Contacts of the helix formed by residues 149 - 155 (chain B) in PDB entry 3QVL
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 PRO 149 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU* 3.5 13.7 - - - +
119B THR* 3.6 4.2 - - - +
120B LEU* 4.2 7.9 - - + -
148B LEU* 1.3 99.0 - - + +
150B VAL* 1.3 66.7 + - - +
151B LEU* 3.2 6.1 - - + +
152B ALA* 3.0 28.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 5HY 3.3 56.8 - - + +
17B MET* 3.6 20.2 - - + +
46B SER* 3.9 10.5 - - - -
47B ILE 3.7 7.9 - - - +
48B GLU* 2.9 33.3 + - + +
119B THR* 4.0 10.8 - - - -
120B LEU* 5.1 5.8 - - + -
123B THR* 5.6 1.3 - - + -
148B LEU 3.7 0.6 + - - -
149B PRO* 1.3 71.3 - - - +
151B LEU* 1.3 58.1 + - - +
152B ALA 3.2 4.7 + - - -
153B LEU* 3.3 23.4 + - - +
184B SER* 4.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B SER* 3.9 21.5 - - - +
17B MET* 4.0 13.2 - - + -
45B PRO* 3.8 38.1 - - + +
46B SER* 3.8 16.3 - - - +
48B GLU* 4.7 0.4 + - - -
149B PRO* 3.2 5.3 - - + +
150B VAL* 1.3 72.0 - - - +
152B ALA* 1.3 58.2 + - - +
153B LEU 3.1 2.5 - - - -
154B GLU* 3.1 25.5 + - + +
155B ASP* 3.4 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 4.1 23.6 - - + -
149B PRO* 3.0 29.0 + - + +
151B LEU* 1.3 77.6 - - - +
153B LEU* 1.3 57.1 + - - +
154B GLU 3.1 1.1 - - - -
155B ASP* 3.0 35.8 - - - +
157B SER* 4.5 1.6 + - - -
159B LEU* 6.4 0.4 - - + -
160B ALA* 3.7 16.9 + - + +
161B GLN* 4.5 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B 5HY 4.8 0.7 - - - +
17B MET* 5.5 0.2 - - + -
119B THR* 3.8 20.4 - - + +
146B ILE* 5.3 0.4 - - + -
150B VAL* 3.3 18.3 + - + +
151B LEU 3.1 0.8 - - - -
152B ALA* 1.3 76.9 - - - +
154B GLU* 1.3 67.9 + - + +
155B ASP* 3.7 0.4 - - - -
156B GLY 5.1 1.3 + - - -
160B ALA* 3.8 24.7 - - + -
161B GLN* 2.9 38.9 + - + +
164B VAL* 4.7 2.9 - - + -
184B SER* 3.3 29.4 - - - +
186B GLY* 4.1 21.2 - - - +
187B MET* 3.8 23.6 - - + -
190B LEU* 5.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B SER* 4.5 2.2 - - - +
16B ALA* 3.3 32.8 - - + +
17B MET* 3.5 50.4 - - + +
20B THR* 3.1 23.9 + - - +
151B LEU* 3.1 16.6 + - + +
153B LEU* 1.3 85.7 - - + +
155B ASP* 1.3 60.8 + - - +
156B GLY 3.2 3.8 + - - -
186B GLY* 4.1 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU 3.4 8.3 + - - +
152B ALA* 3.0 30.8 - - - +
153B LEU 3.7 0.2 - - - -
154B GLU* 1.3 77.0 - - - +
156B GLY* 1.3 61.9 + - - +
157B SER* 2.7 34.1 + - - -
158B GLY 4.1 1.0 + - - -
159B LEU* 6.1 0.7 - - - +
----------------------------------------------------------
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