Contacts of the helix formed by residues 127 - 135 (chain B) in PDB entry 2JDQ
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 127 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 5.7 1.8 - - + -
91B ILE* 4.7 13.0 - - + +
92B PHE* 4.2 12.6 - - + -
106B PHE* 4.7 11.4 - - + -
121B VAL* 4.2 17.7 - - + +
124B THR* 3.2 43.0 + - + +
125B PRO 3.0 7.3 + - - +
126B GLY* 1.3 76.4 - - - +
128B VAL* 1.3 65.7 + - + +
129B ALA 3.4 0.4 - - - -
130B ARG* 3.3 8.0 + - - +
131B PHE* 3.1 47.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 4.9 2.2 - - + +
122B ILE* 4.1 28.2 + - + +
124B THR 5.0 0.4 + - - -
126B GLY* 4.5 0.2 - - - -
127B VAL* 1.3 78.4 - - + +
129B ALA* 1.3 64.4 + - - +
131B PHE* 3.2 10.5 + - + +
132B VAL* 3.2 21.3 + - - +
151B LEU* 4.3 11.9 - - + -
154B ILE* 4.5 15.5 - - + -
164B ILE* 3.6 47.3 - - + +
165B VAL* 4.3 8.5 - - + -
168B ALA* 3.9 9.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
126B GLY* 4.2 13.7 + - - +
127B VAL 3.4 0.4 - - - -
128B VAL* 1.3 78.2 - - - +
130B ARG* 1.3 58.6 + - - +
131B PHE 3.4 0.2 - - - -
132B VAL* 3.6 10.6 + - - +
133B GLU* 3.1 31.7 + - - +
168B ALA* 4.4 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 3.2 45.4 + - + -
92B PHE* 3.5 33.3 + - + +
93B SER 3.3 19.2 + - - -
94B LYS* 5.3 0.8 - - - +
99B GLN* 3.4 8.5 - - - +
126B GLY 3.6 14.2 + - - +
127B VAL* 3.3 14.1 + - - +
128B VAL 3.1 0.2 - - - -
129B ALA* 1.3 77.2 - - - +
131B PHE* 1.3 59.2 + - - +
133B GLU* 3.3 36.4 + - - +
134B PHE* 3.2 43.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 3.5 30.5 - - + -
103B THR* 4.3 16.8 - - + -
106B PHE* 3.9 24.9 - + + -
121B VAL* 4.2 10.3 - - + -
127B VAL* 3.1 36.6 + - + -
128B VAL* 3.2 11.5 + - - +
130B ARG* 1.3 73.5 - - - +
132B VAL* 1.3 65.1 + - - +
134B PHE* 3.4 11.5 + + - +
135B LEU* 3.3 22.9 + - - +
147B SER* 3.9 18.4 - - - -
150B VAL* 3.9 29.2 - - + -
151B LEU* 3.7 23.8 - - + +
154B ILE* 5.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 3.2 19.2 + - + +
129B ALA 3.8 7.0 - - - +
131B PHE* 1.3 72.9 - - - +
133B GLU* 1.3 65.8 + - - +
135B LEU* 3.2 23.7 + - + +
136B LYS* 4.0 4.7 + - - +
151B LEU* 4.3 7.6 - - + -
165B VAL 5.0 0.2 - - - +
168B ALA* 3.6 39.0 - - + +
170B ALA* 4.0 22.0 - - + -
173B ILE* 3.2 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 5.7 0.5 - - - -
129B ALA* 3.1 16.1 + - - +
130B ARG* 3.3 55.9 + - - +
132B VAL* 1.3 76.2 - - - +
134B PHE* 1.3 65.0 + - + +
136B LYS* 3.1 32.1 + - + +
137B ARG* 4.1 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ILE* 3.8 32.1 - - + -
99B GLN* 3.4 46.0 - - + -
103B THR* 4.0 11.9 - - - -
130B ARG* 3.2 35.2 + - + -
131B PHE* 3.4 7.6 + + - +
132B VAL 3.3 0.2 - - - -
133B GLU* 1.3 78.4 - - + +
135B LEU* 1.3 64.8 + - - +
136B LYS 3.1 1.0 + - - -
137B ARG* 3.3 27.0 + - + +
143B LEU* 3.5 25.4 - - + -
144B GLN* 3.6 15.4 + - - +
147B SER* 3.3 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE 3.3 14.8 + - - +
132B VAL* 3.2 14.5 + - + +
133B GLU 3.2 1.0 - - - -
134B PHE* 1.3 76.6 - - - +
136B LYS* 1.3 54.4 + - - +
144B GLN* 2.7 38.4 + - - +
147B SER* 4.3 1.6 - - - -
148B ALA* 3.9 25.6 - - - +
151B LEU* 3.9 10.3 - - + -
170B ALA* 4.5 5.4 - - + +
173B ILE* 3.4 29.8 - - + +
174B PHE* 3.7 37.7 - - + -
177B LEU* 3.9 23.7 - - + +
----------------------------------------------------------
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