Contacts of the strand formed by residues 91 - 96 (chain X) in PDB entry 5K0Y
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 HIS 91 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53X VAL* 4.6 4.3 - - + -
55X GLY* 5.5 6.4 + - - -
57X ARG* 3.7 31.7 + - + +
58X LYS 3.2 10.8 + - - +
59X ALA* 3.3 6.1 - - - +
60X ILE 3.0 22.6 + - - +
80X VAL* 5.6 1.8 - - + -
84X GLU* 3.2 24.0 + - - -
89X GLY 3.6 10.5 - - - -
90X LYS* 1.4 69.9 - - - +
92X VAL* 1.3 61.8 + - - +
93X VAL* 5.5 1.2 - - - +
168X HIS 6.1 1.3 - - - -
172X THR* 3.1 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60X ILE* 3.5 17.0 - - + +
62X ILE* 3.6 31.0 - - + -
80X VAL* 3.1 35.8 - - + +
83X LEU* 3.8 39.0 - - + -
84X GLU 4.5 1.1 - - - +
87X PHE* 4.0 20.9 - - + -
90X LYS 3.7 9.6 + - - +
91X HIS* 1.3 75.2 - - - +
93X VAL* 1.4 68.7 + - - +
94X PHE* 5.1 1.8 - - + -
169X LYS* 5.3 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 93 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60X ILE 3.2 10.3 + - - +
61X ILE* 4.9 7.6 - - + -
62X ILE* 3.5 27.4 + - - +
76X GLN* 5.3 5.2 - - + +
80X VAL* 5.6 0.7 - - + -
91X HIS 5.5 0.7 - - - +
92X VAL* 1.4 78.0 - - - +
94X PHE* 1.4 82.6 + - + +
95X ILE* 4.4 12.8 - - + -
132X ASP 5.2 0.7 - - - +
133X LEU* 3.7 50.7 - - + +
169X LYS* 6.2 2.5 - - + +
172X THR* 5.9 4.7 - - + -
173X PHE* 4.2 16.6 - - + -
176X VAL* 5.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 94 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62X ILE* 3.8 38.6 - - + +
64X VAL* 4.8 4.3 - - + -
69X LEU* 3.7 22.4 - - + -
72X PHE* 3.5 61.2 - + + -
73X GLN* 5.1 0.9 - - - -
76X GLN* 4.5 16.4 - - + -
79X LEU* 4.0 15.7 - - + -
80X VAL* 3.9 25.6 - - + -
83X LEU* 5.1 2.2 - - + -
92X VAL* 5.1 3.1 - - + -
93X VAL* 1.4 85.9 - - + +
95X ILE* 1.4 66.2 + - - +
132X ASP* 4.1 16.9 - - - +
133X LEU* 4.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61X ILE* 3.8 22.0 - - + -
62X ILE 3.0 21.3 + - - +
63X PHE* 3.5 17.0 - - + -
64X VAL* 3.5 16.9 + - - +
93X VAL* 4.4 4.9 - - + -
94X PHE* 1.4 79.6 - - - +
96X ALA* 1.4 72.3 + - - +
97X GLN* 5.5 2.7 - - - +
129X ILE* 3.8 31.0 - - + -
132X ASP* 5.0 1.3 - - - -
133X LEU* 4.0 16.8 - - + -
176X VAL* 3.8 17.0 - - + -
180X LEU* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64X VAL* 3.9 15.0 - - + +
66X VAL* 4.1 24.7 - - + -
69X LEU* 5.2 1.3 - - + -
95X ILE* 1.4 74.3 - - - +
97X GLN* 1.4 60.9 + - - +
98X ARG* 5.6 1.6 - - + +
125X VAL* 4.1 4.5 - - - +
128X ALA* 5.8 4.7 - - + -
129X ILE* 3.3 29.9 - - + +
132X ASP* 3.5 23.8 + - - +
----------------------------------------------------------
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