Contacts of the strand formed by residues 457 - 467 (chain B) in PDB entry 5CP2
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 457 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B LEU* 3.9 29.2 - - + +
451B LEU* 3.4 30.5 + - + -
452B ARG* 4.1 27.8 - - + +
455B GLY* 4.5 4.4 - - - -
456B PHE* 1.3 77.0 - - + +
458B THR* 1.3 63.5 + - - +
460B ASP* 4.5 4.5 - - - +
473B TYR* 3.7 34.1 - - + +
476B VAL 3.4 15.0 - - - +
477B CYS* 4.0 5.6 - - + -
489B LEU* 4.0 27.1 - - + -
491B ILE* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B GLY 4.2 14.4 - - - +
456B PHE 3.5 1.1 + - - +
457B LEU* 1.3 76.5 - - - +
459B ASP* 1.3 72.4 + - - +
476B VAL* 2.9 31.2 + - - +
477B CYS* 4.2 0.9 + - - -
478B ARG* 4.3 21.8 - - + +
486B HIS* 3.4 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ILE* 3.8 33.0 - - + +
378B LYS* 3.2 23.9 + - - -
379B HIS* 2.9 28.2 + - - -
457B LEU 3.6 0.6 - - - -
458B THR* 1.3 92.9 + - - +
460B ASP* 1.3 65.7 + - - +
473B TYR* 3.3 5.0 + - - -
475B GLY* 3.6 0.3 - - - -
476B VAL* 2.9 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B THR* 5.0 4.5 - - - +
372B GLN* 5.7 0.2 + - - -
375B ILE* 3.3 18.3 - - - +
452B ARG* 2.9 40.7 + - - -
457B LEU* 4.5 5.2 - - - +
459B ASP* 1.3 76.6 + - - +
461B LEU* 1.3 63.9 + - - +
462B VAL 6.2 0.7 - - - -
463B SER* 6.1 0.2 - - - +
473B TYR* 2.3 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TRP* 4.0 24.5 - - + -
372B GLN* 3.1 45.7 + - + +
375B ILE* 3.8 36.3 - - + -
376B GLY* 5.1 0.7 - - - +
383B PHE* 5.4 1.1 - - + -
460B ASP* 1.3 76.7 - - - +
462B VAL* 1.3 74.4 + - + +
474B LEU* 2.8 16.6 + - + +
475B GLY* 4.2 7.9 - - - +
476B VAL* 4.4 7.2 - - + -
488B ARG* 3.8 41.3 - - - +
11T G 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B TRP* 4.2 18.2 - - + -
372B GLN* 4.5 5.4 - - + -
460B ASP* 5.2 1.3 - - - +
461B LEU* 1.3 90.4 - - + +
463B SER* 1.3 70.0 + - - +
464B GLN* 4.3 14.4 - - + +
472B LYS 4.1 0.3 - - - +
473B TYR* 3.7 4.1 - - - -
474B LEU* 3.0 45.3 + - + +
10T T 3.9 32.1 - - - +
11T G 4.6 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B PHE* 4.5 10.6 - - - -
448B LEU* 4.8 2.6 - - - +
452B ARG* 5.7 1.2 + - - -
460B ASP* 6.1 0.3 - - - +
462B VAL* 1.3 77.2 + - - +
464B GLN* 1.3 63.8 + - - +
465B GLU* 3.7 21.2 + - - +
472B LYS 3.8 2.2 - - - -
473B TYR* 4.2 13.5 - - - -
10T T 3.5 21.1 + - - +
11T G 5.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B PHE* 5.3 0.7 - - - -
462B VAL* 4.3 14.4 - - + +
463B SER* 1.3 77.4 - - - +
465B GLU* 1.3 63.1 + - - +
466B GLU 3.4 3.6 + - - -
467B ASN* 2.8 33.1 + - - +
471B GLN* 3.4 4.2 - - - -
472B LYS* 2.9 65.3 + - - +
474B LEU* 5.1 7.2 - - + +
9T C 3.6 38.7 + - - +
10T T 3.9 17.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B PHE* 4.4 19.7 - - + -
445B SER* 5.3 7.3 + - - -
463B SER* 3.7 21.8 - - - +
464B GLN* 1.3 72.5 - - - +
466B GLU* 1.3 60.1 + - + +
467B ASN 3.8 0.7 - - - -
468B GLY 5.4 0.2 - - - +
471B GLN* 3.4 29.6 + - + +
10T T 5.0 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B GLN 3.4 0.8 - - - -
465B GLU* 1.3 80.6 - - + +
467B ASN* 1.3 63.2 + - - +
468B GLY 3.1 14.1 + - - +
470B GLN 4.3 0.2 - - - -
9T C 5.5 1.0 + - - +
10T T 4.5 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 467 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B GLN* 2.8 37.5 + - - +
466B GLU* 1.3 73.7 - - - +
468B GLY* 1.3 58.0 + - - +
470B GLN* 2.7 43.1 + - + +
472B LYS* 4.0 15.2 - - - +
492B ILE* 6.0 0.2 - - - +
529B GLU* 5.4 4.0 + - - +
530B HIS* 3.0 24.5 + - + +
9T C 2.8 43.0 - - - +
----------------------------------------------------------
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