Contacts of the helix formed by residues 123 - 132 (chain G) in PDB entry 5DST
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 123 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G SER* 3.0 14.9 + - - -
121G GLY 3.0 6.5 - - - -
122G THR* 1.3 78.8 + - - +
124G ILE* 1.3 65.1 + - - +
125G LEU 3.2 3.4 + - - -
126G SER* 3.2 12.2 + - - -
127G MET* 2.9 30.2 + - - +
149G SER* 4.2 7.4 - - - -
153G ILE* 4.8 8.9 - - - +
164G ILE* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G LEU* 3.7 22.9 - - + -
95G ARG* 4.7 2.7 - - - +
96G THR* 4.4 3.1 - - + -
122G THR* 3.4 7.1 - - - +
123G GLY* 1.3 76.4 - - - +
125G LEU* 1.3 72.2 + - + +
127G MET* 3.3 9.4 + - + +
128G PHE* 3.0 47.8 + - + -
401G SAH 3.5 33.9 - - - +
242H VAL* 4.0 13.0 - - + +
243H TYR* 4.3 3.6 - - + -
245H PHE* 3.7 30.3 - - + -
247H MET* 4.2 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ARG* 5.6 2.7 - - - +
96G THR* 5.6 1.6 - - + -
99G TYR* 3.6 53.4 - - + -
103G MET* 3.8 3.1 - - + +
117G ASP* 3.4 18.7 + - - +
120G SER 4.9 0.4 + - - -
123G GLY 3.3 0.6 - - - -
124G ILE* 1.3 85.8 - - + +
126G SER* 1.3 58.4 + - - +
128G PHE* 3.1 22.7 + - + +
129G ALA 3.0 22.9 + - - -
183G ILE* 3.7 16.6 - - + +
184G SER* 4.3 4.9 - - - +
185G GLU* 4.0 13.9 - - + +
401G SAH 3.6 33.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ASP* 2.7 35.7 + - - +
120G SER* 4.5 2.1 - - - -
123G GLY* 3.2 10.5 + - - -
125G LEU* 1.3 78.5 - - - +
127G MET* 1.3 57.1 + - - +
129G ALA* 3.2 5.9 + - - +
130G ALA* 2.9 28.1 + - - +
137G VAL* 3.6 23.6 - - - +
139G GLY* 4.3 6.8 - - - -
153G ILE* 5.4 0.2 - - - -
162G ILE* 3.7 19.7 - - - +
164G ILE* 5.3 1.1 - - - -
183G ILE* 4.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G GLY* 2.9 15.4 + - - +
124G ILE* 3.6 22.0 - - - +
125G LEU 3.2 0.2 - - - -
126G SER* 1.3 73.8 - - - +
128G PHE* 1.3 63.9 + - - +
130G ALA* 3.4 2.3 + - - +
131G LYS* 3.0 27.4 + - - +
152G ILE* 3.8 22.2 - - + -
153G ILE* 4.0 11.9 - - + -
156G ASN* 3.8 17.5 - - - -
158G LEU* 3.8 9.8 - - + +
162G ILE* 3.8 20.4 - - + -
245H PHE* 3.5 55.9 - - + -
247H MET* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G THR* 3.8 27.4 - - + -
99G TYR 4.4 1.1 - - - -
100G ARG* 3.5 52.7 - - + -
103G MET* 3.8 12.6 - - + -
104G TYR* 3.5 26.3 - - + -
124G ILE* 3.0 39.4 + - + -
125G LEU* 3.3 25.8 - - + +
127G MET* 1.3 75.5 - - - +
129G ALA* 1.3 64.5 + - - +
131G LYS 3.1 1.7 + - - -
132G ALA* 2.9 20.8 + - - +
243H TYR* 4.0 10.8 - - + -
245H PHE* 3.7 20.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G MET* 3.7 16.5 - - - -
110G PHE* 4.5 4.5 - - + +
115G VAL* 4.1 16.6 - - + -
125G LEU 3.0 12.9 + - - +
126G SER* 3.2 9.4 + - - +
128G PHE* 1.3 74.9 - - - +
130G ALA* 1.3 65.9 + - - +
132G ALA* 2.9 20.4 + - - +
133G GLY 3.3 4.5 + - - -
134G ALA* 3.4 9.6 + - - +
137G VAL* 4.1 13.0 - - + -
183G ILE* 4.1 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G SER 2.9 16.3 + - - +
127G MET 3.6 5.6 - - - +
129G ALA* 1.3 76.2 - - - +
131G LYS* 1.3 58.0 + - - +
133G GLY* 2.9 21.0 + - - -
134G ALA 3.8 4.9 + - - +
137G VAL* 4.1 3.9 - - + +
158G LEU* 4.2 17.5 - - + -
161G ILE* 3.8 34.8 - - + +
162G ILE* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G TYR* 3.6 28.8 - - + +
107G LYS* 4.1 13.0 - - - -
127G MET 3.0 19.1 + - - +
128G PHE 3.7 2.2 - - - +
130G ALA* 1.3 76.2 - - - +
132G ALA* 1.3 58.3 + - - +
133G GLY* 3.2 1.8 + - - -
156G ASN 5.4 4.3 + - - -
158G LEU* 4.6 20.9 - - + +
245H PHE* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G MET* 4.0 29.4 - - + +
104G TYR* 4.6 2.6 - - + +
107G LYS* 3.4 32.7 - - + +
110G PHE* 3.6 28.3 - - + +
111G LYS* 4.1 1.2 + - - +
128G PHE 2.9 10.6 + - - +
129G ALA 2.9 12.7 + - - +
131G LYS* 1.3 78.1 - - - +
133G GLY* 1.3 55.8 + - - +
134G ALA 3.7 0.2 - - - -
----------------------------------------------------------
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