Contacts of the helix formed by residues 122 - 132 (chain C) in PDB entry 5HEN
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 ASP 122 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C PHE* 3.5 10.5 - - - +
101C GLN* 3.5 23.7 - - - +
102C PRO* 3.5 28.4 - - + +
103C VAL* 5.3 0.7 - - + +
121C MET* 1.3 81.1 - - - +
123C MET* 1.3 63.0 + - - +
124C GLY* 2.8 25.8 + - - -
125C THR* 2.6 28.6 + - - -
126C ILE* 3.2 24.3 + - - +
148C MET* 3.8 12.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C MET* 3.5 14.9 - - + +
90C LEU* 3.3 36.3 - - + -
91C TRP* 3.7 15.7 - - + +
96C ALA* 4.4 18.6 - - - -
99C PHE* 2.8 34.2 + - + +
100C LEU* 4.5 4.3 - - - -
122C ASP* 1.3 72.3 - - - +
124C GLY* 1.3 51.4 + - - +
126C ILE* 4.3 6.5 - - - -
127C LYS* 2.7 37.1 + - - +
145C PHE* 3.5 23.1 - - + -
148C MET* 3.4 23.3 - - + -
149C PHE* 5.8 0.4 - - + -
169C LEU* 4.8 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TRP* 3.9 13.0 - - - -
100C LEU 3.2 23.4 + - - -
101C GLN* 5.3 0.2 - - - -
122C ASP* 2.8 10.6 + - - -
123C MET* 1.3 70.9 - - - +
125C THR* 1.3 57.0 + - - +
127C LYS* 3.2 3.1 + - - +
128C ARG* 2.8 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PRO* 4.4 6.9 - - - +
121C MET* 3.7 18.8 - - + -
122C ASP* 2.6 32.1 + - - -
124C GLY* 1.3 73.1 - - - +
126C ILE* 1.3 65.8 + - - +
128C ARG* 3.3 22.4 + - - +
129C ARG* 2.9 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C MET* 3.5 21.3 - - + -
121C MET* 3.9 13.7 - - + -
122C ASP 3.2 20.2 + - - +
123C MET* 3.7 3.1 - - - +
125C THR* 1.3 76.3 - - - +
127C LYS* 1.3 57.8 + - - +
129C ARG* 3.1 4.2 + - - +
130C LEU* 2.8 38.1 + - + +
135C TYR* 3.7 24.5 - - - +
141C CYS* 4.1 5.8 - - - +
144C ASP* 3.8 7.2 - - + +
145C PHE* 3.7 58.6 - - + +
148C MET* 4.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C HIS* 4.5 11.4 + - - +
87C MET* 4.0 22.9 - - + -
91C TRP* 3.7 45.8 - - + +
123C MET 2.7 21.3 + - - +
124C GLY* 3.6 4.3 - - - +
126C ILE* 1.3 73.6 - - - +
128C ARG* 1.3 63.3 + - - +
130C LEU* 3.2 6.8 + - - +
131C GLU* 3.0 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C PRO* 6.1 2.6 - - - +
124C GLY* 2.8 24.5 + - - +
125C THR* 3.6 32.5 + - - +
126C ILE 3.2 0.2 - - - -
127C LYS* 1.3 77.1 - - - +
129C ARG* 1.3 57.6 + - + +
131C GLU* 3.3 16.2 + - - +
132C ASN* 3.0 52.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C MET* 3.7 10.7 - - - +
125C THR* 2.9 37.4 + - + +
126C ILE 3.1 6.9 + - - +
128C ARG* 1.3 78.2 - - + +
130C LEU* 1.3 62.2 + - - +
132C ASN* 3.4 1.7 + - - +
133C ASN* 3.2 4.7 + - - -
134C TYR* 3.1 79.1 + - + +
135C TYR* 3.3 31.0 + - + -
144C ASP* 2.7 34.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LEU* 3.7 36.8 - - + +
82C LEU* 4.2 6.5 - - + +
83C HIS* 3.9 40.3 + - + +
87C MET* 4.3 12.1 - - + -
126C ILE* 2.8 33.7 + - + +
127C LYS* 3.7 6.3 - - - +
129C ARG* 1.3 78.2 - - - +
131C GLU* 1.3 61.1 - - - +
132C ASN 3.5 0.5 + - - -
133C ASN* 3.6 14.1 + - - +
135C TYR* 3.8 22.2 - - + -
141C CYS* 4.1 11.7 - - - -
145C PHE* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C HIS* 3.4 24.0 + - + +
127C LYS* 3.0 46.4 + - - +
128C ARG* 3.4 22.6 - - - +
130C LEU* 1.3 79.4 - - - +
132C ASN* 1.3 66.6 + - - +
133C ASN* 3.5 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C ARG* 3.0 36.7 + - - +
129C ARG* 3.4 2.9 + - - +
130C LEU 3.3 0.2 - - - -
131C GLU* 1.3 86.9 - - - +
133C ASN* 1.3 74.8 + - - +
134C TYR* 3.2 5.8 + - + +
----------------------------------------------------------
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