Contacts of the strand formed by residues 177 - 186 (chain C) in PDB entry 6PAI
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 177 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C GLU* 3.5 13.4 + - - +
176C ASN* 1.3 92.2 + - + +
178C ARG* 1.3 66.3 + - - +
179C ASP* 4.9 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157C PHE* 4.8 9.7 - - - +
158C ASN* 4.2 25.5 + - - +
177C HIS* 1.3 77.0 - - - +
179C ASP* 1.3 79.5 + - - +
180C ILE* 4.1 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C GLY 3.8 0.7 - - - +
157C PHE* 3.6 3.1 - - - -
158C ASN 3.3 37.8 + - - +
177C HIS* 4.9 6.7 - - - +
178C ARG* 1.3 81.3 + - - +
180C ILE* 1.3 63.8 + - - +
181C TYR* 3.9 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C PHE* 5.2 1.1 - - + -
156C GLY 3.4 2.9 - - - +
157C PHE* 3.6 35.9 - - + -
178C ARG* 4.1 21.3 + - + +
179C ASP* 1.3 77.4 - - - +
181C TYR* 1.3 66.7 + - - +
182C VAL* 3.9 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 181 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C PHE* 3.8 34.8 - + + -
132C GLU* 3.9 22.0 + - + -
133C GLU 4.7 4.9 + - - -
134C ILE* 3.4 34.4 - - + +
135C TYR 5.7 0.3 + - - -
138C LEU* 4.1 28.7 - - + -
155C PHE* 3.4 2.4 - - - -
156C GLY 2.7 41.2 + - - +
158C ASN 5.1 1.6 - - - -
179C ASP* 3.9 34.1 + - + +
180C ILE* 1.3 75.5 - - - +
182C VAL* 1.3 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C PHE* 4.2 2.6 - - - -
153C ILE* 4.0 25.8 - - + -
154C VAL 3.3 10.3 - - - +
155C PHE* 3.9 24.5 - - + -
180C ILE* 3.9 16.6 - - + +
181C TYR* 1.3 80.3 - - - +
183C SER* 1.3 67.8 + - - +
184C THR* 5.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 183 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LEU* 4.4 17.7 - - - -
129C PHE* 3.2 41.2 + - - -
152C VAL 3.9 0.3 - - - +
153C ILE* 3.3 4.1 - - - +
154C VAL* 2.9 36.4 + - - +
182C VAL* 1.3 73.2 + - - +
184C THR* 1.3 63.4 + - - +
185C VAL* 4.0 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 184 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C TRP* 3.8 20.1 - - + -
151C LYS* 3.9 21.8 - - + -
152C VAL 3.3 14.8 - - - +
153C ILE* 3.6 17.2 - - - +
182C VAL* 5.1 1.9 - - - +
183C SER* 1.3 73.4 - - - +
185C VAL* 1.3 61.4 + - - +
216C PHE* 3.8 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 4.5 7.0 - - + -
111C TRP* 3.5 25.3 - - + -
124C ARG* 5.0 1.8 - - - +
126C VAL* 3.9 27.6 - - + -
127C ARG 5.8 0.2 - - - +
128C LEU* 4.1 26.2 - - + -
151C LYS* 3.5 3.6 - - - -
152C VAL* 2.9 35.4 + - - +
154C VAL* 4.9 2.2 - - + -
183C SER* 4.6 9.6 - - - +
184C THR* 1.3 77.2 - - - +
186C ALA* 1.3 76.0 + - - +
216C PHE* 3.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C TRP* 3.8 7.1 - - - -
124C ARG* 3.1 13.7 + - - +
150C SER 3.8 5.4 - - - -
151C LYS* 4.5 1.6 - - - +
185C VAL* 1.3 85.6 - - - +
187C VAL* 1.3 59.8 + - - +
188C PRO 3.9 0.2 - - - -
213C ARG 3.4 24.0 - - - +
214C HIS 3.6 3.8 - - - +
215C GLY* 3.4 20.9 - - - +
216C PHE* 3.0 28.9 + - + +
----------------------------------------------------------
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