Contacts of the helix formed by residues 202 - 214 (chain A) in PDB entry 1P3C
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 202 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 4.1 2.7 - - - -
119A VAL 3.6 14.4 - - - +
120A THR* 4.9 2.9 - - - +
157A THR 4.0 20.4 - - - +
158A ASN* 4.7 14.3 + - - +
200A LYS* 2.9 30.6 + - + +
201A ALA* 1.3 76.0 - - - +
203A ALA* 1.3 67.0 + - - +
204A ALA* 3.7 13.2 + - - +
205A PHE* 3.1 9.3 + - - +
206A VAL* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 3.9 29.4 + - - +
119A VAL 4.7 1.2 + - - -
202A THR* 1.3 74.9 - - - +
204A ALA* 1.3 57.0 + - - +
206A VAL* 3.3 2.3 + - - +
207A GLU* 2.9 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 6.2 4.5 - - + -
98A PHE* 4.9 4.6 - - + -
202A THR* 3.2 9.0 + - - +
203A ALA* 1.3 76.5 - - - +
205A PHE* 1.3 65.3 + - - +
207A GLU* 3.5 12.6 + - - +
208A PHE* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 4.0 19.1 - - + -
98A PHE* 3.6 46.9 - + + -
116A ILE* 4.3 10.3 - - + -
182A ILE* 4.9 2.7 - - + -
184A GLY* 4.9 2.9 - - - -
185A VAL* 3.6 32.8 - - + -
199A PRO* 4.7 6.5 - - + -
200A LYS 3.8 14.6 - - - +
201A ALA* 3.7 24.7 - - + -
202A THR* 3.1 21.7 + - - +
204A ALA* 1.3 79.3 - - - +
206A VAL* 1.3 65.9 + - + +
208A PHE* 3.2 5.2 + - - +
209A ILE* 3.0 42.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 4.0 25.1 - - + -
118A GLN* 3.9 37.9 - - + +
201A ALA 4.0 6.3 - - - +
202A THR 3.0 15.7 + - - +
203A ALA 3.8 3.8 - - - +
205A PHE* 1.3 79.0 - - + +
207A GLU* 1.3 60.4 + - - +
209A ILE* 3.3 6.3 + - + +
210A ASN* 2.9 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A ALA* 2.9 27.6 + - - +
204A ALA* 3.7 12.7 - - - +
205A PHE 3.3 0.2 - - - -
206A VAL* 1.3 76.2 - - - +
208A PHE* 1.3 62.2 + - - +
210A ASN* 3.4 8.2 + - - +
211A TYR* 3.2 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 3.5 36.6 - - + -
84A VAL 3.9 3.6 - - - -
85A PRO* 3.6 39.5 - - + -
98A PHE* 3.9 28.0 - + + -
99A ALA* 4.5 0.4 - - - -
100A VAL* 4.3 17.9 - - + -
204A ALA 3.2 11.2 + - - +
205A PHE 3.6 7.2 - - - +
207A GLU* 1.3 81.0 - - - +
209A ILE* 1.3 69.6 + - + +
211A TYR* 3.2 26.4 + + - +
212A ALA* 2.9 20.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.9 9.9 - - + -
43A LEU* 3.8 28.7 - - + -
98A PHE* 4.8 3.4 - - + -
100A VAL* 3.9 14.1 - - + -
116A ILE* 3.4 27.4 - - + -
205A PHE* 3.0 42.7 + - + +
206A VAL* 3.6 8.3 - - + +
208A PHE* 1.3 85.5 - - + +
210A ASN* 1.3 61.2 + - - +
212A ALA* 3.2 4.5 + - - +
213A LYS* 2.9 46.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A VAL* 2.9 39.2 + - - +
207A GLU* 3.8 6.9 - - - +
208A PHE 3.2 0.2 - - - -
209A ILE* 1.3 78.4 - - - +
211A TYR* 1.3 64.2 + - - +
213A LYS* 3.5 22.6 + - - +
214A ALA* 3.4 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 4.7 14.6 - + + -
207A GLU 3.2 12.9 + - - +
208A PHE* 3.4 33.4 - + - +
210A ASN* 1.3 76.7 - - - +
212A ALA* 1.3 68.0 + - - +
214A ALA* 3.1 10.3 + - - +
215A GLN* 3.0 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 6.1 0.2 - - + -
41A LYS* 2.8 25.5 + - - +
83A TYR* 4.2 16.6 - - + -
100A VAL* 3.7 36.1 - - + -
208A PHE* 2.9 18.1 + - + +
209A ILE 3.2 4.5 + - - +
211A TYR* 1.3 83.0 - - + +
213A LYS* 1.3 59.0 + - - +
215A GLN* 3.3 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.4 36.2 + - + +
38A ALA* 4.7 13.8 - - + +
41A LYS* 3.0 21.1 + - + +
113A TYR* 6.1 1.2 - - - -
114A ARG 5.5 1.6 + - - -
115A SER* 5.8 1.4 - - - +
116A ILE* 4.4 15.1 - - - +
209A ILE* 2.9 39.4 + - + +
210A ASN* 3.7 20.3 + - - +
211A TYR 3.2 0.2 - - - -
212A ALA* 1.3 77.1 - - - +
214A ALA* 1.3 58.6 + - - +
215A GLN* 3.3 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ASN 3.4 8.2 + - - +
211A TYR* 3.1 12.5 + - - +
213A LYS* 1.3 78.4 - - - +
215A GLN* 1.3 70.1 + - - +
----------------------------------------------------------
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