Contacts of the helix formed by residues 153 - 164 (chain A) in PDB entry 2Q41
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 153 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A SER* 2.6 27.3 + - - -
75A TYR* 3.4 20.2 - - + +
76A GLN* 2.7 37.2 + - - +
151A GLU* 3.9 6.5 - - - +
152A ILE* 1.3 81.4 - - + +
154A LYS* 1.3 62.7 + - - +
155A MSE 3.0 25.9 + - - +
156A VAL* 3.5 17.0 + - + +
157A VAL* 3.5 17.5 + - - +
180A ILE* 5.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 5.5 0.6 - - - -
152A ILE 3.7 3.8 + - - -
153A ASP* 1.3 70.6 + - - +
155A MSE 1.3 63.8 + - - +
156A VAL 3.1 1.8 - - - -
157A VAL* 4.0 4.9 - - + +
158A ASP* 2.7 65.7 + - - +
180A ILE* 3.3 39.5 - - + -
45B PRO* 5.8 1.4 - - - +
46B GLY* 6.3 1.2 - - - -
41C SER* 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 3.4 36.6 - - + -
71A GLY* 3.5 26.9 - - - +
73A SER* 3.9 19.5 - - - +
78A VAL* 3.3 36.6 - - + -
153A ASP* 3.0 13.1 + - - +
154A LYS* 1.3 76.7 - - - +
156A VAL* 1.3 58.0 + - - +
158A ASP* 3.7 5.1 - - - +
159A VAL* 2.9 37.1 + - + +
44B ILE* 4.7 7.0 - - + -
45B PRO* 5.6 5.2 - - + -
51C MSE 3.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLN* 4.0 14.4 - - - +
78A VAL* 4.0 15.9 - - + -
90A LEU* 4.5 6.5 - - + -
92A LEU* 3.5 32.5 - - + -
130A GLY* 3.3 39.9 - - - +
151A GLU* 4.5 4.9 - - - +
153A ASP* 3.5 11.3 + - + +
154A LYS 3.1 0.4 - - - -
155A MSE 1.3 72.8 - - - +
157A VAL* 1.3 71.1 + - - +
158A ASP 2.8 1.8 + - - -
159A VAL* 2.9 5.7 + - - +
160A SER* 2.6 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLY 4.9 0.2 - - - +
151A GLU* 3.5 35.4 - - + +
153A ASP 3.5 8.4 + - - +
154A LYS* 3.6 11.0 + - + +
156A VAL* 1.3 78.7 - - - +
158A ASP* 1.3 58.3 + - - +
160A SER* 3.4 2.0 + - - -
161A LYS* 3.0 60.5 + - - +
171A TYR* 3.7 32.0 - - + +
178A LEU* 4.1 10.3 - - + -
180A ILE* 5.1 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LYS* 2.7 59.5 + - - +
155A MSE 3.7 4.7 - - - +
156A VAL 2.8 2.0 + - - -
157A VAL* 1.3 75.5 - - - +
159A VAL* 1.3 64.7 + - - +
160A SER 3.2 0.2 + - - -
161A LYS* 3.3 13.7 + - - +
162A GLN* 3.2 22.9 + - - +
45B PRO* 3.9 26.7 - - + +
41C SER* 3.7 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PHE* 3.7 36.1 - - + -
78A VAL* 5.3 4.0 - - + -
80A VAL* 3.2 34.1 - - + -
90A LEU* 5.4 0.9 - - + -
155A MSE 2.9 26.5 + - + +
156A VAL* 2.9 7.8 + - - +
158A ASP* 1.3 72.7 - - - +
160A SER* 1.3 59.8 + - - +
162A GLN* 4.7 1.8 - - - +
163A PHE* 2.9 51.9 + - + +
164A PHE* 4.3 1.0 - - - -
45B PRO* 4.6 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 4.0 10.0 - - - +
130A GLY 3.3 20.4 + - - -
131A ASP* 3.9 23.6 - - - -
156A VAL* 2.6 25.9 + - - +
157A VAL* 3.6 7.0 - - - -
159A VAL* 1.3 71.0 - - - +
161A LYS* 1.3 65.4 + - - +
162A GLN 3.1 0.2 - - - -
164A PHE* 3.1 43.2 + - - +
167A VAL* 5.0 0.7 - - - -
168A ALA* 4.2 2.4 - - - +
171A TYR* 4.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL* 3.0 41.5 + - + +
158A ASP* 3.3 11.4 + - - +
160A SER* 1.3 77.0 - - - +
162A GLN* 1.3 61.8 + - - +
164A PHE 3.7 2.1 - - - +
168A ALA* 3.4 26.8 - - + +
171A TYR* 3.7 36.1 - - + +
178A LEU* 4.3 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASP 3.2 14.6 + - - +
159A VAL* 4.1 5.0 - - - +
160A SER 3.1 0.8 - - - -
161A LYS* 1.3 82.3 - - - +
163A PHE* 1.3 95.8 + - + +
164A PHE 4.5 1.4 - - - +
165A PRO* 5.8 0.2 - - - +
45B PRO* 5.3 0.9 - - - +
41C SER* 2.8 30.9 - - - +
42C THR* 4.2 3.9 - - - -
43C VAL* 2.9 44.6 + - - +
45C PRO* 4.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.5 33.9 - - + -
69A PHE* 4.3 5.8 - + + -
80A VAL* 3.8 19.7 - - + -
88A LYS* 3.2 36.7 - - + +
159A VAL* 2.9 50.6 + - + +
162A GLN* 1.3 109.4 - - + +
164A PHE* 1.3 62.4 + - + +
165A PRO* 3.4 6.4 - - - +
43C VAL* 4.9 7.2 - - + -
45C PRO* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.9 27.1 - - + -
88A LYS* 3.3 34.1 - - + -
89A VAL 3.9 5.6 - - - -
90A LEU* 3.8 37.2 - - + -
98A LEU* 4.3 9.9 - - + -
100A GLU* 3.7 22.4 - - + -
131A ASP* 6.0 0.7 - - + -
159A VAL 4.3 1.1 - - - -
160A SER* 3.1 38.9 + - - +
161A LYS 3.7 3.7 - - - +
162A GLN 4.7 1.1 - - - -
163A PHE* 1.3 75.7 - - + +
165A PRO* 1.3 62.9 - - - +
167A VAL* 3.4 29.8 - - + -
168A ALA* 3.2 19.3 + - - +
----------------------------------------------------------
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