Contacts of the strand formed by residues 154 - 157 (chain X) in PDB entry 3RCK
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 PHE 154 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X LEU* 4.1 24.5 - - + -
78X PHE* 3.6 28.3 - + + -
90X TYR* 3.7 25.1 - + - -
95X PHE* 4.5 8.3 - + - -
105X GLN* 3.3 7.2 - - - +
106X ALA* 2.9 52.1 + - + +
107X GLY* 3.8 11.9 - - - -
140X LEU* 3.6 19.7 - - + -
141X SER 3.3 13.9 - - - +
142X MET* 4.6 1.8 - - - -
143X ALA* 3.8 2.7 - - - +
152X SER 3.5 14.4 - - - +
153X GLN* 1.3 73.6 - - - +
155X PHE* 1.3 68.2 + - - +
156X ILE* 4.6 5.8 - - + -
171X PHE* 4.4 10.1 - - + -
200X ILE* 4.4 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 155 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103X MET* 3.1 44.2 - - + -
104X CYS 3.2 9.2 - - - +
105X GLN* 4.0 0.4 - - + -
134X HIS* 4.0 2.2 - + - -
139X VAL 3.7 1.2 - - - +
140X LEU* 3.5 5.2 - - - +
141X SER* 2.8 57.1 + - - -
142X MET 3.5 22.9 - - - -
143X ALA* 3.9 6.1 - - + -
154X PHE* 1.3 78.8 - - - +
156X ILE* 1.3 65.0 + - - +
157X CYS* 3.6 28.5 - - - -
161X THR* 5.6 0.7 - - + -
164X LEU* 3.7 30.3 - - + -
168X HIS* 3.8 10.5 - + - -
210X 1FP 4.0 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X LEU* 4.9 2.2 - - + -
62X VAL* 4.2 16.8 - - + -
64X LEU* 4.3 11.7 - - + -
95X PHE* 4.6 20.6 - - + -
103X MET* 3.4 1.6 - - - -
104X CYS* 2.9 37.3 + - + +
138X GLY* 4.3 2.7 - - - +
139X VAL 3.3 8.5 - - - +
140X LEU* 4.0 15.5 - - + -
154X PHE* 4.6 9.0 - - + -
155X PHE* 1.3 78.5 - - - +
157X CYS* 1.3 71.7 + - - +
158X THR* 4.2 1.9 - - - +
174X VAL* 3.8 20.6 - - + -
181X VAL* 3.9 32.1 - - + -
184X ILE* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 157 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102X PHE 3.6 7.6 - - - +
103X MET* 4.3 1.3 - - - +
134X HIS* 4.1 4.9 - - - -
136X GLY 3.9 9.2 - - - +
138X GLY* 2.8 24.9 + - - -
139X VAL* 2.9 30.8 + - - +
155X PHE* 3.6 24.9 - - - -
156X ILE* 1.3 77.6 - - - +
158X THR* 1.3 62.0 + - - +
159X ILE 3.4 18.4 - - - +
161X THR* 3.4 26.2 - - + -
178X MET* 3.8 1.6 - - - +
----------------------------------------------------------
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