Contacts of the helix formed by residues 121 - 132 (chain H) in PDB entry 5FLX
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 THR 121 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6871 C 3.4 8.4 + - - -
6881 U 2.6 31.2 + - - -
101H LEU 5.0 1.3 - - - -
116H ARG* 3.2 29.1 - - - +
118H ARG* 3.2 29.1 + - - +
120H ARG* 1.3 78.0 - - - +
122H LEU* 1.3 64.2 + - - +
123H THR* 3.9 9.5 + - - +
124H ALA* 3.0 21.7 + - + +
125H VAL* 3.0 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6881 U 4.4 5.6 + - - +
6891 U 3.2 36.8 - - + +
7421 U 4.6 18.4 - - - +
100H ILE* 3.7 36.7 - - + +
101H LEU 5.7 0.2 + - - -
120H ARG 3.6 2.0 + - - -
121H THR* 1.3 76.0 + - - +
123H THR* 1.3 56.8 + - - +
125H VAL* 4.0 6.5 - - + -
126H HIS* 2.4 63.8 + - + +
181H THR* 5.9 2.2 - - + +
183H LYS* 6.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 123 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6861 U 5.7 2.0 - - - +
6871 C 4.7 14.2 + - - +
6881 U 4.3 11.8 + - - -
121H THR* 3.2 10.4 + - - -
122H LEU* 1.3 80.6 - - - +
124H ALA* 1.3 56.9 + - - +
125H VAL 3.5 0.2 + - - -
126H HIS* 3.5 12.2 - - + -
127H ASP* 2.9 44.7 - - - +
32W LYS* 6.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 124 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9131 A 5.6 1.4 + - - -
98H ARG* 4.2 0.5 + - - -
118H ARG* 3.6 27.1 - - + +
119H SER* 4.1 13.7 - - - +
121H THR* 3.0 11.0 + - + +
123H THR* 1.3 80.0 - - - +
125H VAL* 1.3 62.8 + - - +
127H ASP* 4.9 1.3 - - - +
128H ALA* 3.3 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 125 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9131 A 5.0 0.9 - - - +
98H ARG* 2.4 50.5 + - + +
99H ARG 5.3 1.3 - - - +
100H ILE* 3.7 33.2 - - + -
119H SER 3.6 11.7 - - - +
120H ARG* 3.4 16.8 - - - +
121H THR 3.0 18.0 + - - +
122H LEU* 3.0 11.8 + - + +
124H ALA* 1.3 74.8 - - - +
126H HIS* 1.3 62.6 + - + +
127H ASP 3.2 1.8 - - - -
128H ALA 3.1 2.8 + - - -
129H ILE* 2.9 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 126 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H LEU* 2.4 63.8 + - + +
123H THR* 3.5 22.4 - - + -
125H VAL* 1.3 74.7 - - + +
127H ASP* 1.3 78.3 + - - +
129H ILE* 3.3 20.2 + - + +
130H LEU* 2.9 30.3 + - + +
177H TYR* 3.7 28.0 + + + -
181H THR* 4.0 17.9 - - + +
183H LYS* 5.5 7.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H THR* 2.9 36.1 + - - +
124H ALA* 4.9 1.6 - - - +
125H VAL 3.2 0.6 - - - -
126H HIS* 1.3 92.1 + - - +
128H ALA* 1.3 60.2 + - - +
129H ILE 3.1 0.2 - - - -
130H LEU* 3.0 25.9 + - - +
131H GLU* 2.9 24.6 + - - +
142H LYS* 3.6 18.6 + - - +
54W ASP* 5.7 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98H ARG* 3.5 15.9 - - - +
124H ALA 3.3 20.3 + - - +
125H VAL 3.1 5.6 + - - +
127H ASP* 1.3 78.5 - - - +
129H ILE* 1.3 56.9 + - - +
131H GLU* 3.4 12.2 + - - +
132H ASP* 2.9 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H ILE* 4.3 17.0 - - + -
96H ALA 4.7 16.8 - - - +
98H ARG* 3.4 13.0 - - - +
100H ILE* 6.0 0.7 - - + -
125H VAL* 2.9 27.8 + - + +
126H HIS* 3.4 26.2 - - + +
127H ASP 3.1 0.2 - - - -
128H ALA* 1.3 74.8 - - - +
130H LEU* 1.3 58.6 + - - +
132H ASP* 3.1 7.6 + - - -
133H LEU* 2.9 33.3 + - + +
177H TYR* 5.7 5.6 - - + -
180H LEU* 3.9 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H HIS* 2.9 16.0 + - + +
127H ASP* 3.0 32.5 + - - +
129H ILE* 1.3 77.7 - - - +
131H GLU* 1.3 60.9 + - - +
133H LEU* 3.1 36.1 + - + +
134H VAL* 4.2 2.6 + - - +
139H ILE* 5.6 1.0 - - - +
142H LYS* 4.2 18.4 - - + +
154H ILE* 4.9 17.0 - - + -
177H TYR* 3.5 39.9 - - + +
185H VAL* 4.5 10.1 - - + -
187H PHE* 5.8 2.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H ASP 2.9 12.4 + - - +
128H ALA* 3.7 14.0 - - - +
130H LEU* 1.3 76.1 - - - +
132H ASP* 1.3 66.3 + - - +
133H LEU 3.5 0.5 + - - -
134H VAL* 3.8 15.4 + - - +
135H PHE* 4.8 1.6 - - - -
139H ILE* 4.1 44.1 - - + +
142H LYS* 4.6 5.9 - - - +
20N ARG* 5.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H LEU* 4.3 16.4 - - - +
94H PHE 3.4 22.8 + - - +
95H ILE* 5.2 1.1 - - - -
96H ALA* 4.0 26.8 - - - +
98H ARG* 4.0 6.6 + - - -
128H ALA* 2.9 24.7 + - - +
129H ILE* 3.1 9.9 + - - +
131H GLU* 1.3 81.7 - - - +
133H LEU* 1.3 66.1 + - - +
135H PHE* 3.8 24.8 + - + +
----------------------------------------------------------
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