Contacts of the strand formed by residues 323 - 331 (chain C) in PDB entry 2A19
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 TYR 323 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ASP* 2.4 38.1 + - - +
293B TYR* 3.5 13.0 - - - -
324B ASN* 3.4 11.1 + - - -
309C VAL* 4.1 24.6 + - + -
312C LEU* 3.8 40.2 - - + +
313C ALA* 3.9 20.9 - - - -
315C LEU 5.5 3.4 + - - +
321C VAL 3.5 3.0 + - - +
322C HIS* 1.3 82.2 + - - +
324C ASN* 1.3 60.6 + - - +
325C GLY* 3.6 30.4 - - - -
326C CYS* 3.6 13.0 - - - -
364C ILE* 4.4 5.6 - - + -
365C GLN 4.0 7.0 - - - -
366C MET* 4.3 5.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 324 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TYR* 5.0 0.2 + - - -
323B TYR* 3.7 15.4 + - - -
324B ASN* 2.7 57.6 + - - +
365B GLN* 4.1 3.6 + - - -
293C TYR* 3.1 45.3 + - - -
322C HIS* 3.7 11.8 + - - -
323C TYR* 1.3 73.7 - - - +
325C GLY* 1.3 56.9 + - - +
365C GLN* 2.8 30.8 + - - +
366C MET 3.7 0.2 - - - -
367C GLU* 3.6 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 325 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B HIS* 5.6 2.0 - - - -
289B ASP* 5.0 2.0 - - - -
365B GLN* 5.0 8.7 - - - -
323C TYR* 3.6 22.4 - - - -
324C ASN* 1.3 79.7 - - - +
326C CYS* 1.3 61.4 + - - +
327C TRP* 5.4 1.3 - - - -
365C GLN* 2.9 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASP* 5.6 1.0 - - - +
286B HIS* 3.3 40.9 + - - -
288B ILE* 3.8 23.6 - - - -
289B ASP* 4.2 2.7 - - - -
309C VAL* 3.7 31.2 - - + -
323C TYR* 3.6 15.4 + - - +
325C GLY* 1.3 75.6 - - - +
327C TRP* 1.3 67.6 + - - +
362C LEU* 4.2 4.5 - - + -
363C PHE 3.1 16.2 - - - +
364C ILE* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 327 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASP* 5.4 0.9 - - - +
288B ILE* 4.0 10.1 - - - -
260C ASP* 2.8 23.0 + - - -
262C ARG* 3.3 50.9 - - + +
263C PHE* 3.8 25.8 - + + -
266C ASP* 5.9 0.4 - - - -
267C PHE* 3.8 31.0 - + - -
295C ILE* 4.3 12.3 - - + -
325C GLY 5.4 0.4 - - - -
326C CYS* 1.3 82.4 - - - +
328C ASP* 1.3 72.1 + - - +
362C LEU* 3.8 3.3 - - - +
363C PHE* 2.9 63.1 + + + -
365C GLN* 4.5 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 328 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 3.8 14.7 - - + +
262C ARG* 5.8 0.3 - - - +
300C TYR* 3.8 22.9 - - + -
327C TRP* 1.3 87.2 - - - +
329C GLY* 1.3 58.9 + - - +
360C LYS* 3.4 22.9 + - - +
361C CYS 3.2 13.9 - - - +
362C LEU* 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 329 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ASP* 3.6 16.4 - - - -
328C ASP* 1.3 78.3 - - - +
330C PHE* 1.3 65.7 + - - -
360C LYS* 4.5 3.0 - - - +
361C CYS* 2.7 41.7 + - - +
363C PHE* 4.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 330 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C VAL* 4.3 6.2 - - - +
260C ASP* 3.6 20.8 + - - +
329C GLY* 1.3 72.1 - - - -
331C ASP* 1.3 64.8 + - - +
358C LYS* 4.6 23.6 + - + +
359C THR* 3.4 7.0 - - - +
360C LYS* 3.5 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 331 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C THR* 2.9 14.0 + - - -
259C VAL* 2.8 27.1 + - - +
260C ASP 3.5 4.1 + - - -
297C ARG* 2.8 34.6 + - - +
329C GLY 3.7 0.2 + - - -
330C PHE* 1.3 73.5 - - - +
332C TYR* 1.3 71.7 + - - +
333C ASP* 3.1 0.3 + - - -
358C LYS* 2.8 32.3 - - - +
359C THR 2.9 15.4 + - - +
361C CYS* 3.6 18.8 - - - -
363C PHE* 3.1 17.7 - - + -
----------------------------------------------------------
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