Contacts of the helix formed by residues 457 - 465 (chain B) in PDB entry 5E9W
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 SER 457 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B GLU* 4.8 3.0 + - - -
340B ILE* 4.9 0.2 - - - +
456B LEU* 1.3 76.1 - - - +
458B LYS* 1.3 59.7 + - - +
459B SER* 3.6 7.5 + - - -
460B GLU* 2.8 40.8 + - - +
461B TRP* 2.8 28.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LEU* 3.6 14.8 - - + +
452B PRO 6.0 0.2 - - - -
457B SER* 1.3 73.4 - - - +
459B SER* 1.3 58.7 + - - +
461B TRP* 3.1 10.6 + - - +
462B GLU* 3.0 52.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 459 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ASN* 3.3 29.9 + - - +
339B GLU* 2.9 38.5 + - - +
340B ILE* 3.7 12.3 - - - +
457B SER* 3.2 4.1 + - - -
458B LYS* 1.3 78.0 + - - +
460B GLU* 1.3 63.7 + - - +
462B GLU* 3.3 3.5 + - - -
463B ALA* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 460 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B ARG 5.0 7.4 - - - +
169B ILE* 5.9 1.7 - - - -
171B TYR* 3.9 31.7 + - - +
172B LEU* 3.8 18.5 + - + +
340B ILE* 3.5 20.9 - - + +
455B THR 4.8 0.3 - - - +
456B LEU* 3.4 29.6 - - + +
457B SER* 2.8 37.6 + - - +
459B SER* 1.3 76.5 - - - +
461B TRP* 1.3 62.6 + - - +
463B ALA* 3.3 3.0 + - - -
464B THR* 3.1 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B PHE* 3.7 17.3 - + - -
395B PHE 5.4 0.9 - - - -
396B LEU* 3.9 25.6 - - + -
399B TYR* 3.6 38.6 - + + -
451B LEU* 3.8 17.9 - - + -
452B PRO* 3.3 40.5 + - + -
454B GLY 2.8 29.9 + - - -
456B LEU* 3.2 36.5 + - + +
457B SER 2.8 12.9 + - - -
458B LYS* 3.5 9.4 - - - +
460B GLU* 1.3 78.5 - - - +
462B GLU* 1.3 51.3 + - - +
464B THR* 3.4 31.3 - - + +
465B SER* 2.7 40.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 462 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ARG* 2.8 32.4 + - - +
338B ASN* 2.7 37.3 + - - +
341B TYR* 4.2 7.0 - - + +
451B LEU* 3.6 15.0 - - + +
458B LYS* 3.0 47.4 + - - +
459B SER* 3.6 10.4 + - - +
460B GLU 3.3 0.2 - - - -
461B TRP* 1.3 77.0 - - - +
463B ALA* 1.3 61.6 + - - +
465B SER* 3.2 12.6 + - - -
466B ILE* 3.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 3.8 24.9 - - + -
340B ILE* 4.0 9.6 - - + -
341B TYR* 3.9 26.0 - - + -
360B PHE* 5.9 0.7 - - + -
362B LEU* 4.8 3.4 - - + -
459B SER 3.1 13.4 + - - +
460B GLU 3.8 6.7 - - - +
461B TRP 3.3 0.2 - - - -
462B GLU* 1.3 76.2 - - - +
464B THR* 1.3 63.7 + - - +
466B ILE* 3.3 25.0 - - - +
467B TYR* 4.2 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 464 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 3.7 14.6 - - - -
175B PHE* 3.5 14.1 - - + -
176B ASN* 3.6 7.2 + - - -
395B PHE* 3.1 37.9 - - + +
456B LEU* 3.7 7.2 - - + -
460B GLU 3.1 14.3 + - - +
461B TRP* 3.4 40.2 - - + +
463B ALA* 1.3 74.3 - - - +
465B SER* 1.3 61.9 + - - +
466B ILE 3.0 10.8 + - - -
467B TYR* 3.1 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ASN* 5.3 1.6 + - - +
323B GLU* 3.8 14.7 - - - +
327B ARG* 2.9 26.6 + - - -
394B THR* 5.4 4.5 - - - +
395B PHE* 4.6 7.7 + - - -
396B LEU* 3.8 32.3 - - - +
451B LEU* 4.4 6.3 - - - +
461B TRP* 2.7 22.6 + - - -
462B GLU* 3.2 4.2 + - - -
463B ALA 3.3 0.2 - - - -
464B THR* 1.3 76.8 - - - +
466B ILE* 1.3 62.2 + - - +
467B TYR 3.1 6.7 + - - +
----------------------------------------------------------
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