Contacts of the strand formed by residues 206 - 216 (chain C) in PDB entry 6NQN
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 ASN 206 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU 3.3 3.4 - - - +
43C LYS* 3.6 35.5 + - - +
200C HIS* 3.2 5.6 - - - +
201C ASP* 2.8 53.2 + - + +
205C SER* 1.3 84.4 + - - +
207C VAL* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET 3.6 1.4 - - - +
41C ASP* 3.3 6.7 - - - +
42C LEU* 2.8 45.4 + - + +
54C TYR* 3.6 38.4 - - + +
197C ILE* 4.0 22.2 - - + -
199C SER 3.6 3.6 - - - -
200C HIS* 4.0 1.8 - - + -
204C TYR* 3.6 35.7 - - + +
206C ASN* 1.3 80.3 - - - +
208C ASN* 1.3 71.6 + - - +
209C LEU* 4.0 2.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
39C SER* 5.0 2.4 + - - -
40C MET 3.4 12.1 + - - +
41C ASP* 3.2 26.3 + - - +
197C ILE* 3.5 4.2 - - - +
198C LYS* 2.7 46.3 + - - +
199C SER* 2.8 34.7 + - - +
207C VAL* 1.3 71.5 - - - +
209C LEU* 1.3 56.1 + - - +
210C HIS* 3.0 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C SER* 3.1 4.3 - - - -
40C MET* 2.8 42.4 + - + +
42C LEU* 3.9 16.8 - - + -
58C THR* 3.7 34.5 - - + +
61C PHE* 3.8 22.0 - - + -
63C KZ4 3.7 28.5 - - - -
195C ILE* 3.8 16.8 - - + -
196C GLU 3.5 15.9 - - - +
197C ILE* 3.8 10.5 - - + -
207C VAL* 4.4 2.5 - - + -
208C ASN* 1.3 74.0 - - - +
210C HIS* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C GLN 3.4 8.3 - - - -
39C SER* 3.3 29.1 + - - -
63C KZ4 5.0 1.1 - - - -
194C HIS 4.1 0.6 - - - +
195C ILE* 3.5 5.7 - - - +
196C GLU* 2.9 42.1 + - + +
198C LYS* 3.0 41.3 + - + +
208C ASN* 3.0 27.7 + - - -
209C LEU* 1.3 75.2 - - - +
211C GLU* 1.3 62.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLY 3.7 0.3 - - - +
37C LYS* 3.4 5.2 - - - +
38C GLN* 2.7 67.5 + - + +
63C KZ4 3.4 46.9 + - + +
65C ASN 4.9 0.3 - - - +
66C ARG* 4.6 4.7 + - - -
68C PHE 4.6 4.0 - - - +
193C HIS* 3.0 28.6 + - - -
194C HIS 3.5 11.4 - - - +
195C ILE* 4.1 6.1 - - + -
210C HIS* 1.3 76.1 - - - +
212C HIS* 1.3 65.2 + - - +
213C ALA* 3.4 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU 4.1 4.6 + - - -
36C GLY 3.2 10.8 - - - -
37C LYS* 3.7 36.0 + - + -
193C HIS* 3.5 1.2 - - - -
194C HIS* 2.9 39.7 + - + +
211C GLU* 1.3 75.9 - - - +
213C ALA* 1.3 77.2 + - - +
214C GLU* 3.3 27.5 + - - +
219E LEU* 3.3 30.9 - - + +
220E PRO* 5.1 10.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 213 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLY* 2.9 15.6 + - - -
66C ARG* 5.3 0.9 - - - -
68C PHE 3.7 15.0 - - - +
69C ALA* 4.0 4.0 - - + -
70C LYS 3.1 19.8 + - - -
191C VAL* 3.9 9.4 - - + -
192C ASP 3.1 12.8 - - - +
193C HIS* 3.8 9.0 - - + +
211C GLU* 3.4 19.7 - - - +
212C HIS* 1.3 75.5 - - - +
214C GLU* 1.3 68.6 + - - +
219E LEU* 4.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 214 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLU 4.9 0.3 - - - +
70C LYS* 3.7 41.2 - - + +
191C VAL* 4.2 3.4 - - - -
192C ASP* 2.8 38.0 + - + +
212C HIS* 3.3 29.0 + - + +
213C ALA* 1.3 79.7 - - - +
215C ALA* 1.3 66.5 + - - +
216C HIS* 3.9 3.7 - - + -
219E LEU* 4.2 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 215 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ALA* 5.0 0.6 - - - +
70C LYS 2.9 16.1 + - - +
71C TYR* 3.7 44.4 - - + -
72C PRO* 3.7 20.8 - - + +
75C ILE* 4.4 3.1 - - + -
189C HIS* 4.4 0.2 - - + -
190C PHE 3.1 13.9 - - - +
191C VAL* 4.0 5.3 - - + +
214C GLU* 1.3 76.2 - - - +
216C HIS* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 216 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PRO* 5.0 2.9 - - - -
75C ILE* 3.6 10.3 - - - -
143C THR* 4.1 5.4 - - + +
189C HIS* 3.6 5.0 - - - +
190C PHE* 2.9 57.8 + + + +
192C ASP* 2.9 44.1 + - - -
214C GLU* 3.9 9.4 - - + -
215C ALA* 1.3 75.9 - - - +
217C SER* 1.3 60.0 + - - +
218C GLY* 3.0 32.5 + - - +
143E THR* 4.7 5.8 - - - -
192E ASP* 5.4 6.5 - - - -
----------------------------------------------------------
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