Contacts of the helix formed by residues 372 - 384 (chain C) in PDB entry 1AX4
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 372 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C CYS* 4.3 4.7 - - - +
360C LYS* 5.4 3.4 - - + +
363C VAL* 3.6 24.8 - - + +
366C ILE* 3.9 30.3 - - + +
367C PRO 3.6 8.5 - - - +
368C GLY* 3.3 15.5 - - - +
370C GLN 3.7 0.4 - - - -
371C PHE* 1.3 87.1 - - - +
373C ALA* 1.3 66.8 + - - +
375C ALA* 3.3 3.4 + - - +
376C VAL* 3.1 27.0 + - - +
411C GLU* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C CYS* 3.6 13.1 - - + +
371C PHE 3.4 0.6 - - - -
372C PRO* 1.3 81.5 - - - +
374C GLN* 1.3 57.2 + - - +
376C VAL* 3.2 4.5 + - - +
377C ILE* 3.0 34.0 + - - +
390C GLU* 3.8 14.6 + - + +
411C GLU* 3.7 24.9 - - + +
412C PHE 3.5 27.6 - - - +
413C MET* 4.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 374 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C TYR 4.5 0.7 - - - +
35C ASN* 5.0 0.8 - - - +
36C PRO* 3.3 20.7 - - - +
371C PHE* 3.3 20.8 + - + +
373C ALA* 1.3 76.5 - - - +
375C ALA* 1.3 58.4 + - - +
377C ILE* 3.4 19.0 - - - +
378C ASN* 2.8 54.4 + - - +
390C GLU* 3.3 32.4 + - + +
394C PHE* 3.5 17.7 - - + -
447C LEU* 3.8 17.5 - - + -
458C HIS* 4.9 0.7 + - - -
463C LEU* 4.1 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 375 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C ILE* 3.9 23.6 - - + -
371C PHE 3.1 13.7 + - - +
372C PRO 3.7 7.0 - - - +
373C ALA 3.3 0.4 - - - -
374C GLN* 1.3 73.3 - - - +
376C VAL* 1.3 66.8 + - - +
378C ASN* 3.6 4.2 + - - +
379C ALA* 3.1 23.4 + - - +
444C LEU* 3.9 11.0 - - + +
445C LYS 5.7 0.2 - - - +
446C GLY* 4.5 14.8 - - - +
447C LEU* 4.0 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 376 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C CYS* 3.7 28.7 - - + -
362C LEU* 4.6 5.4 - - + -
363C VAL* 4.0 23.1 - - + -
372C PRO 3.1 15.6 + - - +
373C ALA 3.5 6.5 - - - +
375C ALA* 1.3 77.0 - - - +
377C ILE* 1.3 56.9 + - - +
379C ALA* 3.1 4.5 + - - +
380C LEU* 2.8 27.7 + - - +
413C MET* 3.9 20.2 - - + -
434C LEU* 4.3 6.7 - - + -
437C LEU* 4.8 1.0 - - + +
441C PHE* 4.1 23.3 - - + -
444C LEU* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 377 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C PRO* 4.0 10.3 - - + -
373C ALA 3.0 18.2 + - - +
374C GLN* 3.4 23.8 - - - +
375C ALA 3.3 0.2 - - - -
376C VAL* 1.3 74.4 - - - +
378C ASN* 1.3 55.3 + - - +
380C LEU* 3.2 6.5 + - - +
381C TYR* 2.9 28.9 + - + +
386C VAL 4.8 0.9 - - - +
388C ALA* 3.7 25.7 + - + +
389C VAL 3.4 10.8 - - - +
390C GLU* 3.4 40.8 - - + +
413C MET* 3.5 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 378 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 3.9 15.2 - - + +
34C TYR* 2.8 45.5 + - + +
36C PRO* 3.4 12.1 - - - +
374C GLN* 2.8 39.0 + - - +
375C ALA* 3.9 5.6 - - - +
377C ILE* 1.3 73.3 - - - +
379C ALA* 1.3 58.7 + - - +
381C TYR* 3.5 5.0 + - - +
382C LEU* 2.9 35.7 + - + +
447C LEU* 4.1 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 379 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C ALA 3.1 16.7 + - - +
376C VAL* 3.1 6.1 + - - +
378C ASN* 1.3 74.5 - - - +
380C LEU* 1.3 66.8 + - - +
382C LEU* 3.2 8.4 + - - +
383C GLU* 2.9 27.2 + - - +
437C LEU* 3.9 18.6 - - + -
444C LEU* 4.3 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 380 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C VAL 2.8 13.3 + - - +
377C ILE* 3.4 9.4 - - - +
379C ALA* 1.3 75.0 - - - +
381C TYR* 1.3 60.7 + - - +
383C GLU* 3.6 1.6 - - + +
384C SER* 2.6 49.6 + - - +
386C VAL* 4.2 25.6 - - + +
388C ALA* 4.4 7.0 - - + +
413C MET* 4.0 26.0 - - + -
415C LEU* 4.3 12.1 - - + -
430C ILE* 4.8 6.3 - - + +
433C ALA* 3.7 23.6 - - + +
434C LEU* 4.2 21.5 - - + +
437C LEU* 3.7 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 381 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PRO* 4.8 0.2 - - - +
25C ARG* 3.4 49.3 + - + +
28C ALA* 3.9 1.7 - - - +
29C LEU* 4.3 20.4 - - + -
36C PRO* 5.1 7.6 - - + -
39C LEU* 3.8 29.4 - - + -
43C ALA* 2.5 42.2 + - - +
44C VAL* 4.6 2.7 - - + -
377C ILE* 2.9 15.8 + - + +
378C ASN* 3.6 7.4 - - - +
380C LEU* 1.3 77.7 - - - +
382C LEU* 1.3 63.9 + - - +
385C GLY* 2.8 42.1 + - - +
386C VAL 3.3 24.3 + - - +
387C ARG* 4.7 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 382 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ARG* 3.1 36.5 - - - +
25C ARG* 2.7 37.6 + - + +
26C GLU* 3.6 43.7 - - + +
29C LEU* 3.7 24.5 - - + -
34C TYR* 5.3 7.0 - - + -
378C ASN* 2.9 22.0 + - + +
379C ALA* 3.8 6.5 - - - +
381C TYR* 1.3 76.6 - - + +
383C GLU* 1.3 52.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 383 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ARG* 3.1 26.0 + - - +
25C ARG* 3.4 12.6 + - - +
379C ALA 2.9 17.2 + - - +
380C LEU* 3.6 5.6 - - - +
382C LEU* 1.3 76.6 - - - +
384C SER* 1.3 59.8 + - - +
433C ALA* 4.8 8.0 - - + +
436C GLY 6.1 0.4 - - - -
437C LEU* 3.3 25.8 - - + +
440C LYS* 3.3 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 384 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C VAL* 4.3 2.5 - - - +
25C ARG* 4.2 8.3 - - - +
45C TYR* 3.9 5.9 - - - +
380C LEU* 2.6 25.2 + - - +
382C LEU 3.6 0.2 - - - -
383C GLU* 1.3 79.4 - - - +
385C GLY* 1.3 62.0 + - - +
386C VAL* 3.3 17.5 + - - +
429C TYR* 2.7 42.1 + - - -
433C ALA* 3.5 26.9 - - - -
----------------------------------------------------------
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