Contacts of the helix formed by residues 163 - 173 (chain D) in PDB entry 1H69
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 163 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B TRP* 5.4 0.9 + - - -
256B GLY* 3.0 14.7 + - - +
258B HIS* 2.9 34.3 + - + +
155D TYR 3.7 6.6 - - - +
156D SER 3.7 7.0 + - - -
157D LEU* 3.5 21.6 - - + +
162D GLY* 1.3 68.5 - - - -
164D MET* 1.3 66.2 + - - +
165D ASN* 2.9 41.9 + - - +
166D VAL* 3.1 23.7 + - + +
167D ILE* 3.7 6.3 + - - +
255D VAL* 5.5 0.3 - - - +
263D ILE* 5.3 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D LEU* 4.2 17.0 - - + -
146D ILE* 5.8 2.5 - - + -
148D THR* 4.5 4.3 - - + -
155D TYR* 3.1 36.8 + - + +
162D GLY 3.2 2.2 + - - -
163D ASP* 1.3 74.0 + - - +
165D ASN* 1.3 62.7 + - - +
166D VAL 3.1 0.2 - - - -
167D ILE* 3.2 26.3 + - - -
168D LEU* 3.1 44.4 + - + +
188D LEU* 4.0 15.3 - - + -
190D TYR* 3.5 42.8 - - + +
269D ILE* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D LEU* 5.6 0.8 - - - +
163D ASP* 2.9 34.3 + - - +
164D MET* 1.3 78.5 - - - +
166D VAL* 1.3 61.3 + - - +
168D LEU* 3.7 1.7 + - - -
169D TRP* 3.3 15.4 + - - +
255D VAL* 3.7 18.0 - - + +
263D ILE* 5.8 1.1 - - + -
266D ASP* 3.1 41.7 + - - +
267D ASN 4.0 0.9 - - - -
268D GLN* 2.7 45.5 + - + +
269D ILE* 3.2 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B VAL* 3.9 16.2 - - + +
169B TRP* 3.6 30.5 - - + +
170B PRO* 4.7 0.9 - - + +
255B VAL* 3.8 37.7 - - + +
256B GLY* 4.6 1.1 - - - -
258B HIS* 4.1 14.1 - - + -
163D ASP* 3.1 17.6 + - + +
165D ASN* 1.3 73.9 - - + +
167D ILE* 1.3 65.9 + - - +
169D TRP* 3.3 4.2 + - - +
170D PRO* 3.2 19.9 - - - +
255D VAL* 4.1 17.3 - - + -
263D ILE* 5.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B TRP* 4.8 11.0 - - + +
170B PRO* 4.7 13.9 - - + +
103D LEU* 4.6 9.2 - - + -
106D PHE* 3.3 61.7 - - + +
107D GLY* 5.3 0.4 - - - -
155D TYR* 3.7 25.6 - - + -
161D HIS 5.2 4.9 - - - +
162D GLY 4.8 2.7 - - - +
163D ASP 4.1 7.0 - - - +
164D MET* 3.2 27.3 + - - +
166D VAL* 1.3 77.6 - - - +
168D LEU* 1.3 62.5 + - + +
170D PRO* 3.4 10.5 - - - +
171D ILE* 4.3 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D LEU* 6.4 0.4 - - + -
144D LEU* 4.1 13.9 - - + -
146D ILE* 3.6 31.4 - - + -
164D MET* 3.1 36.6 + - + +
165D ASN 3.7 3.3 + - - +
166D VAL 3.3 0.2 - - - -
167D ILE* 1.3 78.9 - - + +
169D TRP* 1.3 65.3 - - - +
171D ILE* 3.1 11.5 + - + +
172D GLN* 2.9 37.5 + - - +
186D PRO* 4.0 8.5 - - + -
188D LEU* 4.6 4.3 - - + -
268D GLN* 3.5 26.0 - - + +
269D ILE* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 6.2 0.8 - - - -
160B ILE 5.7 0.2 - - - -
161B HIS 4.0 20.5 + - - -
162B GLY* 5.1 0.8 - - - -
163B ASP 5.3 0.8 + - - -
166B VAL* 3.3 27.6 - - + +
167B ILE* 4.8 10.3 - - + +
165D ASN 3.3 10.8 + - - +
166D VAL 3.3 8.9 + - - +
168D LEU* 1.3 78.0 - - - +
170D PRO* 1.4 70.6 - - + +
173D SER* 2.8 68.6 + - - -
174D GLY* 3.4 1.4 + - - +
222D PHE* 4.0 11.4 - + + -
254D SER* 3.6 20.2 - - - -
255D VAL* 3.7 11.2 - - + -
256D GLY* 3.2 40.5 - - - -
257D HIS* 4.4 12.8 - + - -
268D GLN* 3.7 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B TRP 4.5 0.8 - - - +
106B PHE* 4.0 31.1 - - + +
166B VAL 4.4 0.4 - - - +
167B ILE* 4.2 18.6 - - + -
170B PRO* 4.1 21.8 - - + -
166D VAL 3.2 16.8 - - - +
167D ILE 3.4 11.2 - - - +
169D TRP* 1.4 99.2 - - + +
171D ILE* 1.3 59.3 + - + +
174D GLY* 3.3 23.8 - - - +
175D ILE* 3.3 10.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D PHE* 4.9 3.8 - - + -
103D LEU* 5.7 2.5 - - + -
107D GLY* 4.3 20.0 - - - -
108D VAL* 3.8 32.1 - - + +
116D PHE* 5.2 5.4 - - + -
144D LEU* 3.7 35.2 - - + -
146D ILE* 5.8 0.4 - - + -
167D ILE* 4.3 15.5 - - + +
168D LEU* 3.1 12.0 + - + +
170D PRO* 1.3 81.0 - - + +
172D GLN* 1.3 60.7 + - - +
175D ILE* 2.9 41.3 + - + +
176D LEU* 3.0 15.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D LEU* 3.7 29.5 - - + +
168D LEU* 2.9 24.1 + - - +
171D ILE* 1.3 71.9 - - - +
173D SER* 1.3 55.0 + - - +
176D LEU* 3.5 10.6 - - + +
177D HIS* 2.8 29.5 + - - +
183D VAL* 3.6 23.2 - - + +
184D LEU 4.4 1.2 + - - -
186D PRO* 3.6 34.6 - - - +
220D LEU* 3.3 8.7 - - - +
222D PHE* 4.1 3.8 - - + -
268D GLN* 2.9 47.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B HIS 5.1 0.7 + - - -
132D TYR* 3.4 20.3 + - - -
169D TRP* 2.8 64.3 + - - -
172D GLN* 1.3 73.8 - - - +
174D GLY* 1.3 60.7 + - - +
175D ILE 3.4 0.2 + - - -
177D HIS* 3.6 2.6 - - - +
178D PHE 3.0 28.2 + - - -
222D PHE* 3.8 13.8 - - - -
257D HIS* 5.9 0.2 - - - -
268D GLN* 4.2 0.2 - - - +
----------------------------------------------------------
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