Contacts of the helix formed by residues 323 - 331 (chain B) in PDB entry 6UWZ
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 323 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B VAL* 3.2 14.8 + - - -
322B LEU* 1.3 76.5 - - - +
324B THR* 1.3 65.9 + - - +
325B ARG* 4.1 9.4 - - - +
326B VAL* 2.9 44.3 + - - +
327B LYS* 3.0 11.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU 3.5 2.0 + - - -
323B SER* 1.3 72.5 - - - +
325B ARG* 1.3 62.6 + - + +
327B LYS* 3.6 17.0 - - - +
328B GLN* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B SER* 3.1 8.9 - - - +
324B THR* 1.3 85.2 - - + +
326B VAL* 1.3 59.8 + - + +
328B GLN* 3.3 6.7 + - + +
329B ILE* 2.9 47.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PHE* 4.8 7.4 - - + -
322B LEU* 4.2 6.5 - - + -
323B SER* 2.9 32.1 + - - +
325B ARG* 1.3 81.5 - - + +
327B LYS* 1.3 57.6 + - - +
329B ILE* 4.4 5.2 - - - -
330B PHE* 2.9 49.7 + - + +
331B LEU 4.2 0.2 + - - -
446B TRP* 4.1 27.8 - - + -
449B VAL* 4.2 9.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 3.6 40.1 - - + +
323B SER 3.0 9.0 + - - +
324B THR* 3.6 17.7 - - - +
325B ARG 3.2 0.2 - - - -
326B VAL* 1.3 74.1 - - - +
328B GLN* 1.3 67.1 + - - +
331B LEU* 2.9 46.3 + - + +
332B GLU* 3.4 16.4 + - - +
445B ASN* 4.0 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B THR* 2.9 18.3 + - - +
325B ARG* 3.6 7.9 - - + +
327B LYS* 1.3 75.4 - - - +
329B ILE* 1.3 67.6 + - + +
332B GLU* 2.8 34.0 + - - +
333B LYS* 2.9 55.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ARG* 2.9 36.3 + - + +
326B VAL* 3.8 3.8 - - - +
328B GLN* 1.3 89.1 - - + +
330B PHE* 1.3 92.9 + - + +
331B LEU 3.6 0.3 + - - -
333B LYS* 3.7 19.9 + - + +
334B LEU* 3.1 42.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PHE* 5.3 6.5 - + - -
326B VAL* 2.9 38.7 + - + +
329B ILE* 1.3 90.7 - - + +
331B LEU* 1.3 69.1 + - - +
334B LEU* 3.9 18.2 - - + -
335B PRO* 3.8 4.1 - - - +
449B VAL* 3.7 26.7 - - + -
452B THR* 2.9 41.1 + - + -
453B ILE* 3.8 31.0 - - + -
456B LEU* 5.0 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 4.9 0.4 - - + -
327B LYS* 2.9 43.8 + - + +
330B PHE* 1.3 83.4 - - - +
332B GLU* 1.3 66.6 + - + +
335B PRO* 3.6 16.7 - - - +
445B ASN* 3.6 33.4 - - + +
448B LEU* 3.3 41.5 - - + -
449B VAL* 3.9 10.8 - - + +
----------------------------------------------------------
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