Contacts of the helix formed by residues 122 - 132 (chain D) in PDB entry 3SWD
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 VAL 122 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D ARG* 5.3 1.1 - - - +
94D ILE* 4.6 16.8 - - + -
111D LEU* 3.6 30.1 - - + -
112D PRO* 4.6 20.4 - - + -
120D ARG 4.1 7.6 - - - +
121D PRO* 1.3 77.9 - - - +
123D ASP* 1.3 63.8 + - - +
124D LEU 3.2 2.9 - - - -
125D HIS* 2.9 34.1 + - + +
126D ILE* 3.4 22.4 + - + +
501D EPZ 3.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D PRO* 3.7 16.9 - - + +
122D VAL* 1.3 76.0 - - - +
124D LEU* 1.3 71.9 + - - +
126D ILE* 3.5 9.2 + - - +
127D SER* 2.9 33.3 + - - -
160D LYS* 5.6 3.5 - - - +
501D EPZ 2.9 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ASP* 1.3 85.0 - - - +
125D HIS* 1.3 59.7 + - - +
127D SER* 4.1 6.6 - - - -
128D GLY* 3.0 25.1 + - - -
158D MET* 3.8 19.6 - - + +
159D ASP* 4.1 33.9 - - + +
160D LYS* 3.7 38.4 - - + +
162D SER* 3.8 20.2 - - - -
165D ALA* 3.7 14.4 - - + +
169D ILE* 4.3 1.0 - - - +
501D EPZ 2.9 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ILE* 4.2 27.2 - - + +
95D TRP* 4.2 5.8 - - - -
97D LEU* 6.0 3.4 - - + -
122D VAL* 2.9 30.8 + - + +
124D LEU* 1.3 74.2 - - - +
126D ILE* 1.3 67.3 + - + +
128D GLY* 3.7 0.9 - - - -
129D LEU* 3.2 28.7 + - + +
164D GLY* 3.2 32.3 - - - -
165D ALA* 3.4 18.2 + - + -
168D THR* 2.8 32.5 + - + +
169D ILE* 5.1 0.4 - - - +
501D EPZ 3.8 21.4 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D ILE* 6.6 0.2 - - + -
97D LEU* 5.6 3.3 - - + +
111D LEU* 5.2 5.4 - - + -
122D VAL* 3.4 24.8 + - + +
123D ASP* 3.8 8.7 - - - +
125D HIS* 1.3 75.6 - - + +
127D SER* 1.3 64.0 + - - +
129D LEU* 3.1 4.2 + - - -
130D GLU* 3.0 36.1 + - - +
136D ILE* 3.6 35.5 - - + +
143D VAL* 4.7 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D ASP* 2.9 20.8 + - - -
124D LEU* 4.1 8.5 - - - +
126D ILE* 1.3 77.1 - - - +
128D GLY* 1.3 62.6 + - - +
130D GLU* 3.3 14.3 + - - +
131D GLN* 3.1 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU 3.0 12.6 + - - -
125D HIS 3.7 0.9 - - - -
127D SER* 1.3 77.1 - - - +
129D LEU* 1.3 62.6 + - - +
131D GLN* 3.3 5.5 + - - -
132D LEU* 3.2 24.5 + - - +
156D ILE* 3.7 13.0 - - - +
158D MET* 5.7 0.2 - - - -
169D ILE* 3.7 33.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D LEU* 3.8 35.9 - - + +
98D GLY* 4.4 8.3 - - - +
101D VAL* 5.2 6.1 - - + -
125D HIS 3.2 15.8 + - - +
126D ILE 3.1 7.4 + - - +
128D GLY* 1.3 75.7 - - - +
130D GLU* 1.3 64.8 + - - +
132D LEU* 2.9 20.8 + - + +
134D ALA* 3.2 24.4 + - + +
136D ILE* 3.9 14.1 - - + -
145D ALA* 5.0 5.2 - - + -
151D LEU* 4.9 6.3 - - + -
168D THR* 4.1 23.8 - - + +
169D ILE* 4.8 0.6 - - - +
172D ALA* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D ILE* 3.0 29.5 + - - +
127D SER* 3.3 14.8 + - - +
129D LEU* 1.3 73.9 - - - +
131D GLN* 1.3 57.7 + - + +
133D GLY* 2.8 22.0 + - - -
134D ALA 3.5 21.5 + - - +
135D THR* 5.6 0.2 - - - -
136D ILE* 4.0 30.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D SER* 3.1 32.3 + - - +
128D GLY* 3.7 7.8 - - - +
129D LEU 3.2 0.4 - - - -
130D GLU* 1.3 77.7 - - + +
132D LEU* 1.3 58.7 + - - +
133D GLY* 3.0 3.2 + - - -
152D LYS* 4.2 1.6 - - - +
154D ALA* 3.6 17.3 - - + +
155D HIS 4.0 5.5 - - - +
156D ILE* 3.6 43.5 - - + +
157D VAL 4.8 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D GLY 3.2 12.2 + - - +
129D LEU* 2.9 15.4 + - + +
131D GLN* 1.3 75.8 - - - +
133D GLY* 1.3 58.2 + - - +
134D ALA 3.5 1.6 - - - -
151D LEU* 3.3 23.4 - - + +
152D LYS* 2.8 47.5 + - - +
154D ALA* 4.0 4.9 - - + +
156D ILE* 3.9 17.9 - - + -
169D ILE* 4.0 14.8 - - + +
172D ALA* 4.0 27.8 - - + -
173D ALA* 4.0 15.7 - - + +
176D ALA* 5.4 0.4 - - + -
180D THR* 3.8 23.3 - - + +
----------------------------------------------------------
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