Contacts of the helix formed by residues 99 - 111 (chain D) in PDB entry 4G5O
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 ALA 99 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLU* 3.1 8.9 - - + +
98D ALA* 1.3 77.5 - - - +
100D ARG* 1.3 86.7 + - - +
101D ALA 3.3 0.9 + - - -
102D ASP* 3.6 23.2 + - - +
103D ASP* 4.4 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D PHE* 3.6 21.5 - - + -
97D GLU* 3.3 26.8 + - + +
98D ALA 3.1 1.2 + - - -
99D ALA* 1.3 98.8 + - - +
101D ALA* 1.3 65.2 + - - +
102D ASP 3.1 5.0 + - - -
103D ASP* 2.8 44.6 + - - +
104D ALA* 3.1 10.0 + - - +
129D ARG* 3.4 51.0 + - - +
130D LEU* 3.9 9.1 - - + +
133D ASP* 3.4 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D PHE* 4.2 24.0 - - + -
98D ALA* 3.1 17.1 + - + +
100D ARG* 1.3 78.6 - - - +
102D ASP* 1.3 61.6 + - - +
104D ALA* 3.5 5.9 - - - +
105D ARG* 3.4 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ALA 5.5 1.1 - - - -
99D ALA* 3.8 16.9 - - - +
100D ARG 3.1 0.6 - - - -
101D ALA* 1.3 75.6 - - - +
103D ASP* 1.3 56.9 + - - +
104D ALA 3.1 1.6 - - - -
105D ARG* 2.9 27.0 + - - +
106D GLN* 2.6 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ALA 4.6 1.6 - - - +
100D ARG* 2.8 41.0 + - - +
102D ASP* 1.3 78.1 - - - +
104D ALA* 1.3 53.9 + - - +
106D GLN* 3.9 8.0 - - - +
107D LEU* 2.7 35.3 + - - +
126D VAL* 3.4 13.3 - - + +
129D ARG* 2.6 38.4 + - - +
130D LEU* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D ILE* 4.5 15.9 - - + -
95D PHE* 3.8 28.3 - - + -
100D ARG 3.1 5.6 + - - +
101D ALA* 3.5 10.5 - - - +
102D ASP 3.1 0.4 - - - -
103D ASP* 1.3 77.0 - - - +
105D ARG* 1.3 61.6 + - + +
107D LEU* 3.6 5.6 - - - +
108D PHE* 3.0 33.1 + - + -
130D LEU* 4.1 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D ALA* 3.4 27.0 + - - +
102D ASP* 2.9 31.3 + - - +
104D ALA* 1.3 77.5 - - + +
106D GLN* 1.3 65.3 + - - +
108D PHE* 3.4 11.4 + - + +
109D VAL* 3.2 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D ASP* 2.6 21.5 + - + +
103D ASP* 3.7 10.3 - - - +
105D ARG* 1.3 70.9 - - - +
107D LEU* 1.3 53.5 + - - +
109D VAL* 3.2 18.4 + - - +
110D LEU* 2.8 56.7 + - + +
122D GLU* 3.0 23.9 - - - +
126D VAL* 4.0 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ILE* 4.6 9.2 - - + -
81D ILE* 4.0 30.1 - - + +
82D ILE* 3.8 33.4 - - + +
85D ILE* 4.8 9.2 - - + -
103D ASP 2.7 21.3 + - - +
104D ALA 3.6 6.7 - - - +
106D GLN* 1.3 73.5 - - - +
108D PHE* 1.3 57.9 + - + +
110D LEU* 3.0 7.2 + - - +
111D ALA* 2.8 33.8 + - - +
123D LEU* 4.0 18.8 - - + -
126D VAL* 3.9 11.4 - - + +
127D ILE* 4.1 11.9 - - + -
130D LEU* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D ILE* 4.5 18.2 - - + -
85D ILE* 3.6 31.9 - - + -
86D ARG* 4.0 39.5 - - + -
104D ALA* 3.0 25.4 + - + -
105D ARG* 3.6 10.8 - - + +
106D GLN 3.3 0.2 - - - -
107D LEU* 1.3 84.5 - - + +
109D VAL* 1.3 62.5 + - + +
111D ALA* 3.3 19.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ARG* 3.2 15.2 + - + +
106D GLN* 3.2 21.3 + - - +
107D LEU 3.1 0.6 - - - -
108D PHE* 1.3 79.5 - - + +
110D LEU* 1.3 65.4 + - + +
111D ALA 3.1 1.6 + - - -
112D GLY 4.2 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D GLN* 2.8 50.8 + - + +
107D LEU 3.0 3.6 + - - +
109D VAL* 1.3 72.6 - - + +
111D ALA* 1.3 64.4 + - - +
112D GLY 2.9 5.3 + - - -
113D SER* 3.2 33.0 + - - +
120D THR* 4.2 14.1 - - + +
122D GLU* 3.5 28.3 - - - +
123D LEU* 3.7 31.3 - - + +
126D VAL* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ILE* 4.3 27.7 - - + +
82D ILE* 4.5 17.9 - - + -
107D LEU 2.8 10.6 + - - +
108D PHE* 3.3 21.1 - - + +
109D VAL 3.1 1.8 - - - -
110D LEU* 1.3 75.2 - - - +
112D GLY* 1.3 56.4 + - - +
113D SER 3.4 3.8 + - - -
114D ALA 4.6 1.2 + - - -
115D GLU* 4.6 5.9 - - - +
123D LEU* 5.6 1.3 - - - -
----------------------------------------------------------
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