Contacts of the helix formed by residues 429 - 441 (chain A) in PDB entry 2I91
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 LEU 429 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A VAL* 6.6 0.7 - - + -
351A GLU* 5.4 9.6 - - + -
354A ASP* 3.0 28.9 - - + +
405A ARG* 5.4 1.8 - - - +
427A ASN 5.0 3.6 - - - +
428A MET* 1.3 74.5 - - - +
430A LEU* 1.3 66.5 + - - +
431A HIS* 3.2 11.7 - - + +
432A GLU* 2.9 26.9 + - + +
433A VAL* 3.0 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU* 4.2 28.7 - - + -
328A LEU* 4.6 9.0 - - + -
354A ASP* 3.3 25.0 + - + +
357A PHE* 3.2 48.9 - - + -
358A TYR* 3.3 31.6 + - + +
394A VAL* 6.3 0.4 - - + -
398A ALA* 4.4 12.1 - - + -
401A MET* 5.9 0.2 - - + -
428A MET 3.9 1.6 + - - -
429A LEU* 1.3 73.0 - - - +
431A HIS* 1.3 60.0 + - - +
433A VAL* 3.1 23.5 - - + +
434A VAL* 3.0 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU* 3.5 14.1 - - + +
332A LYS* 2.8 63.5 + - + +
350A VAL* 4.2 17.2 - - + +
354A ASP* 5.4 0.6 - - - +
429A LEU* 3.1 12.6 + - + +
430A LEU* 1.3 76.8 - - - +
432A GLU* 1.3 75.6 + - + +
434A VAL* 3.6 6.7 - - - +
435A GLU* 3.4 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A MET* 3.1 41.9 - - + +
429A LEU* 2.9 19.3 + - + +
431A HIS* 1.3 87.8 - - + +
433A VAL* 1.3 59.6 + - - +
434A VAL 3.1 0.2 - - - -
435A GLU* 3.8 8.3 + - - +
436A LYS* 2.7 62.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A VAL* 5.0 2.9 - - + +
397A ALA* 4.2 22.4 - - + -
398A ALA* 4.9 6.1 - - + +
401A MET* 4.3 20.0 - - + -
424A ILE* 3.5 28.0 - - + -
428A MET* 4.3 10.7 - - + -
429A LEU 3.0 21.3 - - - +
430A LEU* 3.1 23.1 - - + +
432A GLU* 1.3 74.8 - - - +
434A VAL* 1.3 64.3 + - + +
436A LYS* 3.9 0.8 - - - +
437A MET* 2.9 34.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU* 4.5 14.1 - - + -
328A LEU* 5.4 2.0 - - + -
329A GLU* 3.8 30.7 - - + +
332A LYS* 4.4 1.8 - - - +
390A LEU* 5.1 1.1 - - + -
394A VAL* 3.7 39.1 - - + +
430A LEU* 3.0 20.4 + - + +
431A HIS* 3.6 14.1 - - + +
432A GLU 3.1 0.8 - - - -
433A VAL* 1.3 79.2 - - + +
435A GLU* 1.3 67.3 + - + +
437A MET* 3.2 14.4 + - - +
438A SER* 3.2 10.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LYS* 5.2 5.2 + - - +
431A HIS* 3.4 21.8 + - - +
432A GLU* 4.1 13.1 - - - +
434A VAL* 1.3 81.2 - - - +
436A LYS* 1.3 72.0 + - + +
438A SER* 2.7 31.1 - - - -
439A ASP* 2.8 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A PRO* 3.3 25.6 - - + +
424A ILE* 4.0 15.9 - - + -
428A MET* 3.0 26.9 - - + -
432A GLU* 2.7 44.3 + - - +
433A VAL 4.0 0.4 - - - +
434A VAL 3.1 0.6 - - - -
435A GLU* 1.3 87.3 + - + +
437A MET* 1.3 52.3 + - - +
438A SER 3.0 5.5 + - - -
439A ASP* 3.7 11.1 + - - +
440A ILE* 2.6 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ILE* 3.9 14.4 - - + -
377A VAL* 3.6 31.9 - - + -
391A ASN* 5.4 1.2 + - - -
393A SER* 3.8 14.1 - - - +
394A VAL* 4.3 18.8 - - + -
397A ALA* 3.8 31.9 - - + -
414A ALA* 5.5 0.9 - - + -
423A PRO* 4.0 23.1 - - + -
424A ILE* 4.3 8.3 - - - -
433A VAL 2.9 22.4 - - - +
434A VAL 3.2 7.3 + - - +
436A LYS* 1.3 74.5 - - - +
438A SER* 1.3 66.2 + - - +
440A ILE* 3.5 4.0 - - - -
441A THR* 2.8 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A ASN* 5.9 3.6 - - - +
394A VAL* 5.7 0.9 - - - +
434A VAL* 3.2 6.7 + - - +
435A GLU* 2.7 30.4 - - - +
437A MET* 1.3 79.4 - - - +
439A ASP* 1.3 63.1 + - - +
440A ILE 3.1 1.7 + - - -
441A THR* 3.7 10.6 + - - +
442A MET* 5.5 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A GLU* 2.8 28.6 - - - +
436A LYS* 3.7 8.7 + - - +
437A MET 3.5 0.2 - - - -
438A SER* 1.3 76.7 - - - +
440A ILE* 1.3 57.7 + - + +
442A MET* 3.4 20.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A VAL* 3.8 35.7 - - + +
414A ALA* 4.1 5.6 - - + -
420A LEU* 4.7 13.1 - - + +
421A PRO 4.5 5.4 - - - +
423A PRO* 3.7 35.2 - - + -
436A LYS 2.6 32.1 - - - +
437A MET* 3.5 13.7 - - + -
439A ASP* 1.3 79.0 - - + +
441A THR* 1.3 62.7 + - - +
442A MET* 3.3 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A VAL* 3.2 9.8 - - - +
378A SER 3.4 21.8 - - - +
381A MET 3.9 3.1 - - - +
382A ASN* 3.3 41.8 - - - +
391A ASN* 4.6 3.7 + - - +
393A SER* 2.7 31.8 + - - +
437A MET 2.8 19.9 + - - -
438A SER 3.7 7.3 + - - +
440A ILE* 1.3 71.6 - - - +
442A MET* 1.3 71.0 + - - +
----------------------------------------------------------
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