Contacts of the helix formed by residues 154 - 166 (chain A) in PDB entry 2QDC
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 154 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 3.8 43.7 - - + +
129A ILE* 5.1 7.5 - - + +
148A GLN* 4.6 4.8 + - - +
150A PRO* 3.5 7.0 - - - +
151A MET* 2.8 33.3 + - + +
153A ASN* 1.3 87.4 - - - +
155A VAL* 1.3 60.7 + - - +
156A SER 3.3 2.2 - - - -
157A ASP* 3.3 17.2 + - - +
158A PHE* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A PRO* 4.0 8.3 - - + -
151A MET 3.2 15.7 + - - +
152A PRO* 3.9 12.7 + - + +
153A ASN 3.7 1.0 - - - -
154A THR* 1.3 77.8 - - - +
156A SER* 1.3 62.9 + - - +
158A PHE* 3.3 3.2 + - - +
159A TRP* 3.1 30.7 + - + -
184A VAL* 3.8 24.5 - - + -
186A TYR* 3.9 15.9 - - + -
194A TYR* 3.5 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU* 6.1 4.0 - - - -
153A ASN 5.3 1.7 + - - -
154A THR 3.3 0.6 - - - -
155A VAL* 1.3 79.0 - - - +
157A ASP* 1.3 59.3 + - - +
159A TRP* 3.4 3.6 + - - +
160A GLU* 2.9 40.2 + - - +
194A TYR* 4.2 12.5 - - - +
195A GLY* 3.8 27.5 + - - -
196A PRO* 5.8 1.5 - - - +
197A PHE* 4.8 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 3.2 26.2 + - - +
117A LEU* 4.0 16.9 - - + +
119A ARG* 3.0 28.0 + - - -
124A GLU* 4.8 4.5 - - - +
128A TYR 4.1 6.5 - - - +
129A ILE* 3.9 12.7 - - + +
153A ASN 4.1 2.7 - - - +
154A THR* 3.3 27.7 + - - +
156A SER* 1.3 78.2 - - - +
158A PHE* 1.3 56.4 + - - +
160A GLU* 3.3 9.4 + - - +
161A MET* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE* 3.9 12.2 - - + +
147A THR* 4.2 11.2 - - + -
148A GLN 5.0 1.1 - - - -
150A PRO* 3.7 24.9 - - + -
154A THR 2.9 14.2 + - - +
155A VAL 3.3 8.5 + - - +
157A ASP* 1.3 75.7 - - - +
159A TRP* 1.3 69.8 + + - +
161A MET* 3.2 17.6 + - + +
162A VAL* 3.0 40.6 + - + +
170A ILE* 4.0 18.2 - - + -
186A TYR* 3.4 44.0 - + - -
267A VAL* 4.0 26.5 - - + -
269A HIS* 4.2 9.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL* 3.1 29.5 + - + +
156A SER 4.0 2.7 - - - +
158A PHE* 1.3 75.0 - + - +
160A GLU* 1.3 60.4 + - - +
162A VAL* 3.2 26.1 + - + +
163A TRP* 2.9 28.8 + - - +
170A ILE* 4.0 26.0 - - + -
186A TYR* 2.9 50.0 + + - -
187A TRP* 4.4 8.1 - - + -
194A TYR* 3.7 28.9 - + + -
197A PHE* 3.9 20.1 - - + -
199A ILE* 3.6 31.2 - - + -
215A LEU* 3.8 24.5 - - + -
217A ILE* 3.9 7.9 - - + +
226A VAL* 5.0 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 4.4 9.5 - - + +
119A ARG* 3.0 48.2 + - - -
121A GLN* 5.3 5.5 - - + +
122A SER* 3.0 30.2 + - - -
124A GLU* 3.9 6.2 - - - +
156A SER* 2.9 21.5 + - - +
157A ASP* 3.4 11.6 - - - +
159A TRP* 1.3 77.9 - - - +
161A MET* 1.3 55.7 + - - +
163A TRP* 3.4 2.1 + - - +
164A GLN* 2.9 32.2 + - - +
196A PRO* 5.3 3.8 - - + +
197A PHE* 3.6 24.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.9 25.4 - - + -
117A LEU* 3.8 14.5 - - + +
129A ILE* 4.0 19.7 - - + -
131A ALA* 3.8 22.4 - - - -
145A ILE* 3.9 24.0 - - + -
147A THR* 4.1 19.5 - - + -
157A ASP 2.9 12.3 + - - +
158A PHE* 3.4 19.1 - - + +
160A GLU* 1.3 72.7 - - - +
162A VAL* 1.3 67.8 + - + +
164A GLN* 4.5 2.9 - - - +
165A GLU* 2.9 37.9 + - + +
167A VAL* 5.7 0.2 - - + -
267A VAL* 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A PHE* 3.0 44.3 + - + +
159A TRP* 3.2 33.2 + - + +
161A MET* 1.3 75.6 - - + +
163A TRP* 1.3 64.3 + - - +
166A GLU* 3.2 3.1 + - - -
167A VAL* 3.0 61.4 + - + +
170A ILE* 4.2 7.6 - - + -
217A ILE* 4.4 8.1 - - + -
224A ARG* 4.3 0.9 + - - -
226A VAL* 4.3 12.6 - - + -
267A VAL* 4.8 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLN* 3.3 38.7 - - + +
159A TRP 2.9 9.9 + - - +
160A GLU 3.7 1.3 - - - +
162A VAL* 1.3 75.4 - - - +
164A GLN* 1.3 67.3 + - - +
166A GLU* 3.1 5.2 + - - +
197A PHE* 3.5 28.5 - + + -
217A ILE* 3.5 42.0 - - + -
219A TYR* 3.6 26.5 - + + +
222A GLU* 3.3 42.0 - - + -
224A ARG* 2.7 69.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 4.2 6.9 - - - +
116A CYS 2.8 25.5 + - - -
117A LEU* 3.6 9.6 - - - +
118A GLY* 2.8 29.8 + - - -
119A ARG 4.3 2.3 + - - -
120A ALA 5.6 0.2 + - - -
121A GLN* 5.1 5.8 - - - +
133A TYR* 4.6 0.6 + - - -
160A GLU 2.9 21.7 + - - +
161A MET* 4.0 1.8 - - - +
163A TRP* 1.3 80.0 - - - +
165A GLU* 1.3 83.3 + - - +
166A GLU* 3.6 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.9 1.4 - - + +
133A TYR* 2.7 42.7 + - - -
142A LYS* 5.0 4.3 + - - +
145A ILE* 3.7 18.4 - - + -
161A MET* 2.9 26.1 + - + +
164A GLN* 1.3 101.9 + - - +
166A GLU* 1.3 71.3 + - - +
167A VAL* 3.9 13.9 - - + -
264A GLY* 3.8 2.3 - - - -
265A PRO* 3.3 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL 3.2 3.5 + - - -
163A TRP 3.1 9.9 + - - +
164A GLN 4.3 6.1 - - - +
165A GLU* 1.3 81.8 - - - +
167A VAL* 1.3 64.1 + - - +
168A SER* 3.5 5.4 + - - -
224A ARG* 3.7 31.2 - - - +
262A HIS 5.2 6.2 - - - +
264A GLY* 3.6 19.1 + - - +
----------------------------------------------------------
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