Contacts of the strand formed by residues 198 - 208 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ASP 3.3 14.1 - - - +
195C ILE* 3.0 21.8 - - - +
196C LYS 3.2 2.8 - - - -
197C ASN* 1.3 77.9 - - - +
199C ASP* 1.3 69.2 + - - +
200C PRO* 3.0 5.8 - - - +
203C PHE* 4.3 7.6 - - + -
217C CYS* 3.4 36.8 - - + -
218C LEU 3.5 8.3 - - - +
219C VAL* 3.7 11.9 - - + -
230C ILE* 3.8 13.9 - - + -
273C GLN* 3.4 2.6 - - - -
274C LEU* 3.0 37.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 199 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C ASN 3.4 1.8 + - - -
198C VAL* 1.3 73.2 - - - +
200C PRO* 1.3 64.1 - - - +
201C LYS* 3.0 27.0 + - - +
202C SER* 2.6 47.5 + - - +
203C PHE* 4.5 0.3 - - - -
218C LEU* 3.0 17.1 + - + +
270C GLN* 3.8 32.5 - - - +
271C GLU 5.5 0.3 + - - -
272C TYR 4.0 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C VAL* 3.0 12.9 - - + +
199C ASP* 1.3 83.6 - - - +
201C LYS* 1.3 59.0 + - + +
202C SER 3.1 2.0 + - - -
203C PHE* 3.0 38.0 + - + -
272C TYR* 3.3 40.8 - - + +
273C GLN* 3.8 6.7 - - - +
274C LEU* 4.0 4.3 - - + +
403C TRP* 3.9 27.8 - - + -
406C ILE* 4.1 15.0 - - + -
407C ILE* 3.8 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ASP* 2.9 18.7 + - - +
200C PRO* 1.3 76.5 - - + +
202C SER* 1.3 57.3 + - - +
203C PHE 3.5 2.6 + - - +
271C GLU* 2.9 40.3 + - + +
272C TYR* 4.8 2.5 - - + -
405C GLY 4.5 8.6 + - - -
406C ILE* 3.6 48.7 - - + +
407C ILE* 5.8 0.4 - - - -
408C SER* 5.7 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ASP* 2.6 31.4 + - - +
201C LYS* 1.3 79.1 - - - +
203C PHE* 1.3 65.0 + - - +
204C LYS* 3.4 20.1 - - - +
216C GLN* 3.3 11.7 - - - +
217C CYS* 3.7 3.1 - - - -
218C LEU* 2.9 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C VAL* 4.3 2.2 - - + -
200C PRO* 3.0 39.0 - - + +
201C LYS 3.5 3.4 - - - +
202C SER* 1.3 78.6 - - - +
204C LYS* 1.3 61.8 + - - +
215C ILE* 3.4 28.5 - - + -
216C GLN 3.5 4.3 - - - -
217C CYS* 4.0 24.5 - - + -
232C PHE* 4.1 22.9 - + - -
245C LEU* 4.9 14.6 - - + -
249C LEU* 5.8 1.3 - - + -
274C LEU* 4.2 22.4 - - + -
407C ILE* 3.9 35.2 - - + -
408C SER* 3.6 21.3 - - - +
411C VAL* 3.9 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B SER 4.9 9.9 + - - -
202C SER* 3.4 17.9 - - - +
203C PHE* 1.3 79.9 - - - +
205C LEU* 1.3 69.3 + - - +
206C VAL* 4.4 8.1 - - + -
215C ILE* 3.3 9.0 - - - +
216C GLN* 2.9 48.8 + - - +
229C HIS* 6.3 0.8 - - - -
408C SER* 5.6 0.2 - - - -
410C GLU* 5.4 2.0 - - - +
411C VAL* 3.9 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LYS* 1.3 80.0 - - - +
206C VAL* 1.3 62.5 + - - +
207C GLN* 5.7 0.9 - - - +
213C VAL* 4.6 17.9 - - + -
214C ILE 3.6 2.7 - - - +
215C ILE* 4.2 11.4 - - + -
384C TRP* 5.9 1.8 - - - +
410C GLU* 3.6 51.6 + - + +
411C VAL* 4.2 14.5 - - + +
414C TYR* 3.6 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LYS* 4.4 9.2 - - + -
205C LEU* 1.3 78.8 - - - +
207C GLN* 1.3 77.0 + - - +
213C VAL* 3.1 5.6 - - - -
214C ILE* 2.9 44.3 + - + +
216C GLN* 3.7 43.7 - - + +
231C TYR* 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C LEU 5.7 0.4 - - - +
206C VAL* 1.3 90.5 - - - +
208C ASN* 1.3 61.4 + - - +
209C LYS 5.5 0.2 - - - +
212C GLY 3.4 7.6 + - - +
213C VAL* 4.3 6.1 - - + -
214C ILE* 5.3 1.2 - - - +
352C ASP* 4.5 6.1 - - - +
384C TRP* 3.6 30.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C GLN* 1.3 77.2 + - - +
209C LYS* 1.3 53.9 + - - +
210C TYR* 2.6 48.5 + - - +
211C LEU* 3.1 15.2 + - - +
212C GLY* 2.9 29.7 + - - +
214C ILE* 4.2 26.2 - - + +
352C ASP* 3.1 40.8 + - - +
355C PHE* 3.7 20.8 - - - +
----------------------------------------------------------
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