Contacts of the helix formed by residues 154 - 165 (chain D) in PDB entry 4XQ2
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 154 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LEU 4.7 1.6 + - - -
123D THR* 6.1 0.2 - - - +
128D ILE* 6.1 1.6 - - + -
152D VAL* 4.3 1.5 - - - +
153D VAL* 1.3 70.6 - - - +
155D VAL* 1.3 64.0 + - - +
156D ALA* 3.4 9.4 + - - +
157D GLU* 2.8 42.6 + - + +
158D VAL* 3.0 27.1 + - + +
160D ARG* 4.8 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D ILE* 4.5 12.6 - - + +
144D THR* 3.9 20.6 - - + -
153D VAL 3.0 11.5 + - - +
154D ASP* 1.3 71.7 + - - +
156D ALA* 1.3 56.1 + - - +
158D VAL* 3.9 0.9 - - - +
159D SER* 2.8 39.9 + - - +
171D VAL* 3.8 30.5 - - + -
181D GLN* 4.7 2.9 - - - +
183D PRO* 4.1 2.0 - - + +
186D LEU* 3.6 39.5 - - + -
188D ALA* 4.0 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D ASP* 3.4 6.3 + - - +
155D VAL* 1.3 78.1 - - - +
157D GLU* 1.3 58.5 + - - +
159D SER* 3.3 3.1 + - - -
160D ARG* 2.9 54.2 + - - +
186D LEU* 3.1 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D PRO* 6.0 2.1 - - - +
128D ILE* 5.1 11.2 - - + -
154D ASP* 2.8 36.4 + - + +
156D ALA* 1.3 70.0 - - - +
158D VAL* 1.3 65.5 + - - +
160D ARG* 3.2 42.9 + - - +
161D ARG* 2.9 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D LEU* 4.2 11.9 - - + +
128D ILE* 3.6 37.0 - - + -
132D LEU* 5.0 3.6 - - + +
140D VAL* 3.9 19.7 - - + -
142D ILE* 3.8 24.5 - - + -
153D VAL* 3.7 19.3 - - + -
154D ASP* 3.0 21.0 + - + +
155D VAL 4.1 2.0 - - - +
157D GLU* 1.3 74.4 - - - +
159D SER* 1.3 58.3 + - - +
161D ARG* 3.4 7.8 + - - +
162D ALA* 2.9 27.2 + - + +
169D VAL* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D VAL* 2.8 24.5 + - - +
156D ALA* 3.6 5.8 - - - -
158D VAL* 1.3 75.7 - - - +
160D ARG* 1.3 63.8 + - - +
163D HIS* 2.8 36.1 + - - -
169D VAL* 3.6 25.2 - - - +
187D GLY* 3.6 35.1 + - - -
188D ALA* 3.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D ASP* 4.8 1.6 + - - -
156D ALA* 2.9 34.4 + - - +
157D GLU* 3.2 42.0 + - - +
159D SER* 1.3 79.3 - - - +
161D ARG* 1.3 84.2 + - - +
163D HIS* 3.7 4.9 + - - +
164D GLU* 3.3 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D ILE* 4.0 24.0 - - + -
129D ALA* 5.8 3.6 - - + +
132D LEU* 3.5 16.5 - - + +
157D GLU* 2.9 43.5 + - - +
158D VAL 4.1 2.0 - - - +
159D SER 3.2 0.2 - - - -
160D ARG* 1.3 103.4 - - - +
162D ALA* 1.3 64.2 + - - +
163D HIS 3.2 0.4 - - - -
164D GLU* 3.2 49.0 + - - +
165D ARG* 3.4 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LEU* 3.7 14.5 - - + +
140D VAL* 3.8 22.7 - - + -
158D VAL 2.9 19.7 + - - +
159D SER 3.8 0.4 - - - +
161D ARG* 1.3 76.4 - - - +
163D HIS* 1.3 59.2 + - - +
165D ARG* 3.0 19.4 + - - +
167D ALA* 3.3 18.0 + - + +
169D VAL* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D SER* 2.8 26.2 + - - +
160D ARG* 4.0 4.8 - - - +
162D ALA* 1.3 73.4 - - - +
164D GLU* 1.3 62.8 + - - +
165D ARG 3.0 2.2 - - - -
166D GLY* 3.0 16.2 + - - +
167D ALA 3.6 19.3 - - - +
169D VAL* 3.9 8.2 - - + +
187D GLY 3.0 28.7 + - - -
189D ASP* 2.8 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D ARG* 3.3 10.3 + - - +
161D ARG* 3.2 58.9 + - - +
162D ALA 3.1 0.6 - - - -
163D HIS* 1.3 76.6 - - - +
165D ARG* 1.3 60.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D LEU* 2.3 41.9 + - + +
133D ALA* 4.4 3.1 + - - +
134D GLU 2.7 29.9 + - - -
135D PRO* 4.5 1.4 - - - +
136D ASP 4.4 4.6 - - - +
137D LEU* 4.1 25.1 - - + +
161D ARG 3.4 16.8 - - - +
162D ALA 3.0 8.0 + - - +
163D HIS 3.0 1.0 - - - -
164D GLU* 1.3 78.6 - - - +
166D GLY* 1.3 62.7 + - - +
167D ALA* 3.5 2.0 + - + +
----------------------------------------------------------
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