Contacts of the strand formed by residues 427 - 432 (chain C) in PDB entry 2DB3
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 GLN 427 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 2.9 24.9 + - - +
282C GLY* 3.0 43.4 - - - +
283C ARG 3.0 12.4 - - - +
284C ASP* 3.2 7.4 - - - +
306C LYS* 5.6 3.0 - - - +
394C ARG 2.8 13.7 + - - +
395C PHE* 3.1 40.5 - - + -
396C VAL 3.0 24.8 + - - +
426C HIS* 1.3 78.9 + - - +
428C THR* 1.3 61.1 + - - +
429C LEU* 4.3 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 428 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C ASP* 2.9 15.5 + - - -
285C LEU 3.2 21.3 + - - -
396C VAL* 3.4 16.6 - - + +
398C LEU* 5.1 1.6 - - + -
417C MET* 5.0 7.3 - - + +
426C HIS* 3.2 27.0 + - - -
427C GLN* 1.3 71.4 - - - +
429C LEU* 1.3 66.5 + - - +
430C MET* 4.0 18.6 - - + -
446C PHE* 3.3 28.3 + - + +
447C LEU* 3.6 14.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 429 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 3.6 34.3 - - + -
283C ARG 3.6 22.4 - - - +
285C LEU* 3.5 17.3 - - + +
299C PHE* 4.6 1.6 - - + -
303C ILE* 3.8 26.0 - - + -
395C PHE* 4.3 6.3 - - + -
396C VAL 2.9 10.8 + - - +
397C VAL* 3.4 11.5 - - + +
398C LEU* 2.8 32.6 + - - +
427C GLN* 4.3 11.7 - - + +
428C THR* 1.3 86.6 - - - +
430C MET* 1.3 59.6 + - - +
431C PHE* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C LEU 2.9 12.0 + - - +
286C MET* 3.4 5.4 - - - +
287C ALA 2.8 27.4 + - - +
398C LEU* 3.4 27.4 - - + -
401C ALA* 3.5 15.0 - - + -
405C LEU* 3.9 12.1 - - + -
428C THR* 4.0 11.4 - - + -
429C LEU* 1.3 79.2 - - - +
431C PHE* 1.3 64.8 + - - +
435C PHE* 4.4 9.1 - - + -
443C ALA* 3.5 46.4 - - + +
446C PHE* 4.0 11.9 - - + -
447C LEU* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ILE* 4.3 2.0 - - + -
275C SER* 3.9 11.7 - - - -
279C ILE* 4.1 7.0 - - + -
285C LEU* 3.6 21.8 - - + -
287C ALA* 3.5 24.7 - - + -
295C LYS* 3.9 28.7 - - + -
298C ALA* 3.9 15.5 - - + -
299C PHE* 3.6 41.3 - + + -
397C VAL* 4.7 3.8 - - + -
398C LEU 3.1 7.1 + - - +
399C ASP* 4.1 12.6 - - - +
400C GLU 2.9 26.4 + - - -
401C ALA* 2.9 8.6 + - - +
429C LEU* 4.0 20.9 - - + -
430C MET* 1.3 80.1 - - - +
432C SER* 1.3 61.5 + - - +
435C PHE* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C ALA 3.3 5.5 + - - +
288C CYS* 3.3 27.7 - - - +
289C ALA 3.4 2.8 + - - -
295C LYS* 3.9 12.5 - - - +
399C ASP* 5.4 0.4 - - - -
400C GLU* 4.0 7.3 + - - +
401C ALA 4.0 4.7 - - - -
402C ASP* 2.7 26.2 + - - -
431C PHE* 1.3 77.3 - - - +
433C ALA* 1.3 64.3 + - - +
434C THR 2.8 24.0 + - - +
435C PHE* 4.2 8.5 - - - -
551C ARG* 3.8 8.7 + - - -
575C HIS* 3.9 0.9 - - - -
----------------------------------------------------------
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