Contacts of the strand formed by residues 213 - 219 (chain A) in PDB entry 2IUW
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 ARG 213 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A TYR* 3.9 14.7 + - + +
183A ASN 2.9 29.7 + - - -
184A GLU* 3.6 17.9 + - - +
186A ASP 2.8 25.6 + - - -
211A ALA* 3.4 4.1 + - - +
212A THR* 1.3 83.8 - - - +
214A THR* 1.3 64.1 + - - +
238A PRO* 3.7 0.7 - - - +
239A LEU* 2.9 33.3 + - - +
259A VAL* 3.9 19.4 - - + +
260A PRO 2.8 23.4 + - - -
261A LYS* 3.6 0.6 - - - +
262A GLU* 3.7 14.8 + - - +
266A ARG* 3.8 21.3 - - - +
267A GLU 5.4 1.4 + - - -
269A ARG* 3.4 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A THR* 5.8 0.2 - - - +
213A ARG* 1.3 76.0 - - - +
215A PHE* 1.3 61.9 + - - +
216A GLU* 3.8 23.3 - - + +
236A LYS* 4.0 24.7 - - + -
237A ILE 3.8 9.0 - - - +
238A PRO* 4.3 8.6 - - + +
239A LEU* 5.7 0.2 - - - -
259A VAL* 3.4 13.1 - - - +
260A PRO* 3.2 27.9 - - - +
262A GLU* 3.8 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A SER* 5.9 2.5 - - - -
213A ARG 3.9 1.2 + - - -
214A THR* 1.3 70.0 - - - +
216A GLU* 1.3 60.4 + - - +
217A MET* 3.7 31.6 - - + -
235A VAL 3.9 0.5 - - - +
236A LYS* 3.6 1.0 - - - -
237A ILE* 2.8 50.8 + - + +
239A LEU* 3.6 21.1 - - + -
245A LEU* 3.8 20.9 - - + -
247A MET* 3.7 24.5 - - + -
257A HIS* 3.4 39.9 - + + -
258A ARG 3.6 8.1 - - - -
259A VAL* 4.4 2.2 - - + -
700A AKG 3.9 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A TRP* 3.6 16.8 - - + -
214A THR* 3.8 19.3 - - + +
215A PHE* 1.3 74.0 - - - +
217A MET* 1.3 61.7 + - - +
235A VAL 3.6 4.5 - - - +
236A LYS* 3.6 32.0 + - + +
257A HIS* 3.0 8.3 - - - +
258A ARG* 2.8 69.7 + - + +
260A PRO* 3.7 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.7 23.8 - - + -
90A VAL* 4.1 10.3 - - + -
190A TRP* 3.8 3.6 - - - -
215A PHE* 3.7 30.7 - - + +
216A GLU* 1.3 79.8 - - - +
218A ARG* 1.3 61.5 + - - +
234A ARG* 3.4 7.4 - - - +
235A VAL* 2.7 48.1 + - + +
237A ILE* 4.1 17.5 - - + -
247A MET* 4.6 2.7 - - - -
251A THR* 3.6 31.0 - - + -
255A TRP* 3.8 18.2 - - + -
256A GLN 3.2 7.0 - - - +
257A HIS* 4.2 6.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
190A TRP* 3.4 62.8 - - + +
217A MET* 1.3 73.1 - - - +
219A LYS* 1.3 66.6 + - - +
220A LYS* 6.0 0.4 - - - -
233A GLU* 3.5 5.2 - - - +
234A ARG* 3.8 36.2 - - - +
255A TRP* 3.3 4.7 - - - -
256A GLN* 2.8 64.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
81A SER* 3.3 23.1 - - - -
83A SER* 2.8 30.6 + - - -
84A PRO* 3.6 13.7 - - - +
218A ARG* 1.3 78.3 - - - +
220A LYS* 1.3 77.7 + - - +
221A PRO* 3.5 4.5 - - - +
232A VAL 4.8 6.5 - - - +
233A GLU* 2.9 37.8 + - + +
254A ASP* 3.5 12.0 + - - +
255A TRP* 3.4 27.7 - - + +
----------------------------------------------------------
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