Contacts of the strand formed by residues 206 - 212 (chain A) in PDB entry 5IXC
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 ALA 206 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASP* 5.0 6.1 - - - +
166A VAL 3.1 12.8 - - - +
167A HIS* 4.5 17.5 - - + +
204A ALA 5.2 0.9 - - - +
205A SER* 1.3 76.8 - - - +
207A PHE* 1.3 77.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU 3.7 0.7 - - - +
165A ASP* 3.6 8.4 - - - +
166A VAL* 2.9 47.1 + - + +
168A LEU* 5.1 4.7 - - + -
185A LEU* 3.8 25.4 - - + -
187A LEU* 3.6 21.8 - - + -
197A GLN* 3.7 31.2 - - + +
198A THR* 4.7 5.2 - - - -
199A SER* 3.4 42.0 - - - -
205A SER* 4.2 15.0 - - - -
206A ALA* 1.3 88.2 - - - +
208A ARG* 1.3 61.1 + - - +
209A PHE* 4.6 3.4 - - + -
267A LEU* 5.8 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A CYS* 3.6 28.3 - - - +
164A LEU 3.4 7.4 - - - -
165A ASP* 2.8 28.0 + - - -
194A GLU* 3.4 10.4 - - - +
197A GLN* 2.8 22.2 + - - +
207A PHE* 1.3 75.1 - - - +
209A PHE* 1.3 57.5 + - - +
210A HIS* 3.4 23.5 + - + -
275A PRO* 3.7 33.3 - - - +
276A GLU* 4.0 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A CYS* 3.1 6.6 - - - -
164A LEU* 2.7 54.2 + - + -
166A VAL* 4.8 2.9 - - + -
187A LEU* 3.7 45.5 - - + -
189A LEU* 3.6 30.5 - - + -
192A SER* 3.6 18.4 - - - -
194A GLU* 3.4 12.3 - - - -
195A ASP 3.9 20.9 - - - -
197A GLN* 3.5 32.8 - - + -
207A PHE* 4.6 3.8 - - + -
208A ARG* 1.3 75.8 - - - +
210A HIS* 1.3 61.3 + - - +
211A TYR* 3.7 2.8 - - + -
219A LEU* 4.2 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.5 9.0 - - + -
162A SER 3.7 3.8 - - - -
163A CYS* 3.2 23.8 - - - -
192A SER* 3.1 5.2 - - - -
193A TYR* 3.0 27.6 + - + +
194A GLU* 2.7 31.3 + - - +
208A ARG* 3.4 25.0 + - + +
209A PHE* 1.3 71.9 - - - +
211A TYR* 1.3 62.0 + - - +
274A CYS* 3.6 7.9 - - + -
276A GLU* 3.0 30.2 + - - -
507A PHE* 4.1 20.5 - - + -
510A ARG* 5.5 0.9 - - - -
512A MET* 3.2 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.7 10.2 - - - +
162A SER* 2.9 54.1 + - - +
164A LEU* 3.7 32.5 - - + +
189A LEU* 3.8 17.9 - - + -
191A GLY 4.1 6.5 - - - +
192A SER* 3.8 18.6 - - - +
209A PHE 3.7 4.5 - - - -
210A HIS* 1.3 79.8 - - - +
212A MET* 1.3 81.7 + - - +
213A ALA* 5.2 1.3 - - - -
215A LEU* 4.6 4.5 - - + -
217A THR* 4.6 12.6 - - + -
244A LEU* 3.9 30.1 - - + +
271A ALA* 3.7 24.4 - - - +
507A PHE* 4.6 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A THR 3.7 25.4 - - - +
55A PRO* 4.0 19.3 - - + +
159A ARG* 3.8 36.3 - - + -
160A GLU 3.3 6.1 - - - +
161A LEU* 4.1 9.7 - - + +
191A GLY 4.7 6.0 + - - +
211A TYR* 1.3 89.8 - - - +
213A ALA* 1.3 63.5 + - - +
214A ALA* 3.4 5.8 + - + +
215A LEU* 3.5 42.0 + - + +
507A PHE* 5.2 10.2 - - + -
508A MET* 5.2 4.9 - - + +
608A GLY* 5.5 4.3 - - - +
610A GLN* 3.7 15.5 - - - +
----------------------------------------------------------
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