Contacts of the helix formed by residues 455 - 462 (chain C) in PDB entry 3SRF
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 ASN 455 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C GLU* 3.7 12.5 + - + +
433C SER* 5.5 0.4 - - - +
453C THR* 3.2 12.6 + - - +
454C ARG* 1.3 76.6 - - - +
456C PRO* 1.3 75.0 - - - +
457C GLN* 3.5 15.0 + - - +
458C THR* 2.8 30.3 + - - +
459C ALA 3.3 15.6 + - - -
472C LEU* 3.8 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 456 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C ARG 3.1 11.1 - - - +
455C ASN* 1.3 88.5 - - - +
457C GLN* 1.3 62.1 + - - +
459C ALA* 3.0 15.1 + - - +
460C ARG* 3.1 37.3 + - - +
472C LEU* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 457 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ASP* 4.2 15.4 + - - -
236C VAL 4.4 8.7 + - - -
237C ASP* 3.9 12.5 + - - +
263C ASN* 3.6 30.1 + - - +
264C ILE* 4.5 4.8 - - - +
455C ASN* 3.4 13.8 + - - +
456C PRO* 1.3 75.5 - - - +
458C THR* 1.3 60.0 + - - +
460C ARG* 3.3 17.2 + - - +
461C GLN* 2.9 55.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 458 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C THR* 5.0 3.8 - - + +
432C GLU 2.9 15.7 + - - +
433C SER* 3.8 7.3 + - - +
434C GLY* 3.6 32.8 - - - +
438C HIS* 5.6 1.4 + - - +
453C THR* 3.9 14.8 - - + +
455C ASN* 2.8 35.5 + - - -
456C PRO 3.3 0.2 - - - -
457C GLN* 1.3 78.7 - - - +
459C ALA* 1.3 57.0 + - - +
461C GLN* 3.3 7.7 + - - +
462C ALA* 3.0 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C PRO* 4.0 22.1 - - + +
453C THR* 3.7 21.3 - - + +
455C ASN 3.3 3.8 + - - +
456C PRO 3.0 10.6 + - - +
458C THR* 1.3 80.8 - - - +
460C ARG* 1.3 60.2 + - - +
462C ALA* 3.6 1.8 + - - -
463C HIS* 3.8 4.9 - - - -
470C PRO* 3.2 38.8 - - + +
472C LEU* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 460 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ARG* 6.0 3.1 - - - -
95C GLU* 6.0 0.2 + - - -
104C TYR* 5.2 7.4 + - - -
106C PRO* 4.0 16.2 - - + -
107C VAL 3.2 27.6 - - - +
108C ALA* 3.5 22.0 - - - +
109C VAL* 5.9 0.4 - - - -
235C ASP* 4.5 18.4 + - - -
237C ASP* 2.8 42.0 + - - +
238C MET* 4.3 1.2 - - - +
456C PRO* 3.1 30.6 + - - +
457C GLN* 3.3 21.1 + - - +
459C ALA* 1.3 74.0 - - - +
461C GLN* 1.3 61.2 + - - +
462C ALA 3.2 2.9 + - - -
463C HIS* 3.5 18.2 + - - +
472C LEU* 6.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 461 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ASP* 2.8 36.5 + - + +
238C MET* 4.5 8.3 - - + -
263C ASN* 2.7 31.1 + - - +
264C ILE* 3.8 1.0 - - - +
265C LYS* 3.6 32.9 - - + +
438C HIS* 4.6 3.5 + - + +
457C GLN* 2.9 39.0 + - + +
458C THR* 3.7 5.9 - - - +
460C ARG* 1.3 73.9 - - - +
462C ALA* 1.3 59.8 + - - +
463C HIS 3.3 1.7 + - - -
464C LEU* 3.6 20.8 + - + +
465C TYR* 3.6 11.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 462 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C GLY* 6.3 0.7 - - - -
437C ALA* 6.1 0.4 - - + -
438C HIS* 4.5 6.7 - - + +
451C ALA* 5.5 1.8 - - + -
458C THR* 3.0 18.7 + - + +
460C ARG 3.2 1.2 - - - -
461C GLN* 1.3 74.7 - - - +
463C HIS* 1.3 63.9 + - - +
464C LEU 3.1 2.8 + - - -
465C TYR* 3.4 17.9 + - - +
468C ILE* 3.4 37.5 - - + +
470C PRO* 3.6 26.5 - - + -
----------------------------------------------------------
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