Contacts of the helix formed by residues 169 - 178 (chain B) in PDB entry 1C3B
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 SER 169 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 1.3 75.6 - - - +
170B PHE* 1.3 66.5 + - - +
171B GLU* 3.6 6.6 + - - +
172B GLN* 3.0 34.7 + - - +
173B ALA* 2.8 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 3.6 18.2 - - + -
73B LEU* 3.7 19.6 - - + +
159B GLY* 3.8 27.1 - - - -
160B ALA* 5.6 0.7 - - - -
163B VAL* 3.9 15.8 - - + +
168B LEU 3.9 1.0 + - - -
169B SER* 1.3 73.2 - - - +
171B GLU* 1.3 59.1 + - - +
173B ALA* 3.4 2.1 + - - +
174B MET* 2.9 58.1 + - + +
189B ILE* 4.1 15.0 - - + -
218B ALA* 3.4 30.5 - - + -
219B GLU* 3.7 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B SER* 3.2 6.6 + - - +
170B PHE* 1.3 80.3 - - + +
172B GLN* 1.3 57.4 + - - +
174B MET* 3.2 2.4 + - - +
175B GLN* 2.8 62.1 + - + +
188B TRP* 4.7 1.4 - - - -
189B ILE* 3.5 25.5 - - + +
190B ASN* 3.0 47.8 + - - +
218B ALA* 6.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLY 4.8 0.9 - - - +
168B LEU* 3.3 39.5 - - + +
169B SER* 3.0 31.9 + - - +
171B GLU* 1.3 78.1 - - + +
173B ALA* 1.3 56.6 + - - +
175B GLN* 4.4 6.3 - - - -
176B THR* 2.6 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.1 6.5 - - + -
163B VAL* 3.6 28.5 - - + -
166B SER* 4.7 1.6 - - - +
168B LEU* 3.8 25.6 - - + -
169B SER 2.8 17.8 + - - +
170B PHE 3.7 1.1 - - - +
172B GLN* 1.3 78.1 - - - +
174B MET* 1.3 55.1 + - - +
177B ARG* 2.7 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 3.8 39.9 - - + +
70B THR* 4.0 2.0 - - - +
73B LEU* 3.7 15.2 - - + +
170B PHE* 2.9 49.6 + - + +
171B GLU 3.5 5.2 - - - +
172B GLN 3.2 0.2 - - - -
173B ALA* 1.3 78.4 - - - +
175B GLN* 1.3 57.2 + - - +
178B VAL* 2.9 50.5 + - - +
179B PHE* 2.9 37.2 + - + -
189B ILE* 4.2 11.2 - - + -
223B VAL* 5.5 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLU* 2.8 59.4 + - + +
172B GLN* 4.1 5.6 - - - +
173B ALA 3.4 0.2 - - - -
174B MET* 1.3 72.5 - - - +
176B THR* 1.3 64.9 + - + +
179B PHE* 3.8 33.4 - - + +
180B GLN* 2.8 45.2 + - + +
187B THR 4.3 2.4 + - - +
188B TRP* 3.6 35.1 - - - -
189B ILE* 4.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 4.1 7.0 - - + +
172B GLN* 2.6 29.4 + - + +
173B ALA* 3.4 5.4 + - - -
175B GLN* 1.3 79.9 - - + +
177B ARG* 1.3 68.8 + - - +
180B GLN* 3.9 19.8 - - - +
181B PRO* 3.1 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 4.1 15.3 - - + +
76B ASP* 3.9 10.2 + - - +
77B ALA* 4.6 5.7 - - - +
80B ARG* 3.0 60.1 + - - +
82B GLU* 2.6 38.0 + - - -
163B VAL* 6.3 0.2 - - - +
166B SER* 3.8 20.4 - - - -
168B LEU* 3.9 21.4 - - - +
173B ALA* 2.7 33.0 + - - +
176B THR* 1.3 78.5 + - - +
178B VAL* 1.3 60.1 + - + +
181B PRO* 3.5 13.0 - - - +
248B LEU* 3.9 15.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 4.2 15.5 - - + +
72B VAL* 4.8 1.6 - - + -
73B LEU* 4.0 30.1 - - + +
76B ASP* 5.7 0.9 - - + -
174B MET* 2.9 32.8 + - - +
177B ARG* 1.3 85.7 - - + +
179B PHE* 1.3 69.1 + - + +
180B GLN 3.5 1.1 - - - -
181B PRO* 3.6 2.1 - - - +
182B LEU* 3.4 28.4 + - + +
233B TRP* 4.0 29.4 - - + -
248B LEU* 4.5 15.3 - - + -
----------------------------------------------------------
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