Contacts of the strand formed by residues 452 - 459 (chain C) in PDB entry 5HP1
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 LEU 452 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447C ASN* 2.7 28.7 + - + +
450C THR* 2.8 26.4 + - + +
451C LYS* 1.3 80.7 - - - +
453C GLY* 1.3 59.2 + - - +
469C LEU 3.6 14.1 - - - +
470C THR* 3.7 26.7 - - + -
471C ASN 4.6 0.7 - - - +
472C THR* 4.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 453 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ALA 3.1 13.9 - - - -
446C ALA* 3.8 4.0 - - - -
452C LEU* 1.3 76.2 - - - +
454C LYS* 1.3 68.7 + - - +
468C PRO* 3.8 1.4 - - - +
469C LEU* 2.9 36.3 + - - +
472C THR* 3.9 10.1 - - - +
477C THR* 4.4 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 454 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C GLY* 3.2 2.9 - - - -
445C ALA 2.7 35.4 + - - +
453C GLY* 1.3 78.8 - - - +
455C ALA* 1.3 60.3 + - - +
466C VAL* 4.0 20.0 - - + +
467C VAL 3.5 8.1 - - - +
468C PRO* 4.7 7.0 - - + -
469C LEU* 4.3 4.0 - - - -
477C THR* 3.6 2.8 - - - +
551C LEU 3.8 23.9 + - - +
552C VAL* 3.9 25.6 + - + +
553C SER* 4.8 7.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 455 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C ASP 3.6 4.9 - - - -
444C GLY* 4.1 0.2 - - - -
454C LYS* 1.3 75.1 - - - +
456C GLY* 1.3 59.5 + - - +
466C VAL* 3.3 0.9 - - - -
467C VAL* 2.7 36.5 + - + +
469C LEU* 3.8 9.6 - - + +
477C THR 3.8 4.7 - - - +
480C GLN* 3.7 17.3 - - + -
481C ALA 3.7 25.6 - - - +
484C LEU* 3.5 13.5 - - + +
552C VAL* 4.1 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 456 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C VAL* 3.5 1.9 - - - -
443C ASP 2.9 30.1 + - - +
455C ALA* 1.3 76.3 - - - +
457C TYR* 1.3 67.6 + - - +
465C LYS 3.0 13.9 - - - -
466C VAL* 4.1 2.2 - - - -
481C ALA* 3.6 6.7 - - - +
484C LEU* 3.9 9.8 - - - +
548C VAL* 3.9 4.7 - - - -
552C VAL* 3.8 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 457 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C PHE* 3.7 23.3 - + + -
441C TYR 3.1 14.8 - - - +
442C VAL* 3.9 13.2 - - + -
456C GLY* 1.3 75.9 - - - +
458C VAL* 1.3 64.5 + - - +
459C THR* 3.7 20.0 - - + -
463C ARG* 3.9 20.3 - - + +
464C GLN* 3.4 11.3 + - - +
465C LYS* 3.0 43.1 + - + +
481C ALA 4.7 0.4 - - - -
484C LEU* 3.8 31.6 - - + -
485C ALA 4.0 7.9 - - - -
488C ASP* 2.5 36.5 + - - +
548C VAL* 3.6 8.5 - - - +
551C LEU* 4.6 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 458 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C PHE* 3.6 0.9 - - - -
441C TYR* 2.7 48.2 + - + +
457C TYR* 1.3 74.0 - - - +
459C THR* 1.3 72.4 + - - +
462C GLY* 5.3 2.5 - - - +
463C ARG 3.5 4.5 - - - +
464C GLN* 3.7 28.9 - - + +
544C GLY* 3.6 31.9 - - - +
547C GLN* 4.5 6.5 - - + -
548C VAL* 4.1 10.3 - - + +
551C LEU* 5.2 4.5 - - + -
286D THR* 3.9 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C GLU* 2.9 29.0 + - - +
439C THR 3.1 10.1 - - - -
440C PHE* 3.6 32.5 - - + -
457C TYR* 3.7 9.0 - - + -
458C VAL* 1.3 81.9 - - - +
460C ASN* 1.3 63.2 + - - +
461C LYS* 3.1 6.1 + - - -
462C GLY* 3.2 9.0 + - - -
463C ARG* 3.1 34.7 + - + +
286D THR* 3.1 14.9 - - - +
----------------------------------------------------------
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