Contacts of the helix formed by residues 129 - 139 (chain A) in PDB entry 5TSQ
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 LEU 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PRO* 3.5 36.8 - - + -
127A GLY 4.3 5.8 - - - +
128A GLY* 1.3 72.3 - - - -
130A THR* 1.3 63.7 + - - +
131A ASN 3.4 2.7 - - - -
132A ILE* 3.1 12.3 + - + +
133A ALA* 2.9 22.3 + - - +
151A LEU* 4.2 26.0 - - + -
168A ASN 4.4 3.3 + - - +
169A ILE* 4.0 17.5 - - + -
172A ASP* 4.7 2.8 + - - +
175A ALA* 3.5 16.7 - - + +
176A ALA* 3.7 29.6 - - + +
179A VAL* 4.0 19.7 - - + -
180A PHE* 4.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.8 18.7 - - - +
37A VAL* 5.1 2.6 + - - +
67A CYS* 3.7 16.8 - - + -
69A LYS 3.5 22.3 + - - +
70A PRO* 4.0 4.5 - - - +
71A LEU* 3.9 16.8 - - + +
128A GLY* 3.2 4.8 + - - -
129A LEU* 1.3 74.6 + - - +
131A ASN* 1.3 59.1 + - - +
133A ALA* 3.5 1.4 + - - +
134A MET* 2.9 34.5 + - - +
172A ASP* 2.7 28.4 + - - +
175A ALA* 3.6 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP* 2.9 30.7 + - - +
35A THR 2.9 25.1 + - - -
36A VAL* 3.6 11.6 - - - +
66A GLY* 3.5 4.9 - - - -
67A CYS* 2.8 33.7 + - - +
105A ALA* 3.9 12.1 - - - +
106A VAL* 3.7 14.5 - - + +
109A ILE* 4.2 11.1 - - + +
128A GLY 4.8 0.4 + - - -
129A LEU 3.4 0.6 - - - -
130A THR* 1.3 80.6 - - - +
132A ILE* 1.3 58.6 + - - +
134A MET* 4.5 0.2 - - - -
135A ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 6.3 0.2 - - + -
8A ASP* 4.0 31.6 - - + +
109A ILE* 4.3 12.6 - - + -
123A LEU* 4.1 25.4 - - + -
125A PRO* 3.8 30.5 - - + -
129A LEU* 3.1 13.9 + - + +
131A ASN* 1.3 77.4 - - - +
133A ALA* 1.3 58.9 + - - +
135A ALA* 3.4 6.8 + - - +
136A ALA* 3.0 28.2 + - - +
142A ILE* 6.2 0.2 - - + -
149A VAL* 5.3 2.0 - - + -
179A VAL* 3.8 18.6 - - + -
184A TRP* 3.8 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 4.3 3.8 - - + -
129A LEU 2.9 15.7 + - - +
130A THR 3.8 2.2 - - - +
132A ILE* 1.3 74.5 - - - +
134A MET* 1.3 65.4 + - - +
136A ALA* 3.3 3.5 + - - +
137A ARG* 3.0 28.7 + - - +
175A ALA* 3.6 34.8 - - + +
178A ILE* 3.8 26.6 - - + +
179A VAL* 4.0 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A CYS* 3.9 20.4 - - - -
71A LEU* 3.6 28.0 - - + -
104A HIS* 6.2 0.9 - - + -
106A VAL* 3.8 19.1 - - + -
130A THR 2.9 22.1 + - - +
131A ASN 3.8 3.6 - - - +
133A ALA* 1.3 75.6 - - - +
135A ALA* 1.3 59.4 + - - +
137A ARG* 3.3 5.2 + - - +
138A LEU* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 3.8 16.3 - - + +
109A ILE* 4.0 16.6 - - + -
110A ILE* 3.9 18.6 - - + +
131A ASN 2.9 17.9 + - - +
132A ILE* 3.7 4.9 - - - +
134A MET* 1.3 78.3 - - - +
136A ALA* 1.3 57.1 + - - +
139A GLU* 2.9 31.2 + - - +
142A ILE* 3.7 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ILE 3.0 17.2 + - - +
133A ALA* 3.3 7.6 + - - +
135A ALA* 1.3 77.1 - - - +
137A ARG* 1.3 63.1 + - - +
140A PRO* 3.2 29.1 - - - +
142A ILE* 3.7 11.8 - - - +
143A VAL* 4.1 13.4 - - + +
178A ILE* 4.7 10.1 - - + -
182A GLU* 4.7 4.5 - - + -
184A TRP* 4.0 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ALA 3.0 19.8 + - - +
134A MET* 4.0 4.7 - - - +
136A ALA* 1.3 79.0 + - - +
138A LEU* 1.3 63.1 + - - +
140A PRO* 3.8 12.8 - - - +
178A ILE* 3.7 46.3 + - + +
181A ASN* 6.2 1.6 - - - +
182A GLU* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 4.1 13.2 - - + -
107A HIS* 4.1 20.2 - - + +
110A ILE* 3.7 21.8 - - + -
134A MET* 2.9 23.1 + - + +
135A ALA 4.0 1.8 - - - +
137A ARG* 1.3 76.9 - - - +
139A GLU* 1.3 60.6 + - + +
140A PRO* 3.7 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 3.7 38.8 - - + +
114A MET* 4.1 9.4 - - + +
135A ALA 2.9 7.5 + - - +
136A ALA 3.5 2.4 - - - +
138A LEU* 1.3 79.3 - - + +
140A PRO* 1.3 68.6 - - - +
141A ARG* 2.8 66.6 + - - +
142A ILE* 3.0 30.8 + - + +
----------------------------------------------------------
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