Contacts of the strand formed by residues 211 - 219 (chain A) in PDB entry 1XEH
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 ILE 211 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A MET* 5.1 4.9 - - + -
205A HIS* 3.8 41.7 - - + +
209A GLU 3.9 6.3 - - - +
210A PRO* 1.3 77.2 - - - +
212A SER* 1.3 69.4 + - - +
213A VAL* 4.0 13.4 + - + +
232A VAL* 4.7 20.2 - - + -
269A PHE 3.5 1.7 - - - +
270A ALA* 3.5 4.1 - - - -
271A VAL* 2.7 37.7 + - + +
273A PRO* 3.9 27.8 - - + -
318A TYR* 6.4 0.4 - - + -
320A VAL* 4.7 14.4 - - + -
346A LEU* 5.1 7.9 - - + -
348A LEU* 6.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TRP 3.9 0.5 - - - +
200A MET* 3.8 4.9 - - - -
201A ASP* 3.3 50.8 + - - +
202A ARG* 5.7 1.4 - - - +
205A HIS* 5.2 1.2 + - - -
210A PRO* 4.1 4.0 + - - +
211A ILE* 1.3 74.9 - - - +
213A VAL* 1.3 60.9 + - - +
214A ASN* 4.0 1.5 + - - -
268A SER* 3.8 15.8 + - - -
269A PHE 3.2 10.2 + - - -
270A ALA* 4.3 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ALA* 4.4 6.3 - - + -
199A TRP 3.7 8.3 - - - +
200A MET* 5.9 2.2 - - + -
211A ILE* 4.5 15.7 - - + +
212A SER* 1.3 75.9 - - - +
214A ASN* 1.3 66.8 + - - +
215A VAL* 3.6 25.4 + - + +
230A ILE* 5.2 9.4 - - + -
267A GLN 3.6 3.1 - - - +
268A SER* 3.7 1.1 - - - -
269A PHE* 3.2 34.7 + - + +
271A VAL* 5.6 6.3 - - + -
320A VAL* 3.8 25.1 - - + -
322A VAL* 3.9 19.7 - - + -
344A LEU* 5.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLN 3.8 0.5 - - - +
198A ALA* 3.2 25.3 - - - +
199A TRP* 3.1 45.0 + - + +
201A ASP* 3.0 27.7 + - - +
213A VAL* 1.3 71.4 - - - +
215A VAL* 1.3 60.1 + - - +
216A SER* 5.0 3.6 + - - +
266A SER* 6.2 0.2 - - - +
267A GLN 4.0 4.1 + - - -
268A SER* 4.1 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A LEU* 4.0 24.2 - - + -
197A GLN 3.8 2.5 - - - +
198A ALA* 4.7 1.3 - - + -
213A VAL* 3.9 20.6 - - + +
214A ASN* 1.3 75.4 - - - +
216A SER* 1.3 68.5 + - - +
217A ILE* 4.1 15.5 - - + -
228A ILE* 5.0 7.6 - - + -
230A ILE* 4.8 0.2 - - + -
265A PHE* 3.6 4.9 - - + +
266A SER* 3.5 24.4 + - - -
267A GLN* 3.4 10.9 + - + +
269A PHE* 3.6 32.1 - - + -
322A VAL* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A GLN 3.8 2.8 - - - +
196A LEU* 4.0 0.2 - - - +
197A GLN* 2.9 48.8 + - - +
199A TRP* 5.9 3.3 - - - -
214A ASN* 5.0 4.2 + - - +
215A VAL* 1.3 77.8 + - - +
217A ILE* 1.3 65.7 + - - +
218A ASN* 4.2 6.5 + - - -
265A PHE 3.7 4.5 - - - -
266A SER* 3.5 12.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 3.5 28.3 - - + -
195A GLN 3.7 3.1 - - - +
196A LEU* 3.6 19.1 - - + -
215A VAL* 4.1 7.9 - - + -
216A SER* 1.3 76.5 - - - +
218A ASN* 1.3 66.2 + - - +
219A ASN* 4.0 4.5 - - + +
225A ILE* 4.9 3.1 - - + -
228A ILE* 3.9 10.8 - - + -
259A VAL* 3.5 40.4 - - + -
263A SER 3.7 1.2 - - - +
264A SER* 3.5 24.8 - - - -
265A PHE* 3.4 15.5 + - + +
324A LEU* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LEU* 3.4 1.9 - - - +
195A GLN* 3.1 48.7 + - + +
216A SER* 5.5 6.4 + - - -
217A ILE* 1.3 75.0 - - - +
219A ASN* 1.3 58.7 + - - +
220A CYS* 3.4 19.1 + - - -
263A SER 4.1 2.9 - - - -
264A SER* 3.4 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 5.5 0.9 - - - +
194A LEU* 3.0 29.3 - - + +
217A ILE* 3.7 7.1 - - + -
218A ASN* 1.3 69.5 - - - +
220A CYS* 1.3 57.3 + - - +
221A THR* 3.2 33.7 + - - -
223A LYS* 3.0 27.0 + - - +
225A ILE* 4.2 13.0 - - - +
259A VAL* 4.3 4.5 - - + -
260A ALA 3.8 10.0 + - - +
261A ALA* 3.5 9.7 - - - +
262A ASN* 3.0 28.6 + - - -
263A SER 3.3 17.2 + - - +
----------------------------------------------------------
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