Contacts of ILE 96 (chain A) in PDB entry 1A2P
Residue contacts 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 analyze, use
LPC software
This page presents:
Table I
Solvent accessible surface (Å2) for
ILE 96 (chain A) in PDB entry 1A2P
.
Legend:
In order to see to what extent the residue is
buried, accessible surfaces are given for two
cases: in the protein and "free" (in a vacuum).
---------------------------------
Atom In protein Free
---------------------------------
N 0.0 43.9
CA 0.0 11.4
C 0.0 39.0
O 0.0 37.1
CB 0.0 8.1
CG1 0.0 31.4
CG2 0.0 55.2
CD1 0.0 62.8
TOTAL 0.0 289.0
---------------------------------
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Table II
Residues in contact with ILE 96 (chain A)
in PDB entry 1A2P
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)
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 4.1 5.8 - - + +
14A LEU* 4.3 16.2 - - + -
15A GLN* 3.9 15.0 - - + +
88A ILE* 3.7 34.3 - - + -
89A LEU 3.3 4.0 - - - +
90A TYR* 3.8 17.0 - - + -
94A TRP* 3.7 14.6 - - + +
95A LEU* 1.3 83.5 - - - +
97A TYR* 1.3 65.2 + - - +
108A LYS* 3.7 3.1 - - - -
109A ILE* 3.0 33.4 + - + -
110A ARG* 3.1 40.3 + - + +
----------------------------------------------------------
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Table III
List of putative hydrogen bonds formed by ILE 96 (chain A)
in PDB entry 1A2P
Legend:
Dist - distance (Å) between the atoms
Surf - contact surface area (Å2) between the atoms
-----------------------------------------------------------------
Atom from ILE 96 Contacting atom
----------------- ------------------------- Dist Surf
Name Class Residue Name Class
-----------------------------------------------------------------
N III ARG 110A OXT II 3.1 5.9
O II TYR 97A N III 2.2 0.3
O II ILE 109A N III 3.0 21.5
O II ARG 110A N III 3.2 2.9
-----------------------------------------------------------------
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Table IV
Full list of atomic contacts formed by ILE 96 (chain A)
in PDB entry 1A2P
Total number of contacts is 52
Legend:
Dist - distance (Å) between the atoms
Surf - contact surface area (Å2) between the atoms
* - indicates destabilizing contacts
-----------------------------------------------------------------
Atom from ILE 96 Contacting atom
----------------- ------------------------- Dist Surf
Name Class Residue Name Class
-----------------------------------------------------------------
N III LEU 95A C VI 1.3 56.8
N III LEU 95A CA VII 2.4 4.4*
N III ARG 110A OXT II 3.1 5.9
N III LEU 95A CB IV 3.3 1.0*
N III TYR 97A CD1 V 4.3 0.2
CA VII TYR 97A N III 2.4 4.3*
CA VII LEU 95A C VI 2.4 7.4
CA VII LEU 95A O II 2.8 3.1
CA VII LEU 89A O II 3.3 1.8
C VI TYR 97A N III 1.3 44.2
C VI TYR 97A CA VII 2.4 2.9
C VI TYR 97A C VI 3.5 0.2
C VI TYR 97A CB IV 3.5 1.3
C VI LEU 95A C VI 3.5 0.7
C VI TYR 97A CD1 V 3.5 2.2
C VI ILE 109A N III 4.0 0.2
O II TYR 97A N III 2.2 0.3
O II TYR 97A CA VII 2.8 6.1
O II ILE 109A N III 3.0 21.5
O II ARG 110A N III 3.2 2.9
O II ARG 110A OXT II 3.3 2.3*
O II LYS 108A CA VII 3.7 3.1
O II TYR 97A CD1 V 3.7 0.7
CB IV ARG 110A CB IV 3.8 7.6
CB IV ARG 110A N III 4.0 0.4*
CG1 IV LEU 95A C VI 3.4 0.9
CG1 IV ARG 110A CB IV 3.6 18.4
CG1 IV TRP 94A O II 3.7 5.4*
CG1 IV ARG 110A CG IV 3.9 2.7
CG1 IV GLN 15A NE2 III 3.9 2.7*
CG1 IV GLN 15A CG IV 4.1 1.1
CG1 IV ALA 11A O II 4.8 0.2*
CG2 IV TYR 97A N III 3.5 2.7*
CG2 IV ILE 88A CG1 IV 3.7 27.4
CG2 IV ILE 88A CD1 IV 3.7 7.0
CG2 IV ILE 109A CG1 IV 3.8 11.0
CG2 IV ILE 109A CD1 IV 4.0 0.7
CG2 IV LEU 89A O II 4.0 2.0*
CG2 IV ALA 11A CB IV 4.1 4.0
CG2 IV LEU 89A C VI 4.9 0.2
CG2 IV TYR 90A CB IV 5.0 0.2
CD1 IV LEU 95A O II 3.6 8.5*
CD1 IV LEU 95A C VI 3.8 0.7
CD1 IV TYR 90A CB IV 3.8 16.8
CD1 IV TRP 94A O II 3.9 5.6*
CD1 IV GLN 15A CG IV 4.2 11.2
CD1 IV LEU 14A CD1 IV 4.3 11.9
CD1 IV TRP 94A C VI 4.3 1.6
CD1 IV LEU 14A CB IV 4.4 4.3
CD1 IV ALA 11A O II 4.6 1.6*
CD1 IV TRP 94A CA VII 4.8 1.3
CD1 IV TRP 94A CE3 V 4.9 0.7
-----------------------------------------------------------------
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A short description of the
analytical approach (back to top of page)
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 1 or two or more atoms from class 2
or 3; N if it has covalent bonds with 3 carbon
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