Contacts of the helix formed by residues 179 - 188 (chain A) in PDB entry 3S5O
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 PRO 179 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A MET 5.4 1.8 - - - +
146A SER 5.1 0.4 - - - -
147A SER* 3.3 20.2 - - - +
150A LEU* 3.7 21.5 - - + -
177A ASP* 3.2 11.6 - - + +
178A LEU* 1.4 89.3 - - + +
180A VAL* 1.3 65.0 + - - +
181A ASP* 3.3 19.3 - - - +
182A ALA* 3.1 9.0 + - + +
183A VAL* 3.0 18.9 + - - +
204A ARG* 4.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU 3.5 0.6 + - - -
179A PRO* 1.3 71.9 - - - +
181A ASP* 1.3 64.7 + - - +
183A VAL* 3.1 9.0 + - - +
184A VAL* 2.9 37.9 + - + +
204A ARG* 3.9 27.1 - - + +
207A LEU* 4.3 19.7 - - + -
208A ILE* 4.1 22.4 - - + -
211A LYS* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A SER* 2.7 34.8 + - - -
151A ILE* 5.0 2.4 - - - +
179A PRO* 3.3 7.6 - - - +
180A VAL* 1.3 80.1 - - - +
182A ALA* 1.3 67.2 + - - +
184A VAL* 3.5 6.7 + - - +
185A THR* 3.1 27.8 + - - -
211A LYS* 6.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A SER* 4.0 19.5 - - - +
150A LEU* 4.9 0.2 - - + -
151A ILE* 3.7 28.3 - - + +
178A LEU* 4.1 19.3 - - + -
179A PRO* 3.1 11.6 + - + +
181A ASP* 1.3 79.7 + - - +
183A VAL* 1.3 64.6 + - - +
185A THR* 3.3 1.7 + - - -
186A LEU* 2.9 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 4.4 8.5 - - + -
178A LEU* 3.8 22.9 - - + +
179A PRO 3.0 16.3 + - - +
180A VAL* 3.1 8.3 + - - +
182A ALA* 1.3 75.3 - - - +
184A VAL* 1.3 57.0 + - + +
186A LEU* 3.3 2.0 + - - +
187A SER* 2.9 28.6 + - - -
195A MET* 3.7 24.7 - - + -
208A ILE* 3.7 26.2 - - + -
212A THR* 4.5 2.2 - - + -
217A PHE* 3.6 33.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A VAL* 2.9 32.1 + - + +
181A ASP* 3.8 6.5 - - - +
183A VAL* 1.3 76.0 - - + +
185A THR* 1.3 63.9 + - - +
187A SER* 2.6 25.6 + - - +
188A GLN* 3.8 14.3 + - - +
208A ILE* 5.4 1.6 - - - +
211A LYS* 3.7 50.9 - - + +
212A THR* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ILE* 4.1 35.2 - - + +
181A ASP 3.1 17.9 + - - -
182A ALA 3.7 3.6 - - - -
184A VAL* 1.3 76.1 - - - +
186A LEU* 1.3 64.1 + - + +
188A GLN* 3.2 31.1 + - - +
189A HIS 4.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU 4.3 0.2 - - - +
151A ILE* 3.5 27.6 - - + +
154A TYR* 3.7 41.3 - - + -
155A THR* 3.4 26.0 - - - +
167A LEU* 4.1 19.5 - - + -
178A LEU* 4.8 2.5 - - + -
182A ALA* 2.9 28.6 + - + +
183A VAL 3.8 2.7 - - - +
185A THR* 1.3 71.8 - - + +
187A SER* 1.3 56.8 + - - +
188A GLN 3.0 5.6 - - - -
189A HIS* 3.0 29.2 + - + +
192A ILE* 3.5 25.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A VAL 2.9 15.6 + - - -
184A VAL* 2.6 19.6 + - - +
186A LEU* 1.3 75.3 - - - +
188A GLN* 1.3 55.2 + - - +
189A HIS 3.3 0.2 - - - -
192A ILE 4.7 0.4 - - - -
212A THR* 3.5 18.2 - - - +
215A GLN* 3.4 26.1 - - - +
216A ASP 4.1 0.5 - - - +
217A PHE* 3.5 37.6 - - - -
328A K 2.7 26.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL* 3.9 20.0 + - - +
185A THR* 3.4 21.4 - - - +
186A LEU 3.0 0.6 - - - -
187A SER* 1.3 77.3 - - - +
189A HIS* 1.3 64.3 + - - +
190A PRO* 3.4 6.4 - - - +
215A GLN* 3.5 33.8 - - + +
328A K 4.4 0.4 - - - -
----------------------------------------------------------
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