Contacts of the helix formed by residues 106 - 118 (chain A) in PDB entry 4P4P
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 GLY 106 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 3.6 7.6 - - - -
105A PHE* 1.3 74.2 - - - +
107A PRO* 1.3 77.8 - - - +
108A ARG 3.1 4.1 + - - -
109A ALA 3.2 0.3 + - - -
110A ALA* 2.9 22.9 + - - +
4C T 3.0 31.4 + - - -
5C A 4.4 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 3.9 26.5 - - + +
100A THR* 3.7 8.5 - - + -
106A GLY* 1.3 83.3 - - - +
108A ARG* 1.3 55.5 + - - +
110A ALA* 3.8 0.3 - - - +
111A ALA* 3.0 31.2 + - - +
4C T 3.6 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A GLY 3.1 1.2 - - - -
107A PRO* 1.3 78.0 - - - +
109A ALA* 1.3 65.8 + - - +
111A ALA* 3.5 4.1 + - - +
112A ALA* 3.2 21.9 + - + +
3C G 3.5 37.7 - - - +
4C T 3.2 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 3.6 27.1 - - + -
106A GLY 4.0 1.6 - - - +
108A ARG* 1.3 73.4 - - - +
110A ALA* 1.3 63.3 + - - +
112A ALA* 3.3 6.8 + - - +
113A LEU* 3.0 27.4 + - - +
139A GLN* 3.7 16.8 - - - +
4C T 2.7 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 3.9 26.9 - - + -
99A LEU* 3.8 32.5 - - + +
100A THR* 4.1 5.2 - - + +
105A PHE* 4.8 2.6 - - + -
106A GLY 2.9 16.5 + - - +
107A PRO 3.8 3.4 - - - +
109A ALA* 1.3 78.5 - - - +
111A ALA* 1.3 58.5 + - - +
113A LEU* 3.0 8.1 + - - +
114A PHE* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LYS* 3.8 24.9 - - - +
96A ILE* 4.2 10.6 - - + +
107A PRO 3.0 18.3 + - - +
108A ARG* 3.8 5.2 - - - +
110A ALA* 1.3 75.7 - - - +
112A ALA* 1.3 57.0 + - - +
114A PHE* 3.3 7.1 + - - +
115A ASP* 2.7 38.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 3.2 14.3 + - + +
109A ALA* 3.7 10.8 - - - +
110A ALA 3.2 0.2 - - - -
111A ALA* 1.3 73.0 - - - +
113A LEU* 1.3 60.9 + - - +
115A ASP* 4.4 3.4 - - - +
116A ARG* 2.8 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LEU* 3.8 22.7 - - + -
105A PHE* 3.6 28.3 - - + -
109A ALA 3.0 14.6 + - - +
110A ALA* 3.0 7.8 + - - +
112A ALA* 1.3 76.3 - - - +
114A PHE* 1.3 58.4 + - - +
116A ARG* 4.7 4.7 - - - +
117A GLU* 2.8 36.1 + - + +
118A GLY 2.9 6.8 + - - -
119A ILE* 3.3 13.4 + - + -
125A LEU* 3.7 27.6 - - + -
132A ILE* 4.1 26.7 - - + -
135A LEU* 4.4 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PRO* 4.0 5.8 - - + -
92A LYS* 3.6 43.3 - - + +
95A ALA* 3.4 28.0 - - + -
96A ILE* 5.7 0.7 - - + -
99A LEU* 5.3 0.2 - - + -
110A ALA 2.9 11.9 + - - +
111A ALA* 3.5 11.0 - - - +
113A LEU* 1.3 75.5 - - - +
115A ASP* 1.3 73.3 + - - +
118A GLY* 2.8 28.8 + - - -
119A ILE 3.5 16.7 + - - +
120A PHE* 3.7 39.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LYS* 2.5 35.5 + - - -
111A ALA* 2.7 23.0 + - - +
112A ALA* 4.3 3.1 - - - +
114A PHE* 1.3 83.7 - - - +
116A ARG* 1.3 65.4 + - + +
118A GLY* 4.2 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA* 2.8 57.3 + - - +
113A LEU* 4.1 5.5 - - - +
115A ASP* 1.3 79.8 - - + +
117A GLU* 1.3 94.8 + - - +
132A ILE* 4.2 3.2 - - - +
134A SER* 3.3 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 2.8 19.1 + - + +
116A ARG* 1.3 125.2 + - - +
118A GLY* 1.3 64.2 + - - +
119A ILE* 3.5 21.3 + - + +
128A LYS* 5.2 7.0 - - + +
132A ILE* 3.9 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU 2.9 0.2 + - - -
114A PHE 2.8 18.8 + - - -
115A ASP 4.2 1.3 + - - -
116A ARG 3.6 0.8 - - - -
117A GLU* 1.3 79.6 - - - +
119A ILE* 1.3 60.4 + - - +
120A PHE* 3.4 24.8 - - - -
124A GLU* 4.6 4.5 - - - +
128A LYS* 5.8 1.9 - - - -
----------------------------------------------------------
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