Contacts of the strand formed by residues 327 - 332 (chain g) in PDB entry 5M32
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 LYS 327 (chain g).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201g ALA 5.0 1.1 - - - +
202g ILE* 4.1 24.5 - - + +
205g PRO* 3.8 28.9 - - - -
206g MET* 3.7 25.1 - - + -
219g PRO* 3.8 20.0 - - - +
220g PRO 3.7 24.0 + - - +
221g LYS* 4.5 14.8 - - - +
222g GLY* 5.5 1.8 - - - +
281g SER 3.5 4.9 + - - -
282g ILE* 3.3 18.1 - - + -
283g ILE* 3.0 22.3 + - - +
324g THR* 5.6 4.4 - - - +
325g GLN 4.8 6.8 - - - +
326g VAL* 1.3 84.9 - - - +
328g VAL* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202g ILE* 4.2 5.5 - - - +
222g GLY* 3.2 19.8 - - - +
223g VAL 3.0 20.8 + - - -
272g PHE* 4.9 13.0 - - + -
283g ILE* 3.4 8.5 - - + +
285g ILE* 3.7 25.6 - - + -
317g LEU* 3.7 29.8 - - + -
323g ASN* 6.1 0.2 - - - +
326g VAL* 4.5 7.9 - - + +
327g LYS* 1.3 80.2 - - - +
329g ILE* 1.3 76.1 + - - +
330g ALA* 4.8 2.5 - - + +
348g LEU* 4.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198g LEU* 4.7 10.8 - - + -
202g ILE* 4.5 21.1 - - + -
223g VAL* 3.4 7.2 - - + +
225g MET* 3.7 24.9 - - + -
237g ALA* 5.6 6.1 - - + +
240g CYS* 4.8 12.1 - - + -
241g ALA 6.1 0.2 - - - +
248g PHE* 4.7 10.3 - - + -
282g ILE* 3.9 30.7 - - + -
283g ILE 2.5 15.1 + - - +
284g PHE* 3.3 20.7 - - + -
285g ILE* 2.9 30.1 + - - +
328g VAL* 1.3 80.9 - - - +
330g ALA* 1.3 62.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223g VAL 2.7 16.3 + - - +
224g LEU* 3.8 21.5 - - + -
225g MET* 2.8 31.1 + - - +
284g PHE* 4.3 1.8 - - - -
285g ILE* 3.7 6.3 - - + -
288g LEU* 3.7 19.1 - - + -
328g VAL* 5.2 2.7 - - + -
329g ILE* 1.3 76.1 - - - +
331g ALA* 1.3 63.6 + - - +
348g LEU* 4.5 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 331 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225g MET* 3.3 12.3 - - + +
233g LYS* 4.0 22.2 - - + -
284g PHE* 3.6 29.4 - - + -
285g ILE 3.3 6.8 + - - +
286g ASP* 4.3 5.8 - - - +
287g GLU* 2.9 32.6 + - - +
288g LEU* 3.9 1.2 + - - +
330g ALA* 1.3 79.5 - - - +
332g THR* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 332 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224g LEU* 4.6 15.7 - - + +
225g MET 3.0 6.3 + - - -
226g TYR* 3.4 24.6 - - - +
227g GLY 3.8 0.2 + - - -
233g LYS* 3.5 3.9 - - - +
287g GLU* 4.8 2.5 - - - +
288g LEU* 3.6 39.9 - - + +
289g ASP* 5.0 5.2 - - - -
331g ALA* 1.3 81.5 - - - +
333g ASN* 1.3 62.0 + - - +
334g ARG 2.5 29.4 + - - -
335g VAL* 4.0 7.8 - - - +
337g ILE* 5.8 0.9 - - - -
338g LEU* 4.5 9.8 - - + +
----------------------------------------------------------
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