Contacts of the helix formed by residues 369 - 380 (chain I) in PDB entry 1I43
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 369 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368I GLY* 1.3 76.0 - - - +
370I LEU* 1.3 70.1 + - + +
371I LEU* 2.9 19.6 + - - +
372I THR* 2.9 24.8 + - - -
373I THR* 2.8 25.1 + - - -
419I ASP* 4.2 2.5 - - - -
420I ASN* 4.0 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369I ASP* 1.3 75.0 - - + +
371I LEU* 1.3 78.2 + - + +
374I ALA* 3.3 22.7 + - + +
398I GLN* 3.6 20.9 + - - +
400I ALA* 4.8 1.6 - - + -
401I ILE* 3.8 26.2 - - + -
405I TRP* 4.2 24.2 - - + -
419I ASP* 3.3 49.8 - - + +
96K ILE* 5.0 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369I ASP* 2.9 15.5 + - - +
370I LEU* 1.3 96.2 - - + +
372I THR* 1.3 64.3 + - - +
374I ALA* 3.3 9.1 + - + +
375I LYS* 3.1 19.8 + - - +
96K ILE* 6.0 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 372 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366I VAL* 4.4 3.4 - - + -
367I ASP 4.6 0.9 - - - +
368I GLY* 3.9 18.6 - - - -
369I ASP* 2.9 26.5 + - - -
371I LEU* 1.3 72.3 - - - +
373I THR* 1.3 62.7 + - - +
375I LYS* 2.7 37.6 + - + +
376I PHE* 3.0 5.9 + - - +
445I ILE* 4.0 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 373 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366I VAL* 3.9 14.1 - - + +
369I ASP 2.8 20.5 + - - -
372I THR* 1.3 75.1 - - - +
374I ALA* 1.3 61.5 + - - +
376I PHE* 3.1 21.8 + - - +
377I VAL* 3.2 8.0 - - - +
398I GLN* 3.3 22.9 - - - +
419I ASP 3.4 8.3 + - - +
420I ASN* 3.5 26.5 + - - +
422I VAL* 3.3 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370I LEU* 3.3 18.3 + - + +
371I LEU* 3.4 10.5 - - + +
372I THR 3.1 0.6 - - - -
373I THR* 1.3 75.8 - - - +
375I LYS* 1.3 61.3 + - - +
377I VAL* 3.3 2.1 - - - +
378I ASP* 2.9 37.9 + - - +
398I GLN* 3.4 12.5 + - - +
401I ILE* 5.2 0.9 - - + -
92K THR* 3.5 31.2 - - + -
96K ILE* 6.1 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 375 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371I LEU 3.1 12.2 + - - +
372I THR* 2.7 18.9 + - + +
374I ALA* 1.3 76.6 - - - +
376I PHE* 1.3 62.5 + - - +
378I ASP* 3.6 9.4 + - + +
379I ALA* 3.3 18.5 + - - +
441I ALA 5.2 0.2 - - - +
444I SER* 3.6 29.7 - - - +
445I ILE* 4.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 376 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364I PHE* 3.7 33.2 - + - -
366I VAL* 3.9 14.8 - - + -
372I THR 3.0 4.2 + - - -
373I THR* 3.1 10.7 + - - +
375I LYS* 1.3 74.2 - - - +
377I VAL* 1.3 75.5 + - + +
379I ALA* 2.8 26.3 + - - +
380I LEU* 3.4 25.5 + - + +
396I VAL* 5.6 0.4 - - + -
422I VAL* 4.4 8.5 - - + -
424I PHE* 5.6 1.1 - + - -
438I ILE* 3.8 13.2 - - + -
441I ALA* 3.6 29.4 - - + -
442I LEU* 3.5 34.3 - - + -
445I ILE* 3.1 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 377 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373I THR 3.2 15.4 + - - +
374I ALA* 3.3 4.9 - - - +
376I PHE* 1.3 85.7 - - + +
378I ASP* 1.3 65.1 + - - +
379I ALA 3.3 0.3 + - - -
380I LEU* 3.5 35.0 + - + +
385I ILE* 4.1 24.2 - - + +
396I VAL* 5.0 9.4 - - + +
397I ASP* 5.6 5.4 - - - +
398I GLN* 4.1 14.4 - - + +
422I VAL* 4.2 18.6 - - + -
92K THR* 3.0 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 378 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374I ALA* 2.9 22.5 + - - +
375I LYS* 3.8 10.1 - - + +
376I PHE 3.1 0.2 - - - -
377I VAL* 1.3 79.0 - - - +
379I ALA* 1.3 61.6 + - - +
380I LEU 3.9 4.8 - - - +
385I ILE* 3.9 5.3 - - - +
90K ASN 5.5 2.4 - - - +
91K LYS* 3.7 18.5 - - + +
92K THR* 2.7 46.3 + - - -
93K SER* 4.4 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375I LYS 3.3 11.2 + - - +
376I PHE 2.8 15.2 + - - +
378I ASP* 1.3 76.9 - - - +
380I LEU* 1.3 67.2 + - - +
381I LYS* 3.5 14.6 - - - +
440I GLN* 3.7 10.9 + - - +
441I ALA* 3.4 28.5 - - + +
444I SER* 4.4 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376I PHE* 3.8 20.9 - - + +
377I VAL* 3.5 31.0 + - - +
378I ASP 3.9 6.1 - - - +
379I ALA* 1.3 83.5 - - - +
381I LYS* 1.3 60.4 + - - +
383I PRO* 4.0 13.5 - - + +
396I VAL* 3.8 35.2 - - + -
424I PHE* 4.3 5.4 - - + -
437I ASP* 3.7 17.5 - - - +
438I ILE* 3.9 25.4 - - + -
441I ALA* 3.7 18.8 - - + +
67L ARG* 5.1 2.4 + - - -
----------------------------------------------------------
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