Contacts of ligand TPP1404A in PDB entry 2BFB
Ligand-Protein Contacts (LPC) are derived
with the LPC 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.
On this page you will find:
- 3D ligand structure presentation with
Jmol, an open-source
Java viewer for chemical structures in 3D (top left window)
- Solvent accessible surface of the ligand
complexed with protein and in uncomplexed form
(top right window). Clicking
on "select" buttons highlights atoms in 3D picture
- List of residues in contact
with the ligand
- List of putative hydrogen
bonds formed by the ligand
- Full list of atomic contacts
formed by the ligand
- Values of ligand complementarity
(a function of atomic contact
surface area and the chemical properties of contacting atoms)
- Prediction of complementarity changes as a
function of atomic substitution
in the
ligand
Table II
Residues in contact with ligand TPP1404A
in PDB entry 2BFB (back to top of page)
Legend:
Dist - nearest distance (Å) between atoms of the ligand and the residue
Surf - contact surface area (Å2) between the ligand and the residue
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 contacting ligand by their side chain
(including CA atoms)
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A MET* 5.8 2.7 - - - -
92A GLU* 4.4 0.2 + - - -
113A TYR* 2.4 70.5 + - - +
114A ARG* 2.9 39.7 + - - +
162A SER* 2.8 27.3 + - - -
163A PRO* 3.7 12.3 - - + +
164A LEU* 3.1 60.6 + - + +
192A GLY* 3.3 13.5 + - - -
193A GLU* 3.1 3.8 + - - -
194A GLY* 3.0 18.1 + - - -
195A ALA* 2.9 31.8 + - - +
198A GLU* 3.1 29.7 + - - +
220A ARG* 3.0 26.3 + - - +
222A ASN* 2.9 18.4 + - - -
224A TYR 2.9 6.9 + - - -
225A ALA* 3.3 18.7 - - + +
226A ILE* 3.6 57.6 + - + +
287A ARG* 5.1 2.3 + - - -
1402A MN 2.1 75.9 + - - -
1505A CL 4.7 7.6 - - - -
108B ASP* 5.9 3.4 - - - +
----------------------------------------------------------
Table III
List of putative hydrogen bonds between ligand TPP1404A
and protein in PDB entry 2BFB
(back to top
of page)
Legend:
N - ligand atom number in PDB entry
Dist - distance (Å) between the ligand and protein atoms
Surf - contact surface area (Å2) between the ligand and protein atoms
------------------------------------------------------------------------
Ligand atom Protein atom
----------------- ---------------------------- Dist Surf
N Name Class Residue Name Class
------------------------------------------------------------------------
1 N1' I GLU 198A OE2 II 4.0 4.6
4 N3' I LEU 164A N III 3.1 12.5
6 N4' I SER 162A O II 2.8 22.0
20 O1A I MN 1402A MN I 2.1 37.4
20 O1A I GLY 194A N III 3.0 17.0
20 O1A I GLU 193A OE1 II 3.1 0.7
20 O1A I GLU 193A OE2 II 3.2 2.1
20 O1A I TYR 224A O II 3.4 0.5
20 O1A I GLU 193A N III 3.5 1.0
21 O2A I ALA 195A N III 2.9 25.1
21 O2A I GLY 192A N III 3.8 0.5
21 O2A I ARG 220A NH2 III 4.6 0.3
22 O3A II TYR 113A OH I 3.4 2.8
22 O3A II ARG 220A NH2 III 3.4 7.8
22 O3A II MN 1402A MN I 3.5 0.3
