Contacts of the helix formed by residues 126 - 135 (chain B) in PDB entry 3EU9
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 THR 126 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B HIS* 3.7 2.0 - - - -
117B ASP* 3.2 39.8 + - - +
118B GLN 3.5 2.2 - - - -
119B LEU* 3.5 17.3 - - + -
125B SER* 1.3 76.7 - - - +
127B PRO* 1.3 75.8 - - - +
128B LEU* 3.3 9.6 + - - +
129B HIS* 3.0 40.2 + - + +
130B TRP* 3.2 12.6 + - - -
149B ASP 5.5 1.0 + - - -
152B LEU* 3.9 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 4.6 0.2 - - - +
94B LEU* 3.7 42.6 - - + +
95B HIS* 3.7 24.2 - - + +
98B ALA* 3.4 14.3 - - + +
115B ILE 4.8 1.6 - - - +
116B VAL 3.1 29.2 - - - +
118B GLN 3.5 11.9 - - - +
126B THR* 1.3 85.0 - - - +
128B LEU* 1.3 56.0 + - - +
130B TRP* 3.2 5.6 + - + +
131B ALA 3.0 23.2 + - - -
143B LEU* 3.8 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL 5.1 0.6 + - - -
117B ASP* 4.8 1.8 - - - +
126B THR* 3.1 9.1 + - - +
127B PRO* 1.3 77.5 - - - +
129B HIS* 1.3 55.4 + - - +
131B ALA 3.2 0.3 + - - -
132B THR* 2.8 40.9 + - - +
140B VAL* 3.7 45.3 - - + +
143B LEU* 3.4 18.5 - - + +
144B MET* 4.0 6.7 - - + -
148B ALA* 3.7 25.4 - - + -
149B ASP 4.0 3.6 - - - +
150B PRO* 3.7 39.9 - - + -
160B CYS* 3.6 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 5.3 0.2 - - + -
125B SER* 3.7 12.0 - - - -
126B THR* 3.0 36.2 + - + +
128B LEU* 1.3 76.5 - - + +
130B TRP* 1.3 59.3 + - + +
132B THR* 3.4 4.0 + - - -
133B ARG* 3.0 35.0 + - - +
149B ASP 5.2 1.1 + - - -
152B LEU* 3.2 31.2 + - + +
153B ILE 3.5 9.0 - - - -
154B ASP* 3.4 38.7 + - + +
158B CYS 4.2 2.2 + - - -
160B CYS* 3.6 23.5 + - - -
163B LEU* 3.8 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ASP 5.6 0.2 - - - -
55A ASP* 3.5 35.0 - - + -
57A SER* 5.9 0.6 + - - -
91B VAL* 3.6 26.9 - - + -
95B HIS* 3.4 40.1 - + + +
96B TRP* 3.9 30.5 - + - -
99B ILE* 3.7 37.5 - - + +
120B GLY 4.6 2.0 + - - -
121B GLY* 4.7 5.4 - - - -
123B LEU* 6.1 0.8 - - - +
125B SER* 3.7 23.4 + - - -
126B THR 3.2 13.1 + - - +
127B PRO* 3.4 10.8 - - + +
128B LEU 3.1 0.4 - - - -
129B HIS* 1.3 78.5 - - - +
131B ALA* 1.3 64.6 + - - +
133B ARG* 3.3 17.0 + - - +
134B GLN* 3.2 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 4.1 10.7 - - + +
99B ILE* 4.8 0.9 - - - +
127B PRO 3.0 12.7 + - - +
128B LEU 3.2 6.9 + - - +
130B TRP* 1.3 77.0 - - - +
132B THR* 1.3 63.2 + - - +
134B GLN* 3.3 3.5 + - - +
135B GLY 3.1 17.2 + - - -
136B HIS* 3.1 13.5 + - + +
139B MET* 3.5 36.8 - - + -
140B VAL* 4.1 11.9 - - + -
143B LEU* 4.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LEU* 2.8 25.8 + - - +
129B HIS* 3.6 5.8 - - - -
131B ALA* 1.3 77.6 - - - +
133B ARG* 1.3 63.0 + - - +
135B GLY* 3.1 4.7 + - - -
140B VAL* 3.8 19.1 - - - +
160B CYS* 3.3 46.7 - - + +
163B LEU* 3.9 5.6 - - + -
164B ALA* 3.6 21.2 - - + +
169B HIS* 3.1 20.8 - - - -
172B ILE* 3.9 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER* 5.2 9.5 - - - -
99B ILE* 6.3 1.3 - - + -
123B LEU* 3.4 22.5 - - - +
125B SER* 5.0 6.7 + - - -
129B HIS* 3.0 21.5 + - - +
130B TRP* 3.6 17.5 - - - +
132B THR* 1.3 77.1 - - - +
134B GLN* 1.3 58.0 + - + +
154B ASP* 4.3 4.6 + - - -
156B GLU* 2.6 32.1 + - - -
163B LEU* 3.9 27.0 - - + +
166B GLN* 4.9 2.4 - - - +
167B PHE* 3.1 57.5 - - + -
169B HIS* 2.8 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A HIS* 2.9 34.0 + - - +
71A GLU* 5.3 9.7 - - - +
99B ILE* 3.3 35.7 - - + +
130B TRP 3.2 8.4 + - - +
131B ALA* 3.9 1.3 - - - +
132B THR 3.3 0.2 - - - -
133B ARG* 1.3 82.1 + - + +
135B GLY* 1.3 61.6 + - - +
136B HIS* 3.8 27.2 + - + +
169B HIS* 3.7 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA 3.1 3.8 + - - -
132B THR 3.1 4.6 + - - -
133B ARG 3.2 0.8 - - - -
134B GLN* 1.3 79.3 - - - +
136B HIS* 1.3 62.8 + - - +
137B LEU* 3.3 7.9 + - - +
169B HIS* 3.3 31.9 + - - -
171B SER* 5.4 1.7 + - - -
172B ILE* 3.6 11.7 - - - +
----------------------------------------------------------
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