Contacts of the helix formed by residues 170 - 182 (chain A) in PDB entry 3RU0
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 ASP 170 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 6.0 0.4 - - - -
168A ALA 3.5 3.9 + - - +
169A PHE* 1.3 79.8 - - - +
171A LEU* 1.3 59.9 + - - +
172A PHE* 3.3 13.0 + - - +
173A GLU* 3.0 51.5 + - + +
174A ALA* 2.8 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.7 3.1 - - + -
148A VAL* 3.9 28.3 - - + +
151A PHE* 3.5 46.2 - - + -
152A GLN* 4.1 13.5 - - + +
165A LEU* 6.4 0.7 - - + -
169A PHE* 3.8 30.7 - - + -
170A ASP* 1.3 74.8 + - - +
172A PHE* 1.3 63.3 + - - +
174A ALA* 3.2 2.3 + - - +
175A PHE* 3.1 47.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 4.2 21.5 - - + -
136A LEU* 4.7 2.2 - - + -
141A LYS* 3.7 34.5 - - + -
144A LEU* 3.5 43.8 - - + +
145A ARG* 3.8 22.7 - - + -
148A VAL* 3.7 17.5 - - + +
170A ASP* 3.3 10.3 + - - +
171A LEU* 1.3 77.3 - - - +
173A GLU* 1.3 66.5 + - + +
175A PHE* 3.3 5.4 + - - +
176A ALA* 3.1 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 6.0 0.6 - - + -
127A TYR* 5.4 3.1 - - - -
131A SER* 4.1 8.9 + - - -
133A ILE* 4.6 18.5 - - + +
168A ALA 3.9 17.8 - - - +
170A ASP* 3.0 37.9 + - + +
172A PHE* 1.3 76.7 - - + +
174A ALA* 1.3 59.7 + - - +
176A ALA* 3.2 8.5 + - - +
177A LYS* 2.8 52.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 3.8 11.8 - - + +
126A PHE* 3.8 17.9 - - + -
169A PHE* 3.5 32.8 - - + -
170A ASP 2.8 20.4 + - - +
171A LEU 3.2 6.0 + - - +
173A GLU* 1.3 71.5 - - + +
175A PHE* 1.3 65.0 + - - +
177A LYS* 3.3 5.2 + - - +
178A VAL* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER* 3.6 32.5 - - - -
102A VAL* 3.7 22.4 - - + -
105A LEU* 3.6 19.1 - - + -
144A LEU* 3.6 21.3 - - + +
147A LEU* 3.6 43.1 - - + -
148A VAL* 3.9 14.4 - - + -
151A PHE* 3.8 12.3 - + + -
171A LEU* 3.1 45.4 + - + -
172A PHE 3.3 4.5 + - - +
174A ALA* 1.3 74.2 - - - +
176A ALA* 1.3 63.0 + - - +
178A VAL* 3.1 14.5 + - + +
179A ILE* 3.2 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 3.5 28.8 - - - +
133A ILE* 4.5 4.5 - - + -
136A LEU* 4.3 7.9 - - + -
144A LEU* 3.8 22.8 - - + +
172A PHE 3.1 13.8 + - - +
173A GLU* 3.6 10.3 - - - +
174A ALA 3.2 0.4 - - - -
175A PHE* 1.3 76.4 - - - +
177A LYS* 1.3 61.6 + - - +
179A ILE* 3.4 20.9 + - + +
180A CYS* 3.7 10.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 3.0 56.7 + - + +
127A TYR* 3.0 19.9 + - - +
129A LEU* 2.9 46.2 + - + +
130A GLU 3.7 11.0 - - - +
131A SER* 4.1 7.2 - - - +
173A GLU* 2.8 42.8 + - - +
174A ALA* 3.5 5.8 - - - +
176A ALA* 1.3 75.0 - - - +
178A VAL* 1.3 63.1 + - + +
180A CYS 3.4 0.9 + - - -
181A ASN* 2.8 31.2 + - - +
197A LEU* 5.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER* 3.9 26.2 - - - -
104A LEU* 4.3 17.0 - - + -
105A LEU* 3.8 30.1 - - + -
126A PHE* 5.4 0.4 - - + -
174A ALA 3.1 14.6 + - - +
175A PHE* 3.1 11.6 + - + +
177A LYS* 1.3 77.1 - - + +
179A ILE* 1.3 63.8 + - + +
181A ASN 4.6 0.2 - - - +
182A SER* 2.6 47.6 + - - +
195A VAL* 6.0 0.4 - - + -
197A LEU* 4.5 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 5.0 7.0 - - + -
140A LYS* 3.6 36.1 - - + -
144A LEU* 3.5 29.6 - - + -
147A LEU* 6.0 2.5 - - + -
175A PHE 3.2 11.4 + - - +
176A ALA* 3.6 11.2 - - - +
177A LYS 3.3 0.4 - - - -
178A VAL* 1.3 78.7 - - + +
180A CYS* 1.3 59.0 + - + +
182A SER* 4.8 2.4 + - - -
255A ASP 5.3 0.2 - - - +
256A GLN* 3.0 61.5 + - + +
257A TYR* 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU* 3.1 31.4 - - - -
131A SER 4.5 3.8 - - - -
132A ASN* 3.8 18.8 - - - +
176A ALA 3.8 9.6 - - - -
177A LYS 3.4 0.2 + - - -
179A ILE* 1.3 80.9 - - + +
181A ASN* 1.3 65.5 + - - +
182A SER 3.9 0.4 - - - -
256A GLN 3.9 9.9 - - - +
257A TYR* 3.5 27.4 - - + -
437A SFG 3.4 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 3.9 28.5 - - + +
130A GLU* 2.8 29.7 + - - +
177A LYS* 2.8 26.4 + - - +
178A VAL 4.0 0.7 - - - -
180A CYS* 1.3 81.0 - - - +
182A SER* 1.3 64.9 + - - +
183A PHE* 3.6 9.4 - - - -
197A LEU* 3.7 14.0 - - + +
202A SER* 3.4 28.4 + - - +
437A SFG 2.9 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.5 0.7 - - - +
178A VAL* 2.6 39.3 + - - +
179A ILE 4.8 3.0 + - - -
180A CYS 3.9 0.4 - - - -
181A ASN* 1.3 80.0 - - - +
183A PHE* 1.3 65.7 + - - +
184A THR* 4.3 0.4 + - - -
195A VAL* 3.9 20.8 - - - +
196A GLY 3.8 5.2 - - - -
197A LEU* 4.1 5.7 - - - +
256A GLN* 5.9 3.4 + - - -
257A TYR* 4.7 10.6 + - - -
----------------------------------------------------------
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