Contacts of the strand formed by residues 168 - 179 (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 HIS 168 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C GLU* 3.7 0.2 - - - +
140C GLU* 2.6 37.5 + - + -
160C ALA* 4.0 11.4 - - + -
161C LEU 3.2 15.3 - - - +
162C SER* 3.8 10.0 - - - -
163C LEU* 4.2 9.7 - - - +
167C GLY* 1.3 85.0 - - - -
169C TYR* 1.3 57.6 + - - +
170C ARG* 4.1 0.7 - - + +
147E TYR* 4.2 24.8 - - + +
148E VAL 4.8 6.1 + - - -
149E ARG* 2.6 31.6 + - - +
188E TYR* 3.3 38.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 169 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TYR* 3.2 36.5 - + + +
96C GLU* 3.5 20.6 - - + -
97C ASP* 2.6 44.2 + - + -
125C PHE* 3.7 12.0 - - - -
130C PRO* 3.8 24.2 - - + +
131C VAL* 3.6 20.8 - - + +
136C THR* 4.9 1.1 - - + -
160C ALA* 3.3 2.2 - - - -
161C LEU* 2.8 54.3 + - + +
163C LEU* 3.7 22.9 - - + -
168C HIS* 1.3 72.9 - - - +
170C ARG* 1.3 61.1 + - - +
171C CYS* 4.0 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 170 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C TYR* 3.5 6.1 - - - +
96C GLU* 2.8 53.0 + - + +
158C ASN* 2.9 26.4 + - - +
159C THR 2.8 43.4 + - - +
160C ALA* 4.1 11.0 - - + -
168C HIS 5.4 0.2 - - - -
169C TYR* 1.3 76.5 - - - +
171C CYS* 1.3 68.8 + - - +
172C ASP* 2.9 31.2 + - - -
145E LYS* 6.3 1.3 - - - -
147E TYR* 3.7 30.7 - - + +
149E ARG* 4.6 2.2 - - - +
156E ASP* 2.5 34.6 + - - +
172E ASP* 5.2 0.2 + - - -
174E LYS* 4.3 11.9 - - - +
188E TYR* 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 171 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C MET* 3.7 13.0 - - - -
94C ASN 3.4 13.2 - - - -
95C TYR* 3.6 38.8 - - + -
139C TRP* 4.0 10.3 - - + -
157C VAL 3.9 0.2 - - - +
158C ASN* 3.6 0.2 - - - -
159C THR* 2.9 35.4 + - - +
169C TYR 4.0 0.6 + - - +
170C ARG* 1.3 76.7 + - - +
172C ASP* 1.3 66.2 + - - +
173C PHE* 3.3 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 172 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C SER 3.4 4.9 - - - +
93C MET* 3.5 0.2 - - - -
94C ASN* 2.9 51.8 + - + +
158C ASN* 2.3 42.6 + - - +
170C ARG* 2.9 17.5 + - - +
171C CYS* 1.3 70.8 - - - +
173C PHE* 1.3 62.1 + - - +
174C LYS* 4.6 16.3 + - + +
172E ASP* 4.0 11.3 - - - +
174E LYS* 5.1 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C THR* 3.3 31.4 - - + -
63C KZ4 3.6 30.1 - + + -
91C ARG* 4.0 20.4 - - - -
92C SER 3.5 4.5 - - - +
93C MET* 3.6 17.3 - - + -
139C TRP* 3.8 24.0 - + - -
155C GLY 4.3 1.3 - - - +
156C ASP* 3.4 5.5 - - - +
157C VAL* 2.8 41.4 + - + +
158C ASN* 5.2 0.5 + - - -
159C THR* 3.9 12.6 - - + -
171C CYS* 3.3 28.7 - - - -
172C ASP* 1.3 77.1 - - - +
174C LYS* 1.3 68.0 + - - +
175C THR* 4.2 3.8 - - - +
158E ASN* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 174 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASN* 3.1 18.4 + - - +
91C ARG* 3.2 1.9 - - - +
92C SER* 3.0 40.2 + - - +
147C TYR* 5.7 0.2 - - - +
155C GLY 3.5 2.7 - - - -
156C ASP* 3.3 22.9 - - - +
172C ASP* 4.6 19.1 + - + +
173C PHE* 1.3 79.0 + - - +
175C THR* 1.3 61.6 + - - +
158E ASN* 4.9 4.6 + - - -
170E ARG* 3.8 22.8 - - - +
172E ASP* 5.9 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 175 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C TRP* 4.2 7.0 - - + -
90C GLU 3.2 11.2 - - - +
91C ARG* 2.9 35.9 + - - +
144C GLU* 4.7 2.0 + - - -
154C LYS* 3.3 7.1 - - - +
155C GLY 2.7 40.0 + - - +
156C ASP* 4.4 1.1 + - - +
173C PHE* 4.7 4.0 - - - +
174C LYS* 1.3 73.3 + - - +
176C THR* 1.3 67.1 + - - +
177C TYR* 3.4 44.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASN* 2.6 29.3 + - - +
89C TRP* 3.1 5.5 - - - +
90C GLU* 2.8 40.2 + - - +
152C VAL* 3.8 17.9 - - + -
153C LEU 3.7 2.2 - - - -
154C LYS* 3.2 35.5 - - + +
175C THR* 1.3 72.7 - - - +
177C TYR* 1.3 62.4 + - - +
178C LYS* 3.9 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ARG* 2.9 35.0 + - + -
78C TYR* 3.4 14.1 + - + -
79C PHE* 3.4 35.9 - + + -
87C TYR* 4.0 7.4 - + + -
88C SER 3.6 4.0 - - - +
89C TRP* 3.8 22.2 - + + -
91C ARG* 5.0 0.2 - - - -
144C GLU* 2.6 29.2 + - - -
146C LEU* 3.9 13.9 - - + -
152C VAL* 3.3 8.3 - - - +
153C LEU* 2.8 49.3 + - + +
154C LYS 4.3 0.9 - - - -
155C GLY 4.0 9.2 - - - -
175C THR* 3.4 23.5 + - + +
176C THR* 1.3 72.4 - - - +
178C LYS* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 3.8 20.4 + - - +
125A PHE 4.7 4.0 + - - -
127A ALA* 5.9 3.4 - - - +
78C TYR* 3.6 1.8 - - - -
87C TYR* 3.2 3.8 - - - +
88C SER* 2.8 48.6 + - - +
89C TRP* 6.3 0.2 - - - -
90C GLU* 2.8 30.2 + - - +
152C VAL* 4.1 19.7 - - + -
176C THR* 3.9 22.0 - - + +
177C TYR* 1.3 78.1 - - - +
179C ALA* 1.3 68.4 + - - +
180C LYS* 3.6 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C TYR* 2.7 28.7 + - + +
82C SER* 3.3 23.6 - - - +
87C TYR* 3.7 9.9 - - - -
152C VAL* 5.4 0.4 - - - +
178C LYS* 1.3 77.1 - - - +
180C LYS* 1.3 62.3 + - - +
181C LYS 3.3 19.8 + - - +
183C VAL* 4.2 6.7 - - + -
----------------------------------------------------------
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