Contacts of the strand formed by residues 84 - 90 (chain A) in PDB entry 3SMZ
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 LEU 84 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A HIS* 3.9 48.4 - - + +
79A LEU* 3.9 25.4 - - + +
82A TYR* 3.6 17.6 + - + +
83A GLU* 1.3 78.4 - - - +
85A LYS* 1.4 63.7 + - - +
86A TYR 4.2 7.6 - - - +
87A CYS* 4.2 11.0 - - + -
98A VAL* 3.7 24.2 - - + -
99A THR 3.7 5.4 - - - +
100A LEU* 3.8 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SO4 3.0 38.9 + - - +
59A ARG* 4.8 3.7 - - - +
76A HIS* 6.0 0.8 - - - -
83A GLU 4.0 2.2 + - - -
84A LEU* 1.4 73.6 - - - +
86A TYR* 1.3 97.6 + - + +
99A THR* 2.9 21.2 + - + +
100A LEU* 4.6 4.8 - - - +
101A LEU* 5.1 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SO4 3.9 17.8 + - - -
60A LYS* 6.3 0.4 - - - -
76A HIS* 5.4 0.9 - - - -
84A LEU* 4.2 3.9 - - - +
85A LYS* 1.3 118.4 + - + +
87A CYS* 1.3 63.6 + - - +
88A PHE* 3.5 36.6 - + + -
97A PHE 4.2 2.2 - - - +
98A VAL* 3.3 8.7 - - - +
99A THR* 2.9 52.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 3.1 33.9 - - - +
75A VAL* 3.7 39.0 - - - -
76A HIS* 3.4 31.0 + - + +
84A LEU* 4.2 7.9 - - + -
86A TYR* 1.3 78.5 - - - +
88A PHE* 1.3 71.0 + - - +
89A VAL* 5.2 1.8 - - - -
96A ALA* 5.2 1.1 - - - -
97A PHE 3.5 3.6 - - - -
98A VAL* 4.1 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 3.5 6.1 - - - -
86A TYR* 3.5 50.7 - + + -
87A CYS* 1.3 82.4 - - - +
89A VAL* 1.3 66.2 + - - +
96A ALA* 3.4 2.0 - - - -
97A PHE* 2.9 55.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 4.2 23.6 - - + +
71A THR* 3.8 22.4 - - - +
72A ASN* 2.7 40.4 + - - +
75A VAL* 3.8 20.2 - - + -
87A CYS* 5.2 0.9 - - - -
88A PHE* 1.3 76.7 - - - +
90A ASP* 1.3 59.4 + - - +
91A LYS* 3.8 12.3 + - + +
95A THR 3.4 6.7 - - - +
96A ALA* 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 6.0 0.2 - - - -
88A PHE 3.9 0.2 + - - -
89A VAL* 1.3 70.0 - - - +
91A LYS* 1.3 57.9 + - - +
92A TYR* 3.3 4.5 + - - +
93A LYS* 3.0 28.1 + - + +
94A GLY 3.0 24.3 + - - -
95A THR* 2.7 30.6 + - - +
97A PHE* 3.9 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