TYR* 2.8 29.6 + - - +
418A GLN* 4.0 9.6 - - - +
435A PHE* 4.0 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A GLY 2.8 16.1 + - - +
397A ARG* 3.5 9.6 - - + +
399A MET* 1.3 74.5 - - - +
401A ARG* 1.3 58.6 + - + +
403A TYR* 3.1 24.6 + + + +
404A LEU* 2.8 64.3 + - + +
416A VAL* 3.7 39.7 - - + -
417A GLY 3.7 22.2 - - - -
418A GLN* 3.4 17.8 - - + +
437A PRO* 4.6 3.8 - - + -
493A ARG* 3.1 55.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLU* 5.9 1.8 + - - -
397A ARG 2.9 19.0 + - - +
398A GLN* 2.9 60.7 + - - +
400A TRP* 1.3 74.9 - - + +
402A LYS* 1.3 76.7 + - - +
404A LEU* 3.4 12.8 + - + +
405A GLU* 3.2 55.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ASN 3.3 22.4 + - - +
384A PRO* 3.9 5.6 - - + +
385A GLU* 3.4 39.5 + - - +
387A LEU* 4.9 2.4 - - - +
398A GLN 2.9 14.5 + - - +
399A MET* 3.1 41.2 + - - +
401A ARG* 1.3 88.5 - - - +
403A TYR* 1.3 65.2 + - - +
405A GLU* 3.2 30.5 + - - +
406A ARG* 3.2 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A MET 2.8 15.8 + - - +
400A TRP* 3.4 26.5 - + + +
402A LYS* 1.3 72.1 - - - +
404A LEU* 1.3 61.0 + - + +
406A ARG* 3.0 18.9 + - - +
407A GLU* 2.9 64.8 + - + +
416A VAL* 3.8 16.6 - - + -
437A PRO* 3.7 43.1 - - + -
439A TRP* 3.2 25.5 + - - -
46B ALA* 3.9 13.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A VAL* 4.0 0.9 - - - +
400A TRP* 2.8 66.2 + - + +
401A ARG* 3.8 11.0 - - + +
402A LYS 3.3 0.4 - - - -
403A TYR* 1.3 75.4 - - + +
405A GLU* 1.3 59.8 + - - +
406A ARG 3.3 0.4 + - - -
407A GLU 3.5 15.4 - - - +
408A ASP* 3.2 42.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A VAL* 3.5 15.1 - - - +
380A PRO* 3.0 38.4 - - + +
401A ARG* 3.2 41.4 + - - +
402A LYS* 3.2 28.4 - - - +
404A LEU* 1.3 76.7 - - - +
406A ARG* 1.3 61.8 + - - +
----------------------------------------------------------
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