Contacts of the helix formed by residues 124 - 135 (chain A) in PDB entry 2LBP
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 GLN 124 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASP* 3.0 38.2 + - - +
122A SER 3.0 0.8 - - - -
123A SER* 1.3 77.6 - - - +
125A GLY* 1.3 64.7 + - - +
127A THR* 3.2 7.8 + - - -
128A ALA* 3.1 24.3 + - - +
150A TYR* 4.0 10.5 + - - -
154A LEU* 4.0 8.9 - - + +
198A TYR* 5.5 1.1 - - - +
225A PRO* 3.4 7.0 - - + +
226A GLU* 3.0 19.0 + - - +
247A THR* 2.7 40.9 + - + +
331A PHE* 3.5 39.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER 3.4 4.0 + - - -
124A GLN* 1.3 79.6 - - - +
126A PRO* 1.3 63.1 - - - +
128A ALA* 3.3 0.6 + - - -
129A ALA* 3.1 23.7 + - - +
154A LEU* 3.7 12.4 - - - +
157A SER* 4.0 17.3 - - - -
158A VAL* 3.2 28.1 - - - +
198A TYR* 5.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER 3.0 18.2 - - - +
123A SER* 3.1 14.1 - - - +
125A GLY* 1.3 89.1 - - - +
127A THR* 1.3 61.6 + - - +
129A ALA* 3.9 9.3 - - + +
130A LYS* 3.3 24.8 + - - +
157A SER* 4.2 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A SER 3.1 14.9 + - - -
124A GLN* 3.2 11.5 + - - -
126A PRO* 1.3 76.7 - - - +
128A ALA* 1.3 59.5 + - - +
130A LYS* 3.9 8.6 - - - +
131A TYR* 3.0 29.3 + - - +
247A THR* 4.0 15.3 - - - +
330A ASP* 4.0 22.0 + - + +
331A PHE 3.3 28.9 + - - +
333A VAL* 4.3 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLN 3.1 11.8 + - - +
125A GLY 3.4 8.7 - - - +
127A THR* 1.3 74.9 - - - +
129A ALA* 1.3 65.0 + - - +
131A TYR* 3.1 4.9 + - - +
132A ILE* 3.0 30.8 + - + +
158A VAL* 4.0 3.4 - - + -
198A TYR* 3.8 29.8 - - + -
223A MET* 3.9 17.9 - - - +
247A THR* 4.6 8.5 + - + +
333A VAL* 5.6 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLY 3.1 15.3 + - - +
126A PRO* 4.1 9.6 - - + +
127A THR 3.5 0.2 - - - -
128A ALA* 1.3 75.0 - - - +
130A LYS* 1.3 57.7 - - - +
132A ILE* 3.7 3.3 + - - +
133A LEU* 3.2 35.3 + - + +
157A SER 5.3 0.2 - - - +
158A VAL* 4.3 14.8 - - - +
161A GLY* 4.2 28.7 - - - -
162A LEU* 3.8 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PRO 3.3 18.5 + - - +
127A THR* 3.9 6.5 - - - +
128A ALA 3.3 0.4 - - - -
129A ALA* 1.3 74.9 - - - +
131A TYR* 1.3 63.1 + - - +
133A LEU* 4.6 4.3 - - - -
134A GLU* 2.9 62.5 + - - +
330A ASP* 4.7 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A THR 3.0 18.3 + - - +
128A ALA 3.1 4.5 + - - +
130A LYS* 1.3 80.3 - - - +
132A ILE* 1.3 55.7 + - - +
135A THR* 2.9 50.5 + - + -
136A VAL* 3.2 19.5 + - + -
223A MET* 3.5 20.4 - - + -
245A LEU* 4.3 12.3 - - + +
333A VAL* 3.8 41.3 - - + -
345A ALA* 3.4 13.1 - - + +
346A LYS* 2.2 53.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA* 3.0 26.4 + - + +
129A ALA* 3.8 5.8 - - - +
131A TYR* 1.3 77.3 - - - +
133A LEU* 1.3 57.6 + - + +
136A VAL* 3.8 9.6 - - + -
137A LYS* 2.7 29.3 + - - -
138A PRO* 3.3 26.9 - - + +
141A ILE* 4.0 14.6 - - + -
158A VAL* 4.2 22.4 - - + -
162A LEU* 4.1 13.2 - - + -
196A PHE* 3.4 26.0 - - + -
198A TYR* 4.7 3.6 - - + -
223A MET* 3.1 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 3.2 19.0 + - - +
130A LYS* 4.2 5.4 - - - +
131A TYR 3.2 0.8 - - - -
132A ILE* 1.3 84.8 - - + +
134A GLU* 1.3 61.9 + - + +
137A LYS* 3.2 28.2 - - - +
138A PRO* 6.3 0.7 - - + -
161A GLY 4.1 10.1 - - - +
162A LEU* 3.9 11.7 - - + +
165A ALA* 3.2 37.7 - - + +
167A ALA* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LYS* 2.9 52.9 + - + +
133A LEU* 1.3 82.4 - - + +
135A THR* 1.3 68.3 + - + +
137A LYS* 2.9 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 2.9 55.3 + - + +
134A GLU* 1.3 89.7 - - + +
136A VAL* 1.3 64.6 + - - +
137A LYS* 4.5 2.6 - - - +
346A LYS* 3.4 42.6 + - - +
----------------------------------------------------------
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