Contacts of the helix formed by residues 164 - 180 (chain f) in PDB entry 5T0J
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 ASN 164 (chain f).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163f SER* 1.3 79.0 + - - +
165f VAL* 1.3 61.6 + - - +
166f GLN* 3.4 23.6 - - + +
167f LEU* 3.3 35.1 - - - +
168f ASN* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 165 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163f SER 5.3 1.6 - - - +
164f ASN* 1.3 71.9 - - - +
166f GLN* 1.3 65.6 + - - +
168f ASN* 3.9 13.7 - - + +
169f SER* 2.9 26.4 + - - +
206f VAL* 5.3 11.0 - - + +
208f SER 5.7 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 166 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164f ASN* 3.1 19.1 - - + +
165f VAL* 1.3 77.0 - - - +
167f LEU* 1.3 69.7 + - + +
169f SER* 2.5 31.7 + - - -
170f ASN* 3.6 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142f HIS* 3.9 20.2 + - + +
163f SER* 4.2 12.1 - - - +
164f ASN* 3.3 27.7 + - - +
166f GLN* 1.3 87.8 - - + +
168f ASN* 1.3 57.9 + - - +
170f ASN* 3.4 11.3 + - - +
171f PHE* 2.8 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 168 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160f GLU* 4.9 9.1 + - - +
163f SER* 4.2 12.6 + - - +
164f ASN 2.9 19.8 + - - +
165f VAL* 3.7 16.0 - - - +
166f GLN 3.2 0.2 - - - -
167f LEU* 1.3 75.0 - - - +
169f SER* 1.3 59.3 + - - +
171f PHE* 4.1 16.8 - - - -
172f LEU* 2.9 35.4 + - - +
206f VAL* 5.5 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 169 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165f VAL* 2.9 15.3 + - - +
166f GLN* 2.5 28.1 + - - -
168f ASN* 1.3 77.8 - - - +
170f ASN* 1.3 63.3 + - - +
172f LEU* 4.1 4.1 - - - +
173f ALA* 3.2 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 170 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108f ARG* 6.3 1.3 - - - +
142f HIS* 3.9 17.6 - - + +
166f GLN* 3.6 18.2 + - - +
167f LEU* 3.4 16.3 + - - +
168f ASN 3.4 0.2 - - - -
169f SER* 1.3 87.5 + - - +
171f PHE* 1.3 63.8 + - - +
173f ALA* 4.5 4.7 - - - +
174f LEU* 3.1 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 171 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142f HIS* 3.5 24.3 + + - +
145f PHE* 3.8 47.6 - + + -
160f GLU* 3.7 38.4 - - + -
161f ILE* 5.7 7.6 - - + -
163f SER* 6.0 0.4 - - - +
167f LEU 2.8 19.5 + - - +
168f ASN* 3.8 14.4 - - - +
169f SER 3.3 0.2 - - - -
170f ASN* 1.3 79.0 - - - +
172f LEU* 1.3 61.3 + - + +
174f LEU* 4.1 0.5 - - - +
175f ALA* 3.1 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 172 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168f ASN* 2.9 27.1 + - - +
169f SER* 4.2 3.4 - - - +
171f PHE* 1.3 80.1 - - + +
173f ALA* 1.3 58.4 + - - +
175f ALA* 4.0 3.7 - - + -
176f ARG* 3.1 55.5 + - - +
186f PRO* 4.2 19.3 - - + -
206f VAL* 5.7 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169f SER 3.2 19.1 + - - +
170f ASN* 4.1 4.9 - - - +
171f PHE 3.3 0.2 - - - -
172f LEU* 1.3 75.2 - - - +
174f LEU* 1.3 71.4 + - + +
176f ARG* 3.2 23.6 + - - +
177f GLU* 3.3 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108f ARG* 4.7 12.8 - - - +
142f HIS* 3.6 37.2 - - + +
143f GLY* 5.0 2.2 - - - +
145f PHE* 6.2 0.7 - - - -
146f LEU* 4.7 12.0 - - + +
170f ASN* 3.1 34.7 + - + +
171f PHE 4.6 0.7 - - - +
173f ALA* 1.3 86.7 - - + +
175f ALA* 1.3 60.7 + - - +
177f GLU* 3.3 35.3 - - - +
178f LEU* 3.4 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145f PHE* 4.6 20.2 - - + -
171f PHE* 3.1 28.9 + - + +
172f LEU* 4.1 6.3 - - + +
174f LEU* 1.3 76.8 - - - +
176f ARG* 1.3 59.8 + - - +
178f LEU* 3.2 8.7 + - + +
179f ASP* 2.9 43.1 + - - +
186f PRO* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172f LEU* 3.1 55.9 + - - +
173f ALA* 3.2 13.0 + - - +
175f ALA* 1.3 76.4 - - - +
177f GLU* 1.3 59.5 + - - +
179f ASP* 3.1 16.1 + - - +
180f ILE* 3.2 25.9 + - + +
185f VAL* 6.2 0.4 - - + -
186f PRO* 3.9 28.3 - - + +
187f ASP* 4.0 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146f LEU* 6.5 0.9 - - + -
173f ALA 3.3 7.8 + - - +
174f LEU* 3.3 44.1 - - - +
176f ARG* 1.3 78.0 - - - +
178f LEU* 1.3 58.3 + - - +
180f ILE* 3.2 33.3 - - + +
181f MET* 4.8 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145f PHE* 4.2 24.9 - - + +
146f LEU* 3.7 55.6 - - + +
149f SER* 5.9 2.5 - - - +
174f LEU 3.4 14.0 + - - +
175f ALA* 3.2 10.5 + - + +
176f ARG 3.1 0.6 - - - -
177f GLU* 1.3 78.8 - - + +
179f ASP* 1.3 69.3 + - - +
180f ILE 3.3 0.9 + - - -
181f MET* 3.8 12.9 + - + +
182f GLU* 4.1 11.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 179 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154f GLU* 4.5 12.2 - - - +
175f ALA* 2.9 25.6 + - - +
176f ARG 3.1 2.3 + - - +
178f LEU* 1.3 82.5 - - - +
180f ILE* 1.3 59.1 + - - +
181f MET 3.3 2.5 - - - -
182f GLU* 2.8 50.4 - - - +
184f LYS 3.2 18.5 - - - +
185f VAL* 3.3 6.6 - - - +
186f PRO* 3.4 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain f).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176f ARG* 3.2 22.0 - - + +
177f GLU* 3.2 29.8 - - + +
179f ASP* 1.3 78.1 - - - +
181f MET* 1.3 76.1 + - + +
182f GLU 3.7 3.8 + - - +
185f VAL* 4.4 12.1 - - + -
507f ILE* 3.9 19.2 - - - +
508f GLY* 5.0 7.6 + - - +
----------------------------------------------------------
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