24 O1B I TYR 113A OH I 2.4 29.6
24 O1B I ARG 114A NH2 III 3.0 15.8
24 O1B I ILE 226A N III 5.1 2.8
24 O1B I ARG 287A NH1 III 6.0 0.2
25 O2B I MN 1402A MN I 2.1 37.6
25 O2B I ASN 222A ND2 III 2.9 12.1
25 O2B I TYR 224A O II 2.9 6.4
25 O2B I ARG 114A NH2 III 4.4 0.3
25 O2B I ILE 226A N III 5.2 0.2
25 O2B I ARG 287A NH1 III 5.5 0.3
26 O3B I ARG 114A NE III 2.9 22.2
26 O3B I ARG 220A NH2 III 3.0 15.6
26 O3B I ASN 222A ND2 III 3.7 6.1
26 O3B I ARG 220A NE III 4.0 1.7
26 O3B I MN 1402A MN I 4.1 0.5
26 O3B I GLU 92A OE1 II 4.4 0.2
26 O3B I ARG 220A O II 5.6 0.2
------------------------------------------------------------------------
Table IV
Full list of atomic contacts with ligand TPP1404A
in PDB entry 2BFB (back
to top of page)
Total number of contacts is 107
Legend:
N - ligand atom number in PDB entry
Dist - distance (A) between the ligand and protein atoms
Surf - contact surface area (A**2) between the ligand and protein atoms
* - indicates destabilizing contacts
------------------------------------------------------------------------
Ligand atom Protein atom
----------------- ---------------------------- Dist Surf
N Name Class Residue Name Class
------------------------------------------------------------------------
1 N1' I GLU 198A OE2 II 4.0 4.6
1 N1' I LEU 164A CD1 IV 4.3 0.6*
2 C2' V LEU 164A N III 3.8 0.4
2 C2' V GLU 198A OE2 II 3.8 1.8
2 C2' V LEU 164A CB IV 4.2 2.0
3 CM2 IV GLU 198A OE2 II 3.1 21.1*
3 CM2 IV LEU 164A N III 3.7 12.1*
3 CM2 IV GLU 198A CD VI 4.2 2.2
3 CM2 IV LEU 164A O II 4.2 2.5*
3 CM2 IV PRO 163A CA IV 4.3 5.8
3 CM2 IV PRO 163A CB IV 4.7 2.5
3 CM2 IV ASP 108B OD2 II 5.9 2.7*
3 CM2 IV ASP 108B OD1 II 6.2 0.2*
3 CM2 IV ASP 108B CG VI 6.4 0.4
4 N3' I LEU 164A N III 3.1 12.5
4 N3' I LEU 164A CG IV 3.5 0.2*
4 N3' I PRO 163A CA IV 3.7 4.0*
5 C4' V LEU 164A CG IV 3.5 4.5
6 N4' I SER 162A O II 2.8 22.0
6 N4' I LEU 164A CG IV 3.7 2.0*
6 N4' I SER 162A C VI 3.9 1.6
6 N4' I LEU 164A CD2 IV 4.4 0.4*
6 N4' I SER 162A CB VI 4.7 3.8
7 C5' V LEU 164A CD1 IV 3.8 0.2
8 C6' V LEU 164A CD1 IV 4.1 1.3
9 C7' VI ILE 226A CD1 IV 4.6 4.7
10 N3 I ILE 226A CD1 IV 4.0 0.6*
11 C2 VI LEU 164A CD1 IV 4.2 0.2
11 C2 VI ILE 226A CD1 IV 4.5 3.6
11 C2 VI LEU 164A CG IV 4.6 0.4
11 C2 VI TYR 113A CE2 V 4.6 2.7
11 C2 VI CL 1505A CL IV 4.7 7.6
12 S1 VI TYR 113A OH I 3.1 21.3
12 S1 VI TYR 113A CE2 V 3.7 9.0
12 S1 VI TYR 113A CZ V 3.7 0.7
12 S1 VI LEU 164A CD1 IV 4.1 1.8
12 S1 VI ILE 226A CG1 IV 4.4 4.5
12 S1 VI ILE 226A CD1 IV 4.5 0.2
12 S1 VI MET 87A SD VIII 5.8 2.7
13 C5 IV ILE 226A CG1 IV 3.6 3.1
13 C5 IV LEU 164A CD1 IV 3.7 0.7
14 C4 VI LEU 164A CD1 IV 3.6 2.0
14 C4 VI ILE 226A CD1 IV 3.6 3.8
15 CM4 IV ILE 226A CD1 IV 3.8 10.5
15 CM4 IV LEU 164A CD1 IV 4.0 4.3
15 CM4 IV ILE 226A CG1 IV 4.2 0.9
15 CM4 IV ALA 225A CB IV 5.4 2.9
15 CM4 IV ALA 225A C VI 5.6 0.2
15 CM4 IV ALA 225A O II 5.6 0.2*
16 C6 IV ILE 226A CG1 IV 3.6 14.4
16 C6 IV ILE 226A N III 3.8 8.3*
