Contacts of the strand formed by residues 203 - 209 (chain A) in PDB entry 3WBR
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 203 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER* 3.4 17.5 - - - +
99A THR* 3.3 21.1 - - - +
100A GLY 3.2 15.9 - - - +
101A MET* 4.1 5.3 - - + +
135A LYS* 4.4 9.2 - - - +
137A ASN* 6.0 0.6 - - - +
138A SER* 3.0 34.3 + - - +
139A SER 3.1 10.6 + - - +
140A TYR* 3.6 15.9 - - + -
141A PHE* 2.9 20.6 + - - +
202A GLN* 1.3 80.4 - - - +
204A SER* 1.3 65.5 + - - +
99G THR 4.6 5.5 + - - -
101G MET* 4.0 20.4 - - - +
203G LYS* 4.2 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 3.7 0.9 - - - -
98A SER* 2.8 47.7 + - - -
100A GLY 5.1 0.5 + - - -
107A SER* 3.7 23.6 + - - -
110A ASN* 5.8 1.4 + - - +
111A CYS* 5.1 3.5 - - - -
118A LEU* 3.7 22.8 - - - +
140A TYR* 3.8 4.6 - - - -
141A PHE* 3.9 9.9 - - - +
203A LYS* 1.3 78.8 - - - +
205A ILE* 1.3 67.4 + - - +
206A CYS* 4.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A TYR* 4.7 7.9 - - + -
96A PHE 3.3 10.1 - - - +
97A ILE* 3.9 13.9 - - + -
111A CYS* 4.4 0.7 - - - -
118A LEU* 3.4 9.4 - - - +
119A VAL* 2.8 52.8 + - + +
130A ILE* 3.9 14.8 - - + -
134A LEU* 3.6 28.5 - - + -
140A TYR* 3.8 12.1 - - + -
141A PHE 3.5 6.1 + - - +
142A LEU* 4.6 0.2 - - + -
183A ILE* 3.8 27.1 - - + -
204A SER* 1.3 79.8 - - - +
206A CYS* 1.3 69.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TRP* 3.9 19.5 - - + -
95A TYR* 3.3 6.4 - - - +
96A PHE* 2.8 40.5 + - + +
98A SER* 6.1 1.1 - - - -
110A ASN* 5.7 0.9 - - - -
111A CYS* 2.0 52.7 - - + -
114A MET* 3.8 14.6 - - - -
116A ALA* 4.1 0.9 - - + -
117A ASP 3.1 6.7 - - - +
119A VAL 4.5 0.2 - - - -
204A SER* 5.1 5.6 - - - -
205A ILE* 1.3 76.6 - - - +
207A LYS* 1.3 61.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TRP* 4.2 0.4 - - - -
93A SER* 3.7 23.7 + - - -
94A CYS 3.2 8.5 - - - +
95A TYR* 3.7 16.6 - - + -
116A ALA* 3.3 3.0 - - - +
117A ASP* 2.8 33.8 + - + +
118A LEU 5.2 0.2 - - - +
119A VAL* 4.0 17.7 - - + -
120A VAL* 2.8 28.2 + - - +
122A ASN* 3.1 19.0 - - - +
126A GLU* 2.6 31.1 + - - +
206A CYS* 1.3 76.2 - - - +
208A MET* 1.3 66.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PRO* 3.8 33.4 - - + -
87A TRP* 3.8 37.2 - - + +
93A SER* 3.4 5.6 - - - -
94A CYS* 2.8 39.8 + - + -
114A MET 3.8 22.0 - - - +
115A GLY* 3.7 20.6 - - - +
116A ALA* 3.9 1.8 - - + -
207A LYS* 1.3 80.8 - - - +
209A LYS* 1.3 68.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A SER 3.8 7.9 - - - +
93A SER* 4.5 3.6 - - - +
94A CYS* 4.5 0.2 - - - -
208A MET* 1.3 86.5 - - - +
210A LYS* 1.3 69.5 + - - +
164E ASN 4.6 14.1 + - - -
----------------------------------------------------------
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