Contacts of the strand formed by residues 212 - 219 (chain A) in PDB entry 2C6U
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 212 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A HIS 3.2 1.4 - - - +
120A ASN* 3.2 11.1 + - - -
121A LEU* 3.0 27.8 + - - +
126A SER* 4.1 1.0 + - - -
156A ILE* 3.4 41.1 + - + +
158A TRP* 3.6 43.9 - + + +
197A TYR* 3.8 23.1 - + - -
206A THR* 4.5 2.4 + - - +
210A ASN* 4.3 15.0 + - + +
211A LYS* 1.3 86.5 + - - +
213A TYR* 1.3 73.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE 3.7 6.7 - - - +
118A ARG* 3.6 47.2 - - + -
119A HIS 3.3 9.6 - - - -
120A ASN* 3.8 22.4 + - + -
155A LEU* 3.7 30.5 - - + -
156A ILE 3.7 18.0 + - - +
157A ARG* 3.2 14.0 - - + +
158A TRP* 2.8 23.4 + - - -
212A HIS* 1.3 80.2 - - - +
214A LEU* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 3.0 33.5 + - + +
119A HIS* 3.5 32.3 - - + +
121A LEU* 3.9 16.4 - - + -
126A SER* 3.6 35.7 - - - +
129A TYR* 4.0 15.3 - - + -
130A CYS* 3.6 9.6 - - - -
137A LEU* 4.5 2.0 - - + -
157A ARG* 3.0 14.8 + - - -
158A TRP* 4.0 7.0 - - + +
213A TYR* 1.3 78.3 - - - +
215A MET* 1.3 65.5 + - - +
216A CYS* 3.5 32.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY 3.1 16.6 - - - +
116A PHE* 3.7 32.8 - - + +
117A PHE* 4.6 0.7 - - - +
137A LEU* 3.5 22.3 - - - +
138A LEU* 3.5 30.0 + - + +
149A ILE* 3.6 24.9 - - + -
153A THR* 4.3 2.2 - - + -
157A ARG* 3.8 21.1 - - + -
158A TRP 3.7 11.0 + - - +
159A VAL* 3.6 25.8 - - + -
198A PHE* 3.7 16.8 - - + -
214A LEU* 1.3 78.5 - - - +
216A CYS* 1.3 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 3.8 20.2 - - + -
114A TYR* 3.4 1.9 - - - -
115A GLY 2.8 29.9 + - - -
117A PHE* 4.1 4.9 - - + -
130A CYS* 2.1 50.5 - - - -
133A MET* 3.6 15.7 - - - -
135A ALA* 3.8 5.6 - - + -
136A THR 3.3 6.5 - - - +
138A LEU* 3.1 13.5 - - - +
214A LEU* 3.5 13.9 - - - -
215A MET* 1.3 72.3 - - - +
217A GLU* 1.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TRP* 4.2 0.2 - - - -
112A SER* 2.8 29.6 + - - -
113A CYS 3.3 4.3 - - - -
114A TYR* 3.6 24.6 + - + -
135A ALA* 3.4 4.9 - - - +
136A THR* 2.7 40.6 + - - +
137A LEU 4.5 1.5 - - - +
138A LEU* 3.7 10.3 - - + -
139A LYS* 3.0 38.1 + - - +
216A CYS* 1.3 75.1 - - - +
218A ARG* 1.3 67.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PRO 5.4 0.2 + - - -
102A CYS* 4.2 0.6 - - - +
103A ASP* 3.3 47.4 + - - +
106A TRP* 3.6 49.2 - - + +
112A SER* 3.5 4.6 - - - -
113A CYS* 2.7 52.1 + - + +
133A MET 4.1 13.5 + - - -
134A ASN* 3.8 11.2 - - - +
135A ALA* 3.6 21.3 - - + +
217A GLU* 1.3 74.4 - - - +
219A LYS* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP* 3.2 37.2 - - + +
112A SER* 4.6 3.6 - - - +
113A CYS* 4.6 2.1 - - - -
218A ARG* 1.3 78.8 + - - +
220A ALA* 1.3 71.8 + - - +
221A GLY 3.7 0.9 + - - -
----------------------------------------------------------
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