Contacts of the helix formed by residues 207 - 220 (chain A) in PDB entry 1H4L
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 ASP 207 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 3.8 14.0 - - - +
205A GLY 3.4 1.4 - - - -
206A ASN* 1.3 85.3 + - - +
208A VAL* 1.3 52.8 + - - +
209A ASP* 2.8 17.4 + - - +
210A ASP* 2.8 25.4 + - - +
211A GLN* 2.7 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 4.2 2.4 - - + +
168A ARG* 3.9 24.0 - - - +
173A LEU* 3.9 32.8 - - + +
207A ASP* 1.3 73.5 - - - +
209A ASP* 1.3 66.3 + - - +
211A GLN* 2.9 17.3 + - - +
212A LEU* 3.0 25.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASP* 2.8 14.2 + - - +
208A VAL* 1.3 75.9 - - - +
210A ASP* 1.3 65.1 + - - +
212A LEU* 3.3 4.7 + - - +
213A LYS* 3.1 44.1 + - - +
239A TYR* 2.7 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A GLY* 3.1 7.3 - - - -
206A ASN* 2.8 45.2 + - - +
207A ASP* 2.8 27.2 + - - +
209A ASP* 1.3 74.9 - - - +
211A GLN* 1.3 67.2 + - - +
213A LYS* 3.1 17.5 + - - +
214A ARG* 3.1 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 3.6 29.5 + - + +
166A TRP* 3.4 20.9 + - - +
168A ARG 4.8 2.5 + - - +
173A LEU* 3.5 23.1 - - + -
203A PHE* 2.7 47.6 + - - +
205A GLY* 3.1 19.1 + - - +
207A ASP 2.7 15.8 + - - +
208A VAL 3.3 8.5 - - - +
210A ASP* 1.3 74.6 - - - +
212A LEU* 1.3 64.5 + - - +
214A ARG* 3.4 3.8 + - - +
215A ILE* 3.2 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PRO* 4.2 6.7 - - + +
173A LEU* 3.4 35.0 - - + +
174A PHE* 3.9 26.2 - - + -
208A VAL* 3.0 28.3 + - + +
209A ASP* 3.5 5.8 - - - +
211A GLN* 1.3 77.7 - - - +
213A LYS* 1.3 64.1 + - - +
215A ILE* 3.1 7.3 + - - +
216A PHE* 2.9 43.1 + - + -
235A ASP 5.7 1.1 - - - +
237A LYS* 5.8 2.7 - - + -
239A TYR* 3.3 38.6 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
209A ASP* 3.1 40.1 + - - +
210A ASP* 3.1 20.4 + - - +
212A LEU* 1.3 78.0 - - - +
214A ARG* 1.3 54.3 + - + +
216A PHE* 4.2 0.4 - - - +
217A ARG* 2.7 41.1 + - + +
239A TYR* 3.9 12.6 - - + -
242A TYR* 3.7 29.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU 5.5 0.2 - - - +
203A PHE* 3.7 20.1 - - + -
204A PRO* 3.4 41.4 + - - +
205A GLY* 3.6 12.6 - - - +
206A ASN* 3.8 14.6 + - - +
210A ASP* 3.1 44.8 + - - +
211A GLN 3.4 4.7 + - - +
213A LYS* 1.3 76.7 - - + +
215A ILE* 1.3 63.1 + - - +
217A ARG* 3.6 9.1 + - - +
218A LEU* 3.3 21.3 + - - +
93B SER* 4.5 7.7 + - - -
94B CYS* 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG 4.4 3.6 - - - +
170A PRO* 4.1 9.6 - - + -
173A LEU* 3.9 24.9 - - + -
186A TRP* 3.9 37.0 - - + +
203A PHE* 3.8 26.3 - - + -
211A GLN* 3.2 25.1 - - - +
212A LEU* 3.1 7.7 + - - +
214A ARG* 1.3 76.5 - - - +
216A PHE* 1.3 75.8 + - + +
218A LEU* 3.2 3.8 + - - +
219A LEU* 2.8 32.5 + - + +
269A CYS* 4.2 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A PRO* 4.1 8.7 - - + -
174A PHE* 3.6 36.1 - + - -
212A LEU* 2.9 29.7 + - + +
213A LYS 4.2 0.7 - - - +
215A ILE* 1.3 84.3 - - + +
217A ARG* 1.3 63.2 + - - +
220A GLY* 2.7 34.3 + - - +
221A THR* 3.5 35.2 + - + +
222A PRO* 3.6 28.9 - - + -
239A TYR* 4.1 25.8 - + + -
242A TYR* 4.0 9.4 - - + +
243A PRO 3.9 1.9 - - - +
269A CYS* 3.9 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 2.7 25.9 + - - +
214A ARG* 3.8 8.7 - - - +
215A ILE 3.2 0.2 - - - -
216A PHE* 1.3 73.5 - - - +
218A LEU* 1.3 57.9 + - + +
242A TYR* 4.1 29.5 - - + +
243A PRO* 3.8 9.9 - - - +
245A THR* 3.4 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 4.5 13.5 - - + -
203A PHE* 3.5 31.9 - - + -
214A ARG 3.3 12.3 + - - +
215A ILE 3.2 2.5 + - - +
216A PHE 3.0 0.2 - - - -
217A ARG* 1.3 78.8 - - - +
219A LEU* 1.3 78.7 + - + +
220A GLY 3.4 1.3 - - - -
245A THR* 2.7 52.3 + - - +
246A THR* 3.8 1.0 + - - -
248A LEU* 5.2 6.5 - - + -
250A ASN* 6.3 1.6 - - + -
251A VAL* 4.1 31.9 - - + -
267A LEU* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A TRP* 3.7 22.2 - - + -
203A PHE* 4.5 5.4 - - + -
215A ILE* 2.8 23.2 + - + +
218A LEU* 1.3 99.7 - - + +
220A GLY* 1.3 65.0 + - - +
244A ALA* 3.9 12.9 - - - +
246A THR* 5.5 3.9 - - - +
248A LEU* 4.6 8.3 - - + -
264A GLN* 4.3 23.6 + - - +
267A LEU* 3.0 40.6 - - + +
269A CYS* 4.4 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 220 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PHE* 2.7 25.2 + - - -
218A LEU 3.4 2.4 + - - -
219A LEU* 1.3 82.4 - - - +
221A THR* 1.3 66.6 + - - -
222A PRO* 3.5 6.8 - - - +
226A GLN* 5.6 0.3 - - - +
242A TYR 3.6 2.9 - - - -
243A PRO 3.5 16.8 + - - -
244A ALA* 3.9 8.3 - - - -
269A CYS* 4.8 2.6 - - - -
----------------------------------------------------------
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