Contacts of the strand formed by residues 198 - 208 (chain A) in PDB entry 1M6X
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 VAL 198 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ASP 3.3 14.8 - - - +
195A ILE* 3.0 21.3 - - - +
196A LYS 3.2 3.0 - - - -
197A ASN* 1.3 77.3 - - - +
199A ASP* 1.3 68.7 + - - +
200A PRO* 3.0 6.9 - - - +
203A PHE* 4.3 8.5 - - + -
217A CYS* 3.4 36.6 - - + -
218A LEU 3.5 9.0 - - - +
219A VAL* 3.6 11.7 - - + -
230A ILE* 3.8 13.9 - - + -
270A GLN* 3.9 0.2 - - - -
273A GLN* 3.4 2.6 - - - -
274A LEU* 3.0 35.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASN 3.4 1.8 + - - -
198A VAL* 1.3 71.8 - - - +
200A PRO* 1.3 60.2 - - - +
201A LYS* 3.0 26.4 + - - +
202A SER* 2.6 53.4 + - - +
203A PHE* 4.4 0.5 + - - -
218A LEU* 3.0 16.8 + - + +
270A GLN* 3.5 41.1 - - - +
271A GLU 5.3 0.5 + - - -
272A TYR* 3.9 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A VAL* 3.0 10.6 - - + +
199A ASP* 1.3 76.6 - - - +
201A LYS* 1.3 57.8 - - - +
202A SER 3.0 2.3 + - - -
203A PHE* 2.9 38.5 + - + -
272A TYR* 2.9 52.7 - - + +
273A GLN* 3.8 7.0 - - - +
274A LEU* 4.5 3.4 - - + -
403A TRP* 3.9 28.0 - - + -
406A ILE* 4.1 13.0 - - + -
407A ILE* 3.8 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 2.9 18.2 + - - +
200A PRO* 1.3 76.6 - - + +
202A SER* 1.3 58.4 + - - +
203A PHE 3.5 2.8 + - - +
271A GLU* 3.4 33.3 + - + +
272A TYR* 5.0 2.7 - - + -
405A GLY 4.5 8.6 + - - -
406A ILE* 3.6 48.7 - - + +
408A SER* 5.7 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A ASP* 2.6 32.6 + - - +
201A LYS* 1.3 79.6 - - - +
203A PHE* 1.3 63.5 + - - +
204A LYS* 3.5 16.7 + - - +
216A GLN* 3.3 11.7 - - - +
217A CYS* 3.7 3.3 - - - -
218A LEU* 2.9 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A VAL* 4.3 1.8 - - + -
200A PRO* 2.9 39.7 + - + +
201A LYS 3.5 3.4 - - - +
202A SER* 1.3 77.8 - - - +
204A LYS* 1.3 63.6 + - - +
215A ILE* 3.4 29.2 - - + -
216A GLN 3.5 4.0 - - - -
217A CYS* 4.0 25.4 - - + +
232A PHE* 4.1 21.1 - + - -
245A LEU* 4.9 15.3 - - + -
249A LEU* 5.8 1.6 - - + -
274A LEU* 4.2 22.7 - - + -
407A ILE* 4.0 33.9 - - + -
408A SER* 3.6 21.3 - - - +
411A VAL* 3.9 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER* 3.6 15.5 - - - +
203A PHE* 1.3 80.9 - - - +
205A LEU* 1.3 68.8 + - - +
206A VAL* 3.8 10.4 + - + -
215A ILE* 3.5 4.5 - - - +
216A GLN* 2.9 45.1 + - - +
408A SER* 5.5 0.4 - - - -
410A GLU* 5.3 2.5 - - - +
411A VAL* 3.9 6.9 - - - +
145C LYS* 2.8 35.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LYS* 1.3 76.8 - - - +
206A VAL* 1.3 61.2 + - - +
207A GLN* 5.7 0.7 - - - +
213A VAL* 4.7 15.3 - - + -
214A ILE 3.7 4.3 - - - +
215A ILE* 3.9 18.8 - - + -
384A TRP* 5.9 1.8 - - - +
410A GLU* 3.4 51.3 + - + +
411A VAL* 4.0 15.8 - - + +
414A TYR* 3.5 43.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LYS* 4.3 10.1 - - + +
205A LEU* 1.3 78.8 - - - +
207A GLN* 1.3 75.0 + - - +
213A VAL* 3.1 5.5 - - - -
214A ILE* 3.0 40.7 + - + +
216A GLN* 3.9 42.0 - - + +
231A TYR* 6.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU 5.7 0.7 - - - +
206A VAL* 1.3 89.7 - - - +
208A ASN* 1.3 63.1 + - - +
209A LYS 4.3 0.4 - - - -
212A GLY 3.4 6.3 - - - +
213A VAL* 4.1 6.7 - - + -
214A ILE* 5.7 0.3 - - - +
352A ASP* 4.8 4.0 - - - +
384A TRP* 2.9 37.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLN* 1.3 77.1 - - - +
209A LYS* 1.3 53.5 + - - +
210A TYR* 2.6 41.6 + - - +
211A LEU* 3.4 11.0 + - - +
212A GLY* 2.9 30.5 + - - +
214A ILE* 4.4 27.0 - - + +
352A ASP* 3.3 44.8 + - - +
355A PHE* 3.8 18.0 - - - +
----------------------------------------------------------
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