Contacts of the helix formed by residues 430 - 441 (chain C) in PDB entry 4RYD
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 430 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU 3.8 2.5 - - - -
133C ASN* 2.7 34.9 + - - +
400C THR* 3.7 20.9 + - - +
401C SER* 4.9 0.4 - - - +
402C LYS* 2.9 31.4 + - + +
428C LEU 3.6 0.4 + - - -
429C LEU* 1.3 74.7 - - - +
431C ALA* 1.3 57.0 + - - +
432C GLY 3.2 0.2 + - - -
433C ALA* 3.1 18.2 + - + +
434C MET* 2.9 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C LEU 3.0 14.2 + - - +
133C ASN 3.5 11.7 - - - +
134C VAL* 3.7 14.1 - - + -
137C ALA* 4.0 11.2 - - + -
377C ILE* 3.9 33.9 - - + +
380C LEU* 4.5 4.5 - - + -
429C LEU 4.0 1.0 - - - -
430C ASP* 1.3 70.3 - - - +
432C GLY* 1.3 63.8 + - - +
434C MET* 3.1 2.0 + - - +
435C VAL* 3.0 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ASN* 3.1 24.3 + - - -
136C ALA* 4.1 3.1 - - - -
137C ALA* 4.1 6.9 - - - +
140C GLN* 3.3 16.8 - - - +
430C ASP* 3.2 2.2 + - - -
431C ALA* 1.3 77.3 - - - +
433C ALA* 1.3 61.7 + - - +
435C VAL* 3.2 6.9 - - - +
436C ALA* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ASN* 4.4 1.0 - - - +
400C THR* 3.7 15.8 - - + +
402C LYS* 3.7 13.5 - - - +
430C ASP* 3.1 31.4 + - - +
432C GLY* 1.3 73.1 - - - +
434C MET* 1.3 60.1 + - - +
436C ALA* 3.3 5.2 + - - +
437C LEU* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377C ILE* 4.2 12.3 - - + -
378C ILE* 4.6 8.5 - - + -
381C THR* 3.5 30.3 - - + +
393C MET* 3.9 19.1 - - - -
396C LEU* 3.6 25.4 - - + +
397C VAL* 3.7 24.7 - - + -
400C THR* 3.1 25.6 - - - +
429C LEU* 5.3 6.1 - - + -
430C ASP 2.9 24.0 + - - +
431C ALA* 3.1 10.1 + - - +
433C ALA* 1.3 77.0 - - - +
435C VAL* 1.3 58.3 + - - +
437C LEU* 3.9 1.2 - - - +
438C ALA* 3.0 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 435 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ALA* 3.9 16.6 - - + -
140C GLN* 3.3 23.1 - - - +
142C TYR* 3.8 17.7 - - + -
377C ILE 5.2 0.2 - - - +
380C LEU* 3.7 42.6 - - + +
381C THR* 4.0 4.7 - - - +
384C ALA* 3.8 8.0 - - + +
431C ALA* 3.0 18.0 + - - +
432C GLY 3.2 12.3 - - - +
434C MET* 1.3 75.8 - - - +
436C ALA* 1.3 65.1 + - - +
438C ALA* 3.7 2.5 - - - +
439C GLN* 3.2 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLN* 3.7 17.0 - - - +
432C GLY 3.1 19.5 + - - +
433C ALA* 3.6 7.4 - - - +
434C MET 3.2 0.2 - - - -
435C VAL* 1.3 80.5 - - - +
437C LEU* 1.3 61.9 + - - +
439C GLN* 3.5 17.2 + - - +
440C ASN* 4.2 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LEU* 3.5 24.9 - - + -
399C GLN* 3.6 29.4 - - + +
400C THR* 3.7 21.3 - - + -
433C ALA 2.9 17.2 + - - +
434C MET 4.1 2.2 - - - +
436C ALA* 1.3 74.6 - - - +
438C ALA* 1.3 64.3 + - - +
439C GLN 3.3 0.3 + - - -
440C ASN* 3.4 6.0 + - + +
441C TRP* 3.3 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C THR* 3.6 33.0 - - + +
384C ALA* 4.1 3.1 - - + -
385C ASN* 2.7 33.4 + - + -
388C LEU* 4.1 5.6 - - + -
396C LEU* 3.8 13.6 - - + +
434C MET 3.0 19.5 + - - +
435C VAL 3.7 5.4 - - - +
436C ALA 3.3 0.4 - - - -
437C LEU* 1.3 78.2 - - - +
439C GLN* 1.3 57.9 + - - +
441C TRP* 3.1 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 439 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLN* 3.7 16.6 - - - +
142C TYR* 3.0 37.2 + - - +
384C ALA* 4.1 17.3 - - + +
385C ASN* 4.4 5.5 + - - +
435C VAL 3.2 18.7 + - - +
436C ALA* 3.8 9.4 - - - +
437C LEU 3.3 1.0 - - - -
438C ALA* 1.3 77.6 - - - +
440C ASN* 1.3 70.6 + - - +
441C TRP 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 440 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C ALA 4.2 3.1 + - - +
437C LEU* 3.4 10.1 + - + +
438C ALA 3.3 0.2 - - - -
439C GLN* 1.3 87.3 + - - +
441C TRP* 1.3 64.1 + - - +
442C THR* 3.5 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 441 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C ASN* 4.0 10.0 + - - -
388C LEU* 3.6 19.1 - - + -
392C ASP* 2.8 36.8 + - + +
395C HIS* 3.6 31.2 - + + -
396C LEU* 3.5 24.0 - - + -
399C GLN* 3.6 36.6 - - - -
437C LEU* 3.3 22.1 + - + +
438C ALA* 3.1 19.1 + - - +
439C GLN 3.4 0.8 - - - +
440C ASN* 1.3 76.4 - - - +
442C THR* 1.3 76.0 + - - +
443C THR* 3.8 3.9 + - - -
444C VAL* 3.9 14.1 - - + -
----------------------------------------------------------
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