16 C6 IV ALA 225A CB IV 3.9 4.5
16 C6 IV TYR 113A OH I 4.0 0.7*
17 C7 VIII TYR 113A OH I 3.4 3.6
17 C7 VIII LEU 164A CD1 IV 3.8 9.9
17 C7 VIII ALA 225A CB IV 4.1 1.1
17 C7 VIII LEU 164A CD2 IV 4.5 0.4
17 C7 VIII ALA 195A N III 4.9 1.3
17 C7 VIII GLY 194A CA VI 5.0 0.4
18 O7 II ALA 225A CB IV 3.3 8.0*
18 O7 II ALA 225A CA VII 3.4 1.4
18 O7 II GLY 194A CA VI 4.1 0.2
20 O1A I MN 1402A MN I 2.1 37.4
20 O1A I GLY 194A N III 3.0 17.0
20 O1A I GLU 193A OE1 II 3.1 0.7
20 O1A I GLU 193A OE2 II 3.2 2.1
20 O1A I TYR 224A O II 3.4 0.5
20 O1A I GLU 193A N III 3.5 1.0
20 O1A I GLY 194A CA VI 3.5 0.5
20 O1A I ALA 225A CB IV 3.8 0.2*
21 O2A I ALA 195A N III 2.9 25.1
21 O2A I GLY 192A CA VI 3.3 12.3
21 O2A I ALA 195A CB IV 3.5 5.4*
21 O2A I GLY 192A N III 3.8 0.5
21 O2A I ARG 220A NH2 III 4.6 0.3
21 O2A I LEU 164A CD2 IV 4.9 2.1*
22 O3A II TYR 113A OH I 3.4 2.8
22 O3A II ARG 220A NH2 III 3.4 7.8
22 O3A II MN 1402A MN I 3.5 0.3
22 O3A II GLY 192A CA VI 3.9 0.5
22 O3A II TYR 113A CZ V 4.4 0.2
24 O1B I TYR 113A OH I 2.4 29.6
24 O1B I ARG 114A NH2 III 3.0 15.8
24 O1B I ILE 226A N III 5.1 2.8
24 O1B I ARG 287A CD VII 5.7 0.2
24 O1B I ARG 287A NH1 III 6.0 0.2
25 O2B I MN 1402A MN I 2.1 37.6
25 O2B I ASN 222A ND2 III 2.9 12.1
25 O2B I TYR 224A O II 2.9 6.4
25 O2B I ARG 114A NH2 III 4.4 0.3
25 O2B I ALA 225A CA VII 4.5 0.2
25 O2B I ARG 287A CD VII 5.1 1.6
25 O2B I ILE 226A N III 5.2 0.2
25 O2B I ARG 287A NH1 III 5.5 0.3
26 O3B I ARG 114A NE III 2.9 22.2
26 O3B I ARG 220A NH2 III 3.0 15.6
26 O3B I ARG 114A CG IV 3.5 1.2*
26 O3B I ASN 222A ND2 III 3.7 6.1
26 O3B I ARG 114A CD VII 3.8 0.2
26 O3B I ARG 220A CZ VI 3.9 0.5
26 O3B I ARG 220A NE III 4.0 1.7
26 O3B I MN 1402A MN I 4.1 0.5
26 O3B I GLU 92A OE1 II 4.4 0.2
26 O3B I ASN 222A CG VI 4.6 0.2
26 O3B I GLY 192A CA VI 5.0 0.2
26 O3B I ARG 220A O II 5.6 0.2
26 O3B I ARG 220A CB IV 5.7 0.2*
------------------------------------------------------------------------
Table V
Complementarity values for the ligand TPP1404A
in PDB entry 2BFB (back to top of page)
---------------------------------------------
Theoretical maximum (Å2) 617
Actual value (Å2) 382
Normalised complementarity 0.62
---------------------------------------------
Table VI
Normalised complementarity as a function of atomic
substitution for ligand TPP1404A
in PDB entry 2BFB (back
to top of page)
Legend:
| N | - ligand atom number in PDB entry |
| Bold
| - indicates atomic
substitution which could stabilize the complex |
| Italics | - indicates atomic
substitution which could destabilize the complex |
|
Ligand atom | Atom class |
|---|
| N | Type | Class | I
| II | III | IV | V |
VI | VII | VIII |
|---|
| 1 | N1'
| I |
0.62 |
0.60
|
0.62 |
0.61
|
0.62 |
0.62
|
0.62 |
0.61
|
| 2 | C2'
| V |
0.61 |
0.61
|
0.61 |
0.61
|
0.62 |
0.62
|
0.62 |
0.61
|
| 3 | CM2
| IV |
0.72 |
0.63
|
0.68 |
0.62
|
0.74 |
0.74
|
0.70 |
0.66
|
| 4 | N3'
| I |
0.62 |
0.62
|
0.58 |
0.59
|
0.63 |
