Contacts of the helix formed by residues 125 - 133 (chain B) in PDB entry 3OOT
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 PHE 125 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER* 2.8 19.6 + - - -
124B GLY* 1.3 76.3 - - - -
126B ILE* 1.4 64.7 + - - +
127B GLU* 3.3 15.7 - - - +
128B GLN* 3.0 8.7 + - - +
135B PRO* 3.9 2.9 - - - -
138B ASP* 5.2 2.7 - - - -
184B LEU* 3.8 19.5 - - + -
187B THR* 4.2 4.9 - - - -
188B GLY* 3.3 42.1 + - - +
189B VAL* 3.9 14.1 - - - -
190B TRP* 3.5 47.3 - + - -
315B ARG* 3.5 32.8 - - - +
318B ASN* 3.8 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PHE* 1.4 71.1 - - - +
127B GLU* 1.4 76.2 + - - +
128B GLN 3.2 0.2 - - - -
129B ALA* 3.1 18.3 + - - +
132B ARG* 3.7 37.6 - - + +
133B VAL 4.2 3.8 - - - +
134B THR* 3.9 26.0 - - + +
135B PRO* 3.6 24.8 - - + +
138B ASP* 4.7 12.2 + - - +
315B ARG* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PHE* 3.1 18.0 + - - +
126B ILE* 1.4 87.5 - - + +
128B GLN* 1.3 66.0 + - + +
129B ALA 5.0 1.7 - - - +
187B THR* 4.1 22.7 + - + +
188B GLY* 3.8 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLY 5.9 1.0 + - - -
35B SER* 5.6 3.1 - - - -
36B SER* 3.4 22.2 + - - +
37B ASN* 4.3 1.4 - - - +
125B PHE 3.0 4.5 + - - +
127B GLU* 1.3 81.9 - - + +
129B ALA* 1.4 62.0 + - - +
130B ILE* 3.5 10.7 + - - +
186B LYS* 5.9 1.9 + - - -
188B GLY 3.1 24.0 - - - +
189B VAL* 4.6 16.0 - - + +
294B PRO* 5.5 6.2 - - - +
295B THR* 3.5 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER* 3.7 17.7 - - - +
37B ASN* 3.5 11.0 - - - +
125B PHE 3.5 3.0 + - - -
126B ILE* 3.1 22.4 + - + +
127B GLU 5.0 1.2 - - - +
128B GLN* 1.4 75.0 - - - +
130B ILE* 1.3 63.4 + - - +
131B GLY 3.5 0.5 + - - -
132B ARG* 3.4 14.2 + - - +
133B VAL 3.3 31.2 - - - +
135B PRO* 4.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASN* 2.9 26.5 + - - +
71B LEU* 3.8 16.3 - - + +
72B THR 3.4 29.2 - - - +
73B LEU* 3.8 28.3 - - + -
74B ARG* 4.2 15.0 - - + +
128B GLN 4.3 8.3 - - - +
129B ALA* 1.3 71.0 - - - +
131B GLY* 1.3 62.4 + - - +
133B VAL* 3.2 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 5.7 2.2 - - - -
84B LEU* 5.4 8.1 - - - +
129B ALA 3.5 0.8 + - - -
130B ILE* 1.3 75.2 - - - +
132B ARG* 1.4 66.7 + - - +
133B VAL* 3.1 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 3.7 27.2 - - + +
129B ALA* 3.4 15.9 + - - +
130B ILE 3.3 2.4 - - - -
131B GLY* 1.4 77.4 - - - +
133B VAL* 1.4 61.4 + - - +
134B THR* 3.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER 4.8 1.4 - - - +
37B ASN* 3.5 17.0 - - - +
84B LEU* 4.3 23.6 - - + -
99B GLN* 4.5 0.2 - - - +
100B MET* 3.4 45.3 - - + +
126B ILE* 4.4 0.4 - - - -
129B ALA* 3.3 20.0 - - - +
130B ILE 3.2 21.7 + - - +
131B GLY* 3.1 7.0 + - - +
132B ARG* 1.4 74.7 - - - +
134B THR* 1.3 71.7 + - - +
135B PRO* 3.3 4.7 - - - +
----------------------------------------------------------
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