Contacts of the strand formed by residues 141 - 148 (chain A) in PDB entry 1RC9
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 141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 3.5 45.2 - + - +
58A GLU* 4.1 2.6 - - - +
79A MET* 3.1 9.0 - - - +
80A SER* 3.0 35.4 + - - +
81A PRO 3.4 21.3 - - - -
82A TYR* 3.4 18.6 - + - -
83A PRO* 3.5 28.6 - - + +
132A ALA 3.5 3.1 - - - +
133A TYR* 3.5 29.1 - + - -
139A TYR* 3.2 0.4 - - - +
140A SER* 1.3 89.3 - - - +
142A PHE* 1.3 60.7 + - - +
143A PHE* 3.8 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TRP* 4.0 6.1 - + - -
53A ALA* 3.7 32.1 - - - +
56A CYS* 4.5 3.4 - - - -
57A ILE 3.4 26.9 - - - -
58A GLU* 3.7 35.9 - - + +
59A SER 3.7 15.0 - - - -
77A ILE* 4.0 22.4 - - + -
78A TYR 3.5 11.2 - - - -
79A MET* 4.1 10.5 - - + -
130A ALA 4.2 0.2 - - - +
131A ALA* 3.5 3.1 - - - -
132A ALA* 2.9 34.6 + - + +
134A CYS* 4.1 11.9 - - - -
141A TYR* 1.3 75.6 - - - +
143A PHE* 1.3 64.6 + - - +
144A VAL* 3.7 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 4.2 12.1 - + - -
7A GLU* 5.9 1.8 - - + -
77A ILE* 3.3 3.8 - - - +
78A TYR* 2.7 56.1 + + + +
80A SER* 3.7 22.0 - - - -
84A MET* 4.1 25.8 - - + -
86A TRP* 3.8 30.1 - + + -
89A ILE* 3.4 34.5 - - + -
93A TRP* 5.2 2.5 - - + -
130A ALA 3.6 2.7 - - - -
131A ALA* 3.9 18.2 - - + -
141A TYR* 3.8 23.1 - + + -
142A PHE* 1.3 74.8 - - - +
144A VAL* 1.3 68.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA* 3.8 11.7 - - + +
52A TRP* 4.2 6.3 - - + -
53A ALA* 3.9 19.3 - - + -
75A GLU* 3.7 33.2 - - + +
76A ASN 3.6 3.8 - - - +
77A ILE* 4.0 4.3 - - + -
86A TRP* 4.3 0.4 - - - -
93A TRP* 5.3 0.2 - - - -
129A CYS* 3.1 3.2 - - - +
130A ALA 2.8 38.2 + - - -
142A PHE* 3.7 32.8 - - + -
143A PHE* 1.3 81.0 - - - +
145A CYS* 1.3 64.8 + - - +
146A GLN* 4.1 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ILE* 4.8 2.0 - - - -
22A HIS* 5.1 0.7 - - - -
75A GLU* 3.4 2.4 - - - +
76A ASN 3.0 32.7 + - - +
86A TRP* 3.4 24.5 - - - -
90A ILE* 5.6 0.2 - - - -
93A TRP* 3.9 20.1 - - + -
127A ILE* 4.1 9.6 - - + -
128A GLY 3.4 4.0 - - - -
129A CYS* 2.0 44.2 - - - -
144A VAL* 1.3 72.4 - - - +
146A GLN* 1.3 63.2 + - - +
147A TYR* 3.5 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA* 4.0 14.6 - - + +
48A ASN* 2.8 39.0 + - - +
49A ALA* 3.7 23.6 + - + +
52A TRP* 4.7 4.9 - - - +
61A SER* 3.8 2.6 + - - -
66A ARG* 3.7 16.7 - - - +
68A ILE* 3.9 5.4 - - + +
73A CYS* 5.0 5.6 - - + -
74A GLY 3.3 11.9 - - - +
75A GLU* 2.9 27.9 + - + +
126A ARG 3.8 0.2 - - - +
127A ILE* 3.4 6.6 - - - +
128A GLY 2.8 32.4 + - - +
144A VAL* 4.1 3.4 - - + +
145A CYS* 1.3 78.0 - - - +
147A TYR* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A HIS* 2.8 41.5 + + - -
39A MET* 3.6 22.7 - - + -
73A CYS* 3.0 4.2 - - - +
74A GLY 2.6 34.6 + - - -
75A GLU 4.3 1.8 - - - -
76A ASN* 3.1 35.4 + - + -
93A TRP* 3.7 9.7 - - - -
118A GLN* 3.4 43.5 - - + +
119A ILE* 3.9 1.9 - - - +
124A SER* 4.2 4.9 - - - -
126A ARG 3.4 4.9 - - - +
127A ILE* 3.6 17.8 - - + +
145A CYS* 3.5 22.9 - - + -
146A GLN* 1.3 76.8 - - - +
148A CYS* 1.3 62.6 - - - +
149A PRO 3.5 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A TYR* 3.7 34.3 - - + -
45A ALA* 4.3 5.4 - - - -
68A ILE* 4.0 9.2 - - - -
71A ILE* 4.9 4.3 - - + -
73A CYS* 2.0 45.3 - - - -
124A SER* 4.2 1.8 - - - -
125A TYR* 3.4 3.8 + - - -
126A ARG* 2.9 46.1 + - + +
146A GLN 5.1 0.2 - - - -
147A TYR* 1.3 73.8 - - - +
149A PRO* 1.3 65.9 - - + +
----------------------------------------------------------
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