Contacts of the strand formed by residues 359 - 367 (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 THR 359 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C LYS* 3.8 29.8 - - - +
301C ASN* 6.3 1.6 - - + -
330C PHE* 3.4 11.3 - - - -
331C ASP 2.9 26.8 + - - +
333C ASP* 4.0 18.0 - - + +
334C PRO* 4.5 1.2 - - - +
358C LYS* 1.3 78.9 - - - +
360C LYS* 1.3 71.7 + - - +
361C CYS* 3.4 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C LYS* 4.0 3.1 - - - +
300C TYR* 3.0 78.2 + - + +
301C ASN* 5.6 0.4 - - - +
328C ASP* 3.4 25.3 + - + +
329C GLY* 3.8 7.2 - - - +
330C PHE* 3.5 22.6 - - + -
359C THR* 1.3 81.1 + - - +
361C CYS* 1.3 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ARG* 4.3 4.5 - - + -
298C VAL 3.5 5.8 - - - +
300C TYR* 3.7 5.7 - - - +
328C ASP* 3.2 10.9 - - - +
329C GLY 2.7 35.5 + - - +
331C ASP* 3.6 20.2 - - + -
332C TYR 4.2 1.6 - - - -
334C PRO* 3.6 35.4 - - - -
359C THR 3.5 14.6 - - - -
360C LYS* 1.3 75.8 - - - +
362C LEU* 1.3 60.9 + - - +
363C PHE* 3.8 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 4.2 16.4 - - + -
296C LYS 3.4 3.5 - - - +
297C ARG* 3.4 2.6 - - - -
298C VAL* 2.7 47.1 + - + +
300C TYR* 3.9 31.8 - - + +
305C ALA* 3.3 36.1 - - + +
306C GLU* 4.7 0.7 - - - +
309C VAL* 3.9 20.0 - - + -
326C CYS* 4.2 11.4 - - + -
327C TRP 3.8 15.7 - - - +
361C CYS* 1.3 74.1 - - - +
363C PHE* 1.3 62.9 + - - +
364C ILE* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C ASP* 3.6 28.0 - - + -
263C PHE* 3.9 17.5 - + - -
295C ILE* 4.2 12.8 - - + -
296C LYS 3.2 4.3 - - - +
297C ARG* 3.6 28.0 - - + -
326C CYS* 3.1 28.1 - - - +
327C TRP* 2.9 62.1 + + + +
329C GLY 4.3 5.6 - - - -
331C ASP* 3.1 32.8 - - + -
361C CYS* 3.8 17.0 - - + -
362C LEU* 1.3 74.7 - - - +
364C ILE* 1.3 61.1 + - - +
365C GLN 4.1 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C VAL* 3.4 2.6 - - - +
295C ILE* 3.2 6.0 - - - +
296C LYS* 2.8 49.3 + - + +
298C VAL* 4.4 13.0 - - + -
305C ALA 5.2 0.4 - - - +
308C GLU* 3.8 29.8 - - + +
309C VAL* 3.5 26.9 - - + -
312C LEU* 4.5 3.8 - - + -
323C TYR* 4.4 17.3 - - + -
325C GLY 3.8 2.9 - - - -
362C LEU* 4.2 15.5 - - + +
363C PHE* 1.3 74.7 - - - +
365C GLN* 1.3 61.7 + - - +
366C MET* 3.6 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ASN 4.4 5.2 + - - +
325B GLY* 5.6 2.9 - - - -
267C PHE* 3.6 23.5 - - + -
286C HIS* 4.5 6.0 + - - -
289C ASP* 5.1 0.2 + - - -
293C TYR* 3.2 55.1 - - + -
294C VAL 3.4 4.3 - - - +
295C ILE* 4.3 6.5 - - + -
323C TYR* 3.8 4.3 - - - -
324C ASN* 2.8 48.4 + - + +
325C GLY* 2.9 23.5 + - - +
327C TRP* 4.5 13.5 - - + -
363C PHE 4.1 1.2 + - - -
364C ILE* 1.3 71.1 - - - +
366C MET* 1.3 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C TYR* 3.5 7.8 - - - -
294C VAL* 2.7 44.2 + - + +
296C LYS* 4.9 10.8 - - + -
308C GLU* 3.6 23.1 - - - +
312C LEU* 3.4 26.2 - - + -
321C VAL* 3.9 19.3 - - + -
322C HIS 3.2 20.0 - - - +
323C TYR* 4.3 8.1 - - - -
324C ASN* 3.7 5.2 - - - -
364C ILE* 3.7 23.6 - - + +
365C GLN* 1.3 74.2 - - - +
367C GLU* 1.3 64.5 + - - +
431C GLY 4.9 9.6 - - - +
433C PHE* 6.1 0.4 - - + +
2640C ANP 4.8 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ASP* 4.2 1.5 - - - +
291C LYS* 5.5 9.1 - - - +
293C TYR* 4.3 7.2 - - + -
294C VAL* 4.1 1.1 - - - +
321C VAL* 4.1 4.0 - - + -
322C HIS* 2.9 54.4 + - + +
324C ASN* 3.6 7.8 + - - +
366C MET* 1.3 74.6 - - - +
368C PHE* 1.3 64.2 + - - +
369C CYS* 3.5 26.5 - - - -
423C VAL* 3.9 6.2 - - - +
429C LYS* 2.9 31.4 + - - +
2640C ANP 3.0 24.4 + - - -
----------------------------------------------------------
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