Contacts of the strand formed by residues 464 - 470 (chain C) in PDB entry 1P4K
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 464 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C ASP 3.5 1.2 - - - +
372C GLU* 3.2 22.2 + - - +
457C ALA 3.2 15.7 - - - +
458C LEU* 3.7 26.5 - - + -
463C ASN* 1.3 73.8 - - - +
465C SER* 1.3 70.7 + - - +
493C VAL* 3.8 14.1 - - + -
494C ASP 3.9 11.7 - - - +
495C ASN* 2.9 19.5 + - - +
498C GLY* 3.6 31.6 - - - +
499C ALA* 4.5 10.3 - - + -
560C LEU* 4.0 21.3 - - + +
561C ASN 4.4 4.5 - - - +
562C LYS* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 465 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C ALA* 3.7 8.4 - - - +
332C LEU* 3.4 36.3 + - - -
335C VAL* 3.8 4.5 - - - +
370C MET 3.3 11.7 - - - -
371C ASP* 3.4 14.4 - - - -
372C GLU* 3.6 7.6 + - - -
456C ILE* 3.3 4.3 - - - +
457C ALA 3.0 30.1 + - - -
464C LEU* 1.3 80.9 + - - +
466C GLY* 1.3 59.6 + - - +
493C VAL* 4.1 8.5 - - - -
499C ALA* 5.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 466 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C VAL* 3.7 4.7 - - - -
369C ILE* 3.3 8.8 - - - +
370C MET 3.0 30.8 + - - -
455C MET 3.1 11.7 - - - -
456C ILE* 4.1 2.2 - - - -
465C SER* 1.3 77.9 - - - +
467C ALA* 1.3 62.4 + - - -
491C LEU* 3.6 21.1 - - - -
493C VAL* 3.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 467 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335C VAL* 3.9 29.8 - - + +
339C VAL* 4.0 8.1 - - + +
368C CYS 3.5 7.0 - - - -
369C ILE* 4.4 2.5 - - + -
389C ILE* 3.6 25.6 - - + -
453C ILE 3.9 0.7 - - - +
454C GLY* 3.4 1.9 - - - -
455C MET* 2.8 32.1 + - - +
466C GLY* 1.3 74.1 - - - +
468C CYS* 1.3 62.2 + - - +
491C LEU* 3.8 4.9 - - - +
501C THR* 4.4 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 468 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C ALA* 3.0 24.9 - - - +
368C CYS 3.0 15.2 + - - +
389C ILE* 4.0 1.0 - - - +
452C THR* 4.9 2.2 - - - -
453C ILE 3.4 11.7 - - - -
454C GLY* 4.2 1.3 - - - -
467C ALA* 1.3 75.8 - - - +
469C THR* 1.3 63.6 + - - +
484C SER* 3.4 43.9 - - - +
490C GLY* 4.2 4.3 - - - -
491C LEU* 4.4 10.3 - - + -
501C THR* 4.0 18.6 - - - +
502C ALA 4.1 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 469 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C VAL* 3.8 18.2 - - + -
343C GLU* 2.7 32.5 + - + +
351C VAL* 3.8 14.7 - - + +
352C GLY 5.0 0.7 + - - -
366C ASP 3.4 5.2 - - - -
367C ALA* 3.7 6.4 - - - +
388C PRO* 3.5 14.2 - - - +
389C ILE* 4.5 2.7 - - - -
452C THR* 4.0 0.5 - - - -
453C ILE* 3.1 45.2 + - + +
468C CYS* 1.3 77.3 - - - +
470C THR* 1.3 67.1 + - - +
484C SER* 4.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 470 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C GOL 3.2 31.4 - - - +
350C SER 2.9 15.6 + - - -
351C VAL* 4.1 6.5 - - - +
352C GLY 4.4 2.6 + - - -
365C LEU* 3.5 6.6 - - - +
366C ASP* 3.0 39.1 + - - +
450C HIS* 4.2 1.7 + - - -
452C THR* 3.2 23.7 - - - +
469C THR* 1.3 78.5 + - - +
471C SER* 1.3 66.6 + - - +
472C GLY* 2.8 13.3 + - - +
484C SER* 3.3 12.1 - - - +
----------------------------------------------------------
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