Contacts of the helix formed by residues 144 - 156 (chain C) 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 SER 144 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASP 5.0 1.0 + - - +
81C ALA* 3.3 22.2 + - - +
142C CYS 3.9 0.6 + - - -
143C SER* 1.3 70.8 + - - +
145C ILE* 1.3 63.9 + - - +
146C SER* 3.0 6.5 - - - -
147C ASP* 3.1 25.8 + - - +
148C TYR* 4.1 8.2 - - - -
166C LYS* 3.9 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C TYR 3.6 12.6 - - - +
81C ALA* 3.8 20.6 - - - +
83C PHE* 4.7 8.1 - - - -
86C HIS* 3.7 30.3 - - + +
121C GLY* 3.9 20.0 - - - -
122C THR* 4.2 5.8 - - + +
141C GLU* 3.6 28.9 - - + -
143C SER* 3.0 9.6 + - - -
144C SER* 1.3 80.2 + - - +
146C SER* 1.3 66.8 + - - +
148C TYR* 2.9 25.5 + - + +
149C SER* 3.0 10.2 + - - -
250D ILE* 4.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C GLU* 3.9 20.4 - - - -
143C SER 2.7 23.1 + - - -
144C SER 3.8 0.2 - - - -
145C ILE* 1.3 80.7 - - - +
147C ASP* 1.3 62.8 + - - -
149C SER* 2.8 27.1 + - - -
150C GLU* 3.1 14.3 + - - +
164C ILE* 4.1 11.9 - - - -
166C LYS* 3.0 34.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C SER* 3.1 19.5 + - - +
146C SER* 1.3 82.1 + - - +
148C TYR* 1.3 68.4 + - + +
150C GLU* 3.5 16.0 + - - +
151C LYS* 3.4 31.1 + - - +
166C LYS* 3.1 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ALA 5.5 4.7 - - - -
144C SER 4.1 14.1 - - - -
145C ILE* 2.9 20.6 + - + +
147C ASP* 1.3 79.6 - - + +
149C SER* 1.3 67.1 + - - +
150C GLU 3.1 0.2 - - - -
151C LYS* 3.2 20.3 + - - +
152C ILE* 2.8 30.0 + - + +
249D CYS* 3.6 39.4 - - + -
250D ILE* 4.0 27.1 - - + -
253D VAL* 3.1 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C SER* 3.9 1.1 + - - -
121C GLY 3.2 24.3 + - - -
122C THR* 3.3 22.8 - - - +
123C GLY* 3.9 6.5 - - - -
145C ILE 3.0 5.6 + - - -
146C SER* 2.8 25.2 + - - -
148C TYR* 1.3 74.7 - - - +
150C GLU* 1.3 55.5 + - - +
152C ILE* 3.3 2.6 + - - +
153C ILE* 2.8 41.0 + - - +
164C ILE* 3.6 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C SER* 3.1 14.9 + - - +
147C ASP* 3.7 16.9 - - - +
148C TYR 3.1 0.4 - - - -
149C SER* 1.3 76.7 - - - +
151C LYS* 1.3 58.1 + - + +
153C ILE* 3.4 7.0 + - - +
154C LYS* 3.0 30.5 + - - +
159C ASP* 5.7 0.5 - - - +
164C ILE* 3.9 36.6 + - + +
166C LYS* 6.1 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ASP* 3.4 19.0 + - - +
148C TYR* 3.2 27.2 + - + +
150C GLU* 1.3 78.3 - - + +
152C ILE* 1.3 57.5 + - - +
154C LYS* 3.4 6.1 + - - +
155C ALA* 2.9 29.7 + - - +
249D CYS* 3.9 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C THR* 3.7 20.0 - - + +
127C MET* 3.8 22.2 - - + -
148C TYR* 2.8 29.2 + - + +
149C SER* 3.5 4.7 - - - +
151C LYS* 1.3 74.6 - - - +
153C ILE* 1.3 64.6 + - + +
155C ALA* 3.1 12.4 + - - +
156C ASN* 2.5 38.7 + - - +
246D ASP 3.6 8.7 - - - +
247D MET* 3.9 28.9 - - + -
249D CYS* 3.6 16.2 - - - -
250D ILE* 3.9 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C GLY* 4.8 8.7 - - - +
127C MET* 4.1 26.9 - - + -
149C SER* 2.8 29.2 + - - +
150C GLU* 3.8 4.7 - - - +
152C ILE* 1.3 72.6 - - + +
154C LYS* 1.3 65.1 + - - +
156C ASN* 3.0 12.5 + - - +
157C HIS 3.2 8.7 + - - -
158C LEU* 3.2 40.9 + - + +
159C ASP* 3.6 10.3 - - + +
162C ILE* 3.6 33.2 - - + +
164C ILE* 3.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C GLU 3.0 18.9 + - - +
151C LYS* 3.7 6.3 - - - +
153C ILE* 1.3 77.1 - - - +
155C ALA* 1.3 62.1 + - - +
157C HIS* 3.0 20.4 + - - -
159C ASP* 3.5 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LYS 2.9 15.0 + - - +
152C ILE* 3.1 13.0 + - - +
154C LYS* 1.3 76.9 - - - +
156C ASN* 1.3 60.8 + - - +
157C HIS* 3.5 15.6 + - - -
246D ASP* 4.1 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C MET* 3.9 9.5 - - - -
131C LYS* 5.3 4.5 + - - -
152C ILE* 2.5 35.0 + - - +
153C ILE 3.0 6.9 + - - +
155C ALA* 1.3 77.9 - - - +
157C HIS* 1.3 75.0 + - - +
158C LEU* 3.3 14.3 + - + +
244D GLY 4.5 1.4 - - - +
245D PHE* 3.3 26.6 - - + +
246D ASP* 2.7 44.9 + - - +
----------------------------------------------------------
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