0.63
|
0.59 |
0.63
|
| 5 | C4'
| V |
0.60 |
0.60
|
0.60 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
| 6 | N4'
| I |
0.62 |
0.55
|
0.62 |
0.56
|
0.63 |
0.63
|
0.63 |
0.56
|
| 7 | C5'
| V |
0.62 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
| 8 | C6'
| V |
0.61 |
0.61
|
0.61 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
| 9 | C7'
| VI |
0.60 |
0.60
|
0.60 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
| 10 | N3
| I |
0.62 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
| 11 | C2
| VI |
0.58 |
0.58
|
0.58 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
| 12 | S1
| VI |
0.60 |
0.59
|
0.60 |
0.55
|
0.62 |
0.62
|
0.62 |
0.61
|
| 13 | C5
| IV |
0.61 |
0.61
|
0.61 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
| 14 | C4
| VI |
0.60 |
0.60
|
0.60 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
| 15 | CM4
| IV |
0.56 |
0.56
|
0.56 |
0.62
|
0.62 |
0.62
|
0.62 |
0.62
|
| 16 | C6
| IV |
0.59 |
0.59
|
0.56 |
0.62
|
0.65 |
0.65
|
0.62 |
0.65
|
| 17 | C7
| VIII |
0.58 |
0.58
|
0.58 |
0.60
|
0.62 |
0.62
|
0.61 |
0.62
|
| 18 | O7
| II |
0.62 |
0.62
|
0.61 |
0.64
|
0.64 |
0.64
|
0.64 |
0.64
|
| 20 | O1A
| I |
0.62 |
0.61
|
0.56 |
0.43
|
0.62 |
0.62
|
0.56 |
0.61
|
| 21 | O2A
| I |
0.62 |
0.62
|
0.53 |
0.56
|
0.64 |
0.64
|
0.56 |
0.64
|
| 22 | O3A
| II |
0.62 |
0.62
|
0.59 |
0.58
|
0.62 |
0.62
|
0.59 |
0.62
|
| 24 | O1B
| I |
0.62 |
0.62
|
0.56 |
0.46
|
0.62 |
0.62
|
0.56 |
0.62
|
| 25 | O2B
| I |
0.62 |
0.60
|
0.57 |
0.43
|
0.62 |
0.62
|
0.57 |
0.60
|
| 26 | O3B
| I |
0.62 |
0.62
|
0.47 |
0.47
|
0.62 |
0.62
|
0.48 |
0.62
|
A short description of the
analytical approach (back to top of page)
The analysis of ligand-protein contacts used in this page
is based upon the surface complementarity approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
The complementarity function
therein is defined as:
Where Sl is the sum of all
surface areas of legitimate atomic contacts between
ligand and receptor, Si is the sum of
all surface areas of illegitimate atomic
contacts, and E is a repulsion term.
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 ligands are automatically
assigned based on the atomic coordinates. However, in
three cases the automatic assignment is
currently ambiguous (due to low resolution). In these
three cases, the user is advised to manually analyze
the full list of contacts (Table IV).
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).
IN YOUR STRUCTURE, the following atoms
fall in these ambiguous cases:
Ligand MN 1402
3. Nitrogen ("hydrophilic")
1 N
Ligand TPP 1404
1. Carbon (in rings)
2 C2' 5 C4' 7 C5' 8 C6'
3. Nitrogen ("hydrophilic")
1 N1' 4 N3' 6 N4' 10 N3
Ligand GOL 1344
2. Oxygen ("hydroxy" or "carbonyl")
2 O1 4 O2 6 O3
Ligand MRD 1345
2. Oxygen ("hydroxy" or "carbonyl")
3 O2 7 O4
Please E-mail any questions and/or suggestions
concerning this page to
Vladimir.Sobolev@weizmann.ac.il