Contacts of the strand formed by residues 429 - 435 (chain B) in PDB entry 6AHU
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 MET 429 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B SER* 4.3 6.9 + - - +
250B TYR 5.7 1.0 - - - +
252B CYS* 5.1 11.4 - - - -
328B TRP* 3.6 43.7 - - + -
425B LEU* 5.2 5.2 - - + -
426B THR 5.4 1.4 - - - +
427B MET* 5.2 3.8 - - - +
428B GLU* 1.3 98.0 + - + +
430B ASN* 1.3 67.1 + - - +
431B ARG* 4.3 0.5 + - - +
553B ILE* 4.4 16.6 - - + +
559B CYS* 5.2 9.0 - - - -
621B LEU* 3.9 25.1 - - + +
622B LEU 3.2 13.0 - - - +
623B PRO* 3.9 7.9 - - + -
624B LYS* 4.0 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B LEU* 4.5 2.3 - - - +
203B GLU* 2.7 39.0 + - - +
204B THR* 5.7 0.6 + - - -
248B SER* 2.8 27.8 + - - +
427B MET* 4.8 5.2 - - - +
429B MET* 1.3 76.7 - - - +
431B ARG* 1.3 61.5 + - - +
432B PHE* 4.3 12.3 - - + -
621B LEU* 3.4 6.9 - - - +
622B LEU* 3.0 48.0 + - + +
623B PRO 4.0 2.6 + - - -
624B LYS* 3.6 16.9 + - - +
627B GLY* 4.4 11.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ASP* 3.8 2.3 - - - +
247B LEU* 3.1 44.1 + - + +
248B SER* 4.5 4.9 - - - +
250B TYR* 3.8 34.8 - - - +
309B THR* 4.6 4.2 + - - +
330B TRP* 3.3 50.0 - - + +
429B MET 5.5 0.9 - - - +
430B ASN* 1.3 76.7 - - - +
432B PHE* 1.3 75.0 + - - +
433B ARG* 3.7 17.5 - - - +
602B GLN* 3.1 30.5 - - - +
619B ASP* 3.1 24.9 + - + -
620B VAL 3.9 6.3 - - - +
621B LEU* 4.4 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B THR* 4.3 10.1 - - - -
244B LEU* 5.5 1.3 - - + -
245B GLN 3.5 10.1 - - - +
246B ASP* 3.2 24.5 - - - -
247B LEU 4.6 0.2 - - - +
430B ASN* 4.3 14.6 - - + -
431B ARG* 1.3 81.6 - - - +
433B ARG* 1.3 60.6 + - - +
434B LEU* 3.4 18.6 - - + +
619B ASP* 3.3 4.6 - - - -
620B VAL* 3.0 34.2 + - + +
622B LEU* 3.6 44.4 - - + -
627B GLY* 4.3 20.2 - - - -
630B PHE* 5.5 2.5 - - + -
631B TRP* 3.5 38.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B LEU* 3.3 2.4 - - - -
245B GLN* 2.9 39.0 + - + +
247B LEU* 3.6 39.4 - - + +
250B TYR* 4.7 15.0 + - - -
309B THR* 6.2 0.8 - - - +
431B ARG* 3.7 22.5 - - - +
432B PHE* 1.3 69.9 - - - +
434B LEU* 1.3 61.5 + - - +
435B ILE* 3.7 30.4 + - + +
602B GLN* 3.6 25.3 + - - +
617B GLY* 4.8 4.3 - - - -
618B TRP 3.3 5.4 - - - +
619B ASP* 3.3 16.2 + - - +
647B SER* 5.5 3.2 + - - -
650B HIS* 3.8 26.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B LEU 3.7 4.0 - - - -
244B LEU* 3.7 24.2 - - + -
432B PHE* 3.4 30.5 - - + +
433B ARG* 1.3 71.0 - - - +
435B ILE* 1.3 55.6 + - - +
439B SER* 3.3 20.3 + - - +
442B ILE* 4.2 4.9 - - + -
443B LEU* 3.8 23.6 - - + -
616B SER 4.0 0.9 - - - +
617B GLY* 3.3 0.3 - - - -
618B TRP* 2.5 49.4 + - + +
620B VAL* 3.7 18.8 - - + +
634B PHE* 4.0 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ALA 4.4 0.9 - - - +
238B MET* 3.7 34.0 - - + +
242B CYS 4.0 0.3 - - - -
243B LEU* 2.8 51.8 + - + +
245B GLN* 4.3 19.5 - - - +
433B ARG* 3.7 29.8 + - + +
434B LEU* 1.3 76.2 - - - +
436B GLY* 1.3 61.5 + - - +
439B SER* 3.7 2.5 - - - -
614B TRP 5.5 0.4 - - - +
615B GLY* 4.8 1.3 - - - -
616B SER 3.4 20.2 - - - +
617B GLY* 3.7 8.5 - - - +
646B GLU* 5.2 0.2 - - - +
650B HIS* 3.6 29.2 - - + +
----------------------------------------------------------
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