Contacts of the strand formed by residues 440 - 447 (chain D) in PDB entry 5SUY
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 ARG 440 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ARG* 3.4 34.2 - - - +
444A TRP* 3.6 26.8 - - - +
449C ILE 3.4 2.4 - - - +
451C ASN* 4.3 4.0 - - - -
452C ALA* 2.9 36.2 + - - +
453C PHE* 5.7 1.6 - - - -
454C LEU* 3.6 31.3 - - - +
457C ASP* 4.7 1.2 + - - -
502C TYR* 3.7 25.8 + - - -
439D VAL* 1.3 79.6 - - - +
441D ASP* 1.3 59.2 + - - +
442D ARG* 3.3 29.6 + - + +
444D TRP* 5.7 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 441 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C THR* 3.3 19.3 + - + +
449C ILE 3.1 29.0 + - - -
450C PRO* 4.1 14.4 - - + -
451C ASN 4.9 0.7 - - - +
440D ARG* 1.3 70.6 - - - +
442D ARG* 1.3 89.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 442 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C LYS* 4.2 34.7 - - + +
447C ILE 3.3 9.2 - - - +
448C THR* 5.0 2.7 - - - +
449C ILE 4.5 2.5 - - - +
452C ALA* 5.3 1.9 - - - +
502C TYR* 4.1 4.2 + - - -
440D ARG* 3.3 31.4 - - + +
441D ASP* 1.3 108.4 + - - +
443D MET* 1.3 63.5 + - - +
444D TRP* 4.6 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 443 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C LEU 3.6 0.9 - - - +
446C LYS* 3.4 6.4 - - - +
447C ILE* 2.9 48.1 + - + +
449C ILE* 3.5 31.4 - - + -
452C ALA* 5.2 3.8 - - + -
491C THR* 3.3 28.5 - - - +
492C VAL* 4.8 4.3 - - + -
502C TYR* 3.6 33.7 - - + -
442D ARG* 1.3 76.9 - - - +
444D TRP* 1.3 70.2 + - - +
445D LEU* 3.6 42.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 444 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C TRP* 4.2 41.9 - + + -
445C LEU 3.5 17.9 - - - -
446C LYS* 3.9 36.1 - - + -
502C TYR* 3.8 32.5 - - + +
440D ARG* 5.7 4.0 - - - -
442D ARG* 4.6 17.4 - - + +
443D MET* 1.3 83.7 - - - +
445D LEU* 1.3 61.9 + - - +
502D TYR* 6.3 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C MET 3.8 0.7 - - - +
444C TRP* 3.4 7.7 - - - -
445C LEU* 2.9 44.0 + - + +
447C ILE* 4.9 10.1 - - + -
492C VAL* 3.9 37.2 - - + -
443D MET* 3.6 19.5 - - + -
444D TRP* 1.3 76.5 - - - +
446D LYS* 1.3 67.1 + - - +
447D ILE* 3.6 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 446 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A ASP* 3.2 21.6 + - - +
460A ASP* 3.2 26.9 + - - +
440C ARG* 5.3 1.4 - - - +
442C ARG* 3.5 46.8 - - + +
443C MET 3.5 9.2 - - - +
444C TRP* 3.7 37.2 - - + +
445D LEU* 1.3 80.3 - - - +
447D ILE* 1.3 75.6 + - - +
448D THR* 4.2 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 447 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C ARG* 3.2 5.9 - - - +
443C MET* 2.9 53.9 + - + +
445C LEU* 5.3 5.8 - - + -
445D LEU* 3.6 35.4 - - + +
446D LYS* 1.3 80.8 - - - +
448D THR* 1.3 67.4 + - - +
449D ILE* 3.4 22.9 + - + -
----------------------------------------------------------
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