Contacts of the strand formed by residues 454 - 457 (chain C) in PDB entry 1M7X
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 VAL 454 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ASN* 3.5 41.9 + - + +
238C GLN* 5.8 0.7 - - - -
239C PHE* 5.7 0.2 - - + -
394C ILE* 5.9 0.5 - - - +
400C ASP 3.7 0.4 + - - -
401C ALA* 3.2 12.0 - - + +
402C LEU* 3.2 21.5 + - - +
452C GLY* 3.3 15.0 + - - +
453C ALA* 1.3 75.0 - - - +
455C THR* 1.3 60.9 + - - +
456C MET* 5.0 5.4 - - + -
478C TRP* 3.6 39.3 - - + +
479C TYR* 4.3 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 455 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C ILE* 6.2 0.7 - - + -
402C LEU* 3.3 15.0 - - + -
404C VAL* 6.2 0.9 - - - -
443C ASN* 2.5 31.9 + - - +
446C LEU* 3.5 30.1 - - + -
453C ALA 4.4 4.3 - - - +
454C VAL* 1.3 79.3 - - - +
456C MET* 1.3 60.8 + - - +
477C PHE* 3.5 10.9 - - - -
478C TRP* 2.6 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 456 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C ASN* 6.2 0.2 - - - +
243C ILE* 6.2 0.9 - - - -
245C ILE* 4.4 10.1 - - + -
283C HIS* 5.9 0.2 - - - +
285C GLU* 4.7 3.6 - - - +
333C ILE* 3.2 51.4 - - + -
401C ALA* 4.1 11.0 - - + -
402C LEU 2.8 9.7 + - - +
403C ARG* 4.3 12.1 - - + -
404C VAL 3.1 21.5 + - - -
454C VAL* 5.0 4.5 - - + -
455C THR* 1.3 75.5 - - - +
457C ALA* 1.3 63.6 + - - +
477C PHE* 3.1 13.2 - - - -
479C TYR* 3.3 46.2 - - + +
481C TRP* 5.3 7.0 - - + +
520C VAL* 4.3 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 457 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C ARG* 4.7 2.2 - - - +
404C VAL 3.3 8.7 - - - +
407C VAL* 4.2 6.7 - - + -
456C MET* 1.3 76.3 - - - +
458C GLU* 1.3 62.7 + - - +
459C GLU 4.2 0.4 - - - -
466C VAL* 3.8 20.2 - - + -
477C PHE* 3.4 33.4 - - + -
479C TYR 3.0 7.8 + - - +
480C LYS* 3.6 3.2 - - - -
481C TRP* 3.1 33.4 + - - -
----------------------------------------------------------
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