Contacts of the helix formed by residues 167 - 176 (chain A) in PDB entry 1P13
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 THR 167 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LYS 4.2 5.6 - - - +
166A ILE* 1.3 80.6 - - - +
168A ARG* 1.3 65.5 + - - +
169A ARG* 3.5 7.5 + - - +
170A GLU* 3.0 31.3 + - + +
171A SER* 2.9 22.3 + - - -
188A ARG* 4.4 1.3 - - - +
191A GLU* 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR* 1.3 73.8 - - - +
169A ARG* 1.3 65.4 + - - +
171A SER* 2.8 22.2 + - - -
172A GLU* 3.0 27.7 + - + +
188A ARG* 3.8 17.7 - - - +
212A VAL 5.6 0.2 + - - -
214A HIS* 3.5 27.5 - - - +
1D CYS* 3.8 26.8 - - - +
2D ASP 2.8 41.2 + - - +
3D PTR 2.8 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR* 3.2 8.2 + - - +
168A ARG* 1.3 82.8 - - - +
170A GLU* 1.3 61.9 + - + +
172A GLU* 3.2 9.5 + - + +
173A ARG* 3.1 61.9 + - + +
178B PRO 3.0 14.5 + - - -
179B GLU* 2.9 32.5 + - - +
180B ASN 3.7 7.4 + - - -
181B PRO* 3.8 23.2 - - - +
182B ARG* 5.0 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 3.7 22.3 - - + +
167A THR* 3.0 23.5 + - + +
169A ARG* 1.3 73.7 - - + +
171A SER* 1.3 67.8 + - - +
173A ARG* 2.8 38.5 + - - +
174A LEU* 3.0 25.6 + - - +
178B PRO* 4.3 13.8 - - + +
210B LEU* 5.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 3.8 12.0 - - - +
167A THR 2.9 15.6 + - - -
168A ARG 2.8 14.6 + - - -
170A GLU* 1.3 78.3 - - - +
172A GLU* 1.3 60.7 + - - +
174A LEU* 3.2 3.0 + - - +
175A LEU* 2.9 29.3 + - - +
186A LEU* 4.1 21.1 - - - -
188A ARG* 3.7 19.9 + - - -
200A SER* 3.8 3.5 + - - -
214A HIS* 3.6 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG* 3.0 36.5 + - - +
169A ARG* 3.2 10.4 + - + +
171A SER* 1.3 77.8 + - - +
173A ARG* 1.3 63.3 + - + +
176A LEU* 2.9 46.1 + - + +
212A VAL* 4.2 22.2 - - + +
214A HIS* 2.7 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ARG* 3.1 48.6 + - + +
170A GLU* 2.8 45.8 + - - +
171A SER 3.3 0.2 - - - -
172A GLU* 1.3 79.0 - - + +
174A LEU* 1.3 63.7 + - - +
176A LEU* 3.9 2.8 + - - -
177A ASN* 4.2 5.0 + - - +
177B ASN 5.3 0.4 + - - -
178B PRO* 3.5 22.4 + - - +
180B ASN 3.3 16.0 + - - -
181B PRO* 5.2 1.2 - - - +
182B ARG* 5.3 0.8 - - - +
204B PHE* 3.6 40.0 - - + +
210B LEU* 3.6 42.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A PHE* 3.6 31.4 - - + -
166A ILE* 3.9 22.4 - - + -
170A GLU* 3.0 11.4 + - - +
171A SER* 3.5 7.6 - - - +
172A GLU 3.2 0.2 - - - -
173A ARG* 1.3 80.6 - - + +
175A LEU* 1.3 59.5 + - + +
176A LEU 3.5 0.3 + - - -
177A ASN* 3.6 8.0 + - - +
180A ASN* 3.1 17.5 + - - -
186A LEU* 4.3 2.7 - - + -
258A CYS* 3.8 19.8 - - - -
259A PRO 4.0 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A SER 2.9 21.5 + - - +
174A LEU* 1.3 71.9 - - - +
176A LEU* 1.3 59.7 - - - +
177A ASN 3.2 6.4 - - - +
180A ASN* 3.2 16.2 + - - +
184A THR* 3.6 31.0 - - + +
185A PHE* 3.9 4.3 - - - -
186A LEU* 4.1 11.0 - - + -
200A SER* 3.6 39.7 - - - +
201A VAL* 4.2 0.9 - - - +
202A SER* 3.6 20.6 - - - -
210A LEU* 6.0 0.7 - - - +
212A VAL* 3.8 22.9 - - + -
258A CYS* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLU* 2.9 40.3 + - + +
173A ARG 4.7 0.2 - - - -
174A LEU 3.3 0.4 - - - -
175A LEU* 1.3 76.5 - - - +
177A ASN* 1.3 65.6 + - - +
178A PRO* 3.1 1.6 - - - +
202A SER* 5.9 0.7 - - - -
210A LEU* 3.9 19.5 - - + +
211A ASN* 3.8 25.1 - - - +
212A VAL* 3.5 22.2 - - + +
204B PHE* 3.7 21.3 - - + -
206B ASN* 3.0 43.5 - - - +
----------------------------------------------------------
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