Contacts of the helix formed by residues 103 - 117 (chain D) in PDB entry 4RBO
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 SER 103 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D VAL 4.2 0.2 + - - -
102D PHE* 1.3 79.4 - - - +
104D SER* 1.3 60.3 + - - +
105D THR* 2.7 27.5 + - - -
106D GLN* 3.3 15.4 + - - +
107D LEU* 3.0 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D SER* 1.3 71.2 - - - +
105D THR* 1.3 62.3 + - - +
107D LEU* 4.2 11.2 - - - +
108D CYS* 2.8 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D SER* 2.7 25.9 + - - +
104D SER* 1.3 80.0 - - - +
106D GLN* 1.3 63.5 + - - +
108D CYS* 3.8 4.5 - - - +
109D VAL* 3.7 17.7 + - - +
----------------------------------------------------------
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 PHE* 3.4 25.7 - - + +
103D SER* 3.3 18.7 + - - +
104D SER 3.2 0.4 - - - -
105D THR* 1.3 83.2 + - - +
107D LEU* 1.3 66.4 + - - +
108D CYS 3.0 1.8 - - - -
109D VAL* 3.0 6.7 - - - +
110D LEU* 2.9 28.7 + - + +
132D LEU* 2.5 62.4 + - + +
134D LEU* 3.4 22.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
101D VAL* 6.5 1.1 - - + -
102D PHE* 5.0 12.9 - - + +
103D SER 3.0 16.8 + - - +
104D SER* 3.9 9.6 - - - +
106D GLN* 1.3 76.1 - - - +
108D CYS* 1.3 57.5 + - - +
110D LEU* 3.5 7.3 - - - +
111D ASN* 2.9 54.4 + - - +
142D TRP* 3.8 28.9 - - + +
146D GLN* 5.3 1.6 - - - +
5F A 4.9 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D SER* 2.8 21.5 + - - +
105D THR* 3.8 6.7 - - - +
107D LEU* 1.3 73.5 - - - +
109D VAL* 1.3 64.2 + - - +
111D ASN* 3.0 9.7 + - - +
112D ASP* 2.8 31.6 + - - +
----------------------------------------------------------
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 THR 3.7 11.4 + - - +
106D GLN* 3.0 17.3 - - - +
108D CYS* 1.3 78.8 - - - +
110D LEU* 1.3 57.4 + - + +
112D ASP* 3.5 9.7 - - + +
113D ARG* 2.9 31.0 + - + +
128D LEU* 4.6 15.0 - - + -
131D ILE* 5.6 4.5 - - + -
132D LEU* 3.7 31.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
102D PHE* 4.9 12.6 - - + -
106D GLN* 2.9 29.9 + - + +
107D LEU* 3.5 8.3 - - - +
109D VAL* 1.3 80.6 - - + +
111D ASN* 1.3 58.2 + - - +
113D ARG* 3.2 5.3 + - - +
114D PHE* 2.8 28.1 + - - +
128D LEU* 4.3 21.8 - - + -
132D LEU* 3.3 27.8 - - + -
134D LEU* 5.3 6.5 - - + -
139D VAL* 5.4 9.0 - - + -
142D TRP* 3.4 53.6 - - + +
143D PHE* 4.7 1.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D LEU* 2.9 44.0 + - - +
108D CYS* 3.5 5.4 - - - +
110D LEU* 1.3 73.2 - - - +
112D ASP* 1.3 57.5 - - - +
114D PHE* 3.1 6.7 + - + +
115D GLN* 2.8 31.0 + - - +
142D TRP* 3.1 24.1 - - - -
146D GLN* 4.0 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D CYS* 2.8 16.4 + - - +
109D VAL* 3.5 14.5 - - + +
111D ASN* 1.3 78.6 - - - +
113D ARG* 1.3 62.2 + - - +
115D GLN* 3.4 21.3 + - - +
116D ARG* 2.3 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109D VAL* 2.9 18.5 + - + +
110D LEU* 3.6 5.4 - - - +
112D ASP* 1.3 77.0 + - - +
114D PHE* 1.3 64.2 + - - +
116D ARG* 3.3 37.8 + - - +
117D GLN* 3.0 41.5 + - - +
120D LEU* 3.1 29.5 - - + +
124D GLN* 3.7 25.3 + - - +
127D GLU* 4.8 9.9 + - - +
128D LEU* 4.6 29.3 - - + +
143D PHE* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LEU 2.8 14.8 + - - +
111D ASN* 3.4 11.2 - - - +
113D ARG* 1.3 77.3 - - - +
115D GLN* 1.3 67.7 + - - +
116D ARG 3.1 1.0 + - - -
117D GLN 3.3 19.6 + - - +
118D LYS* 3.5 40.3 - - + +
142D TRP* 3.9 12.8 - + + -
143D PHE* 4.1 18.3 - + + -
146D GLN* 3.5 54.5 - - + -
147D ARG* 4.1 9.2 - - + -
150D SER* 4.1 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ASN 2.8 19.5 + - - +
112D ASP* 3.7 13.8 - - - +
113D ARG 3.3 0.4 - - - -
114D PHE* 1.3 79.5 - - - +
116D ARG* 1.3 57.8 + - + +
118D LYS* 2.9 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LYS* 3.9 25.6 + - - +
5B C 5.8 2.9 - - - -
112D ASP* 2.3 44.5 + - - +
113D ARG* 3.5 37.0 - - - +
115D GLN* 1.3 79.8 - - + +
117D GLN* 1.3 64.7 + - + +
118D LYS* 5.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TYR* 3.0 17.0 + - - -
151A LYS* 4.1 24.6 + - - +
4B C 3.5 8.5 + - - +
113D ARG* 3.0 38.9 + - - +
114D PHE* 3.3 11.9 + - - +
116D ARG* 1.3 87.0 + - + +
118D LYS* 1.3 60.3 + - - +
119D TYR 2.9 27.8 + - - +
120D LEU* 3.5 22.5 - - + +
124D GLN* 3.1 19.9 + - - -
143D PHE* 4.0 0.9 - - - -
----------------------------------------------------------
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