Contacts of the strand formed by residues 87 - 93 (chain B) in PDB entry 5K79
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 TYR 87 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B THR 4.4 4.9 + - - -
60B ASP* 3.4 28.3 + - + -
78B GLU* 3.6 29.2 - - + +
79B CYS 3.3 17.3 - - - -
80B GLU* 3.6 39.7 + - + +
84B GLY 5.3 0.4 - - - -
85B TYR* 3.4 21.0 + - - -
86B THR* 1.3 85.7 - - - +
88B ILE* 1.3 63.4 + - - +
89B PRO* 4.8 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP 4.7 0.9 - - - +
46B GLY* 3.3 37.2 - - - +
47B THR* 6.0 1.1 - - - +
78B GLU* 3.6 4.3 - - - -
79B CYS 2.9 25.1 + - - +
81B ARG* 3.8 28.7 - - + +
86B THR* 5.6 0.4 - - + -
87B TYR* 1.3 76.4 - - - +
89B PRO* 1.3 87.8 - - + +
90B THR* 3.6 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA 3.5 8.7 - - - +
78B GLU* 3.4 22.6 - - - +
87B TYR 4.8 0.4 - - - +
88B ILE* 1.3 106.6 - - + +
90B THR* 1.3 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLY 3.4 16.8 - - - +
47B THR* 3.7 6.6 - - - +
48B LEU* 3.0 33.7 + - + +
76B ALA* 3.3 3.8 - - - +
77B ALA 2.9 36.5 + - - +
79B CYS* 3.4 34.8 - - + -
88B ILE 4.1 0.2 - - - +
89B PRO* 1.3 76.2 - - - +
91B GLU* 1.3 68.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 6.1 0.3 - - - +
48B LEU* 4.5 2.1 - - - +
65B ALA* 5.6 2.1 - - - +
67B SER* 3.0 30.8 + - - -
68B LEU 5.2 1.0 + - - -
74B VAL* 3.8 24.8 - - + +
75B LEU 3.3 6.1 - - - +
76B ALA* 4.0 16.6 - - + +
90B THR* 1.3 85.9 + - - +
92B ILE* 1.3 62.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 4.1 13.5 - - + -
48B LEU* 3.7 39.5 - - + +
49B SER 4.1 0.9 - - - +
50B TRP* 3.5 56.3 - - + +
74B VAL* 3.2 6.7 - - - -
75B LEU* 2.9 60.5 + - + +
91B GLU* 1.3 75.7 - - - +
93B GLU* 1.3 61.6 + - - +
94B LEU* 3.3 5.6 + - + -
96B GLU* 4.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 2.5 39.3 - - - +
89A PRO* 3.4 18.9 - - + +
50B TRP* 3.3 6.8 - - - -
70B THR* 5.5 0.9 + - - +
72B THR* 3.7 24.4 + - - +
73B TYR 3.5 7.0 - - - +
74B VAL* 4.0 6.1 - - + -
91B GLU 6.0 0.4 - - - -
92B ILE* 1.3 72.7 - - - +
94B LEU* 1.3 65.5 + - - +
95B ASP 3.2 0.9 - - - -
96B GLU* 3.1 41.1 + - + +
----------------------------------------------------------
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