Contacts of the helix formed by residues 138 - 149 (chain B) in PDB entry 2QJ3
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 ASP 138 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLY* 1.3 68.7 - - - -
139B GLU* 1.3 72.4 + - - +
140B THR* 3.3 31.5 + - - -
141B GLU* 3.1 37.7 + - + +
142B VAL* 3.1 13.2 + - - +
180B ALA 4.9 3.6 + - - -
181B LYS* 5.3 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLY 3.2 6.0 + - - -
138B ASP* 1.3 73.1 + - - +
140B THR* 1.3 65.6 + - - +
142B VAL* 3.1 7.0 + - - +
143B LEU* 3.1 38.0 + - + +
156B ARG* 3.4 24.6 + - - +
162B ILE* 4.9 12.5 - - + +
251B ASP* 4.9 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASP* 3.2 14.0 + - - -
139B GLU* 1.3 78.9 + - - +
141B GLU* 1.3 56.9 + - + +
143B LEU* 3.4 7.5 + - - +
144B SER* 2.7 44.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASP* 3.1 31.9 + - + +
140B THR* 1.3 76.9 - - + +
142B VAL* 1.3 60.8 + - + +
144B SER* 4.1 5.3 - - - -
145B ARG* 3.1 28.9 + - - +
179B PRO* 4.5 10.3 - - + +
180B ALA* 4.1 24.2 + - - +
181B LYS* 6.0 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 3.8 35.0 - - + -
136B GLY* 4.6 1.8 - - - -
137B GLY 3.9 21.8 - - - +
138B ASP 3.2 15.5 - - - +
139B GLU* 3.1 7.9 + - - +
141B GLU* 1.3 75.8 - - + +
143B LEU* 1.3 64.6 + - - +
145B ARG* 3.4 5.9 - - - +
146B LEU* 3.1 31.8 + - + +
162B ILE* 3.9 32.5 - - + -
179B PRO* 4.5 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLU* 3.1 30.3 + - + +
140B THR* 3.4 6.7 + - - +
142B VAL* 1.3 77.2 - - - +
144B SER* 1.3 61.5 + - - +
146B LEU* 3.4 7.5 + - + +
147B GLU* 3.2 24.9 + - - +
153B PRO* 3.7 35.6 - - + +
156B ARG* 3.4 43.5 - - - +
162B ILE* 4.6 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B THR* 2.7 31.8 + - - +
141B GLU* 4.1 6.0 - - - -
143B LEU* 1.3 72.9 - - - +
145B ARG* 1.3 68.1 + - - +
147B GLU* 3.2 18.1 + - - +
148B GLN* 3.4 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLU 3.1 18.4 + - - +
142B VAL 3.4 6.1 - - - +
144B SER* 1.3 81.0 - - - +
146B LEU* 1.3 62.3 - - + +
147B GLU 3.4 0.2 + - - -
148B GLN* 3.1 45.1 + - - +
149B LEU* 3.5 35.3 + - - +
173B LYS 4.9 0.4 + - - -
174B LEU* 3.8 15.4 - - + +
177B ASP* 2.5 54.1 + - - +
178B PRO 4.4 1.0 + - - -
179B PRO* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 4.9 1.6 - - + -
142B VAL* 3.1 28.8 + - + +
143B LEU* 3.7 7.4 - - - +
144B SER 3.2 0.2 - - - -
145B ARG* 1.3 76.5 - - + +
147B GLU* 1.3 63.2 + - - +
149B LEU 3.1 6.8 + - - -
151B LEU* 2.9 61.8 + - + +
152B VAL 4.1 0.4 - - - +
153B PRO* 3.9 32.3 - - + -
162B ILE* 4.4 10.1 - - + -
164B ALA* 3.6 35.0 - - + -
174B LEU* 4.3 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU 3.2 13.3 + - - +
144B SER* 3.2 12.9 + - - +
146B LEU* 1.3 77.4 - - - +
148B GLN* 1.3 59.4 + - + +
149B LEU 2.9 6.6 + - - -
150B ASP* 3.1 17.4 + - - +
151B LEU 4.2 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B SER* 3.4 20.9 + - - +
145B ARG* 3.1 38.0 + - - +
146B LEU 3.3 0.4 - - - -
147B GLU* 1.3 78.1 - - + +
149B LEU* 1.3 67.9 + - + +
150B ASP* 3.5 2.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ARG* 3.5 41.0 + - - +
146B LEU 3.1 7.0 + - - +
147B GLU 3.0 1.2 - - - -
148B GLN* 1.3 93.6 - - + +
150B ASP* 1.3 73.2 + - - +
151B LEU* 3.9 10.7 - - + +
170B ALA* 3.5 26.6 - - + +
173B LYS* 4.6 13.2 - - + -
174B LEU* 3.9 42.6 - - + +
----------------------------------------------------------
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