Contacts of the strand formed by residues 170 - 175 (chain o) 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 LYS 170 (chain o).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77o ARG* 3.8 27.7 - - - +
79o ILE* 4.2 16.4 - - - -
103o LEU* 4.0 33.9 - - + -
104o ILE 3.2 22.4 - - - +
105o ASP* 3.9 9.3 + - - +
106o SER* 3.1 9.1 + - - -
165o GLN* 3.0 17.2 - - - +
168o GLN* 3.1 24.4 + - + +
169o GLY* 1.4 87.9 + - - +
171o LEU* 1.4 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67o TRP* 5.9 2.7 - - + +
103o LEU* 3.5 6.1 - - - -
104o ILE* 3.0 40.0 + - + +
105o ASP 3.9 4.0 - - - +
106o SER* 3.3 26.7 - - - +
109o TYR* 3.5 41.1 - - + -
162o LEU* 4.8 1.3 - - + +
165o GLN* 3.5 33.9 - - + +
166o PHE* 3.9 19.7 - - + -
170o LYS* 1.4 73.1 - - - +
172o LEU* 1.3 69.8 + - - +
189o VAL* 4.4 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82o VAL* 3.8 29.6 - - + -
101o ILE* 4.0 8.7 - - + -
102o VAL 3.5 2.2 - - - +
103o LEU* 3.8 12.6 - - + -
165o GLN* 3.2 16.3 + - + +
168o GLN* 3.9 23.8 - - - +
171o LEU* 1.3 73.3 - - - +
173o ALA* 1.4 60.1 + - - +
189o VAL* 3.8 5.0 - - - +
190o LEU* 3.1 30.0 + - + -
195o LEU* 3.7 33.4 - - + -
198o TYR* 6.2 1.3 - - + -
199o LEU* 4.5 15.9 - - + -
202o ILE* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65o PHE* 3.5 31.0 - - + -
101o ILE* 3.4 4.7 - - - -
102o VAL* 2.9 39.3 + - + +
104o ILE* 4.1 15.7 - - + -
172o LEU* 1.4 75.1 - - - +
174o CYS* 1.4 59.9 + - - +
188o TYR 3.6 9.6 - - - +
189o VAL* 4.0 7.4 - - - -
190o LEU* 4.0 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 174 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65o PHE* 4.4 1.3 - - - -
99o ASN* 3.9 23.8 - - - -
100o CYS 3.6 2.7 - - - -
101o ILE* 4.0 16.4 - - + -
173o ALA* 1.4 72.2 - - - +
175o ILE* 1.4 74.0 + - - +
176o ALA 3.4 0.5 + - - -
187o GLY* 3.1 4.2 - - - -
188o TYR* 2.9 56.1 + - + +
190o LEU* 3.9 23.3 - - + +
198o TYR* 5.1 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain o).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65o PHE* 4.2 16.8 - - + -
78o ILE* 5.0 1.6 - - + -
96o LEU* 4.1 13.5 - - + -
97o VAL 4.0 24.2 - - - +
98o LYS* 3.8 0.8 - - - +
99o ASN* 3.0 30.6 + - - +
100o CYS* 3.1 20.4 + - + +
102o VAL* 3.9 22.4 - - + -
174o CYS* 1.4 71.0 - - - +
176o ALA* 1.4 59.2 + - - +
177o SER* 3.1 26.5 - - - +
179o PRO* 4.2 9.0 - - + -
185o ALA* 4.3 19.7 - - + -
186o ASP 3.5 11.2 - - - +
187o GLY* 4.2 0.2 - - - -
----------------------------------------------------------
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