Contacts of the helix formed by residues 141 - 150 (chain A) in PDB entry 5JEI
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 GLY 141 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 4.7 4.0 - - - -
62A GLY 4.6 6.0 + - - -
63A ALA* 5.0 2.8 - - - +
96A ARG* 4.2 8.7 - - - -
140A SER* 1.3 79.6 + - - +
142A SER* 1.3 65.8 + - - -
143A THR 3.3 3.4 + - - -
144A LYS* 3.4 4.0 + - - +
145A GLU* 3.1 30.0 + - - +
301A FWD 3.4 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A THR* 3.2 25.4 + - - +
93A THR* 4.0 19.1 - - - -
96A ARG* 4.1 4.4 - - - +
141A GLY* 1.3 72.9 - - - -
143A THR* 1.3 58.0 + - - +
145A GLU* 3.9 6.9 - - - +
146A PHE* 2.9 30.1 + - - +
193A GLU* 3.2 23.6 + - - -
218A LYS* 4.4 6.9 + - - -
301A FWD 2.9 19.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.9 25.3 - - + +
137A THR* 3.8 27.6 - - + -
138A LEU 5.4 1.3 - - - -
142A SER* 1.3 77.8 + - - +
144A LYS* 1.3 63.9 + - - +
146A PHE* 3.2 2.8 + - - +
147A PHE* 3.2 36.3 + - + -
191A LEU 4.1 11.0 - - - +
193A GLU* 3.9 11.8 + - - +
301A FWD 2.8 37.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A THR* 3.9 12.7 + - - +
138A LEU 3.6 15.5 + - - +
139A ASP* 3.0 32.2 + - - +
140A SER* 4.2 2.0 - - - +
141A GLY 3.4 11.3 + - - +
142A SER 3.4 0.2 - - - -
143A THR* 1.3 79.8 - - - +
145A GLU* 1.3 69.7 + - - +
147A PHE* 3.3 5.4 + - - +
148A ARG* 3.0 23.5 + - + +
159A TRP* 3.9 13.8 - - + -
170A PHE* 3.9 14.6 - - + -
307A PG4 2.5 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ALA* 4.9 16.2 - - + +
64A ARG 6.3 0.2 - - - -
140A SER* 6.0 0.5 - - - -
141A GLY* 3.1 25.8 + - - +
142A SER* 3.9 6.7 - - - +
144A LYS* 1.3 84.5 - - - +
146A PHE* 1.3 63.8 + - - +
148A ARG* 2.7 42.7 + - - +
149A ARG* 3.1 38.8 + - - +
307A PG4 5.2 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 3.5 26.2 - - + -
142A SER 2.9 18.9 + - - +
143A THR 3.2 4.5 + - - +
145A GLU* 1.3 77.5 - - - +
147A PHE* 1.3 76.7 + + - +
149A ARG* 3.9 3.6 - - - +
150A SER* 3.1 31.3 + - - -
152A ILE* 4.6 7.9 - - + -
155A PHE* 3.6 44.6 - + + -
215A LEU* 4.7 3.4 - - + -
216A ASP* 3.7 29.2 - - + -
218A LYS* 4.5 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ILE* 4.1 11.2 - - + -
137A THR* 4.0 6.5 - - + -
143A THR* 3.2 37.1 + - + -
144A LYS* 3.8 3.8 - - - +
146A PHE* 1.3 86.3 - + - +
148A ARG* 1.3 62.0 + - - +
149A ARG 3.2 0.7 + - - -
150A SER* 3.3 16.0 + - - +
155A PHE* 3.7 36.1 - + + +
156A ASP* 5.1 0.2 - - - -
158A MET* 3.9 20.2 - - + -
159A TRP* 3.3 35.7 - - + +
162A MET* 3.6 15.9 - - + -
191A LEU* 3.8 23.8 - - + -
215A LEU* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LYS* 3.0 19.3 + - + +
145A GLU* 2.7 36.4 + - - +
147A PHE* 1.3 76.8 - - - +
149A ARG* 1.3 79.9 + - - +
150A SER 3.8 1.0 + - - +
151A LYS* 5.3 4.7 + - - -
159A TRP* 3.6 34.5 + - + +
302A PO4 4.3 15.5 + - - +
307A PG4 3.8 30.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.1 22.4 - - - +
95A VAL* 3.6 31.8 - - - +
145A GLU* 3.1 28.1 + - - +
146A PHE* 4.2 2.9 - - - +
148A ARG* 1.3 106.2 - - - +
150A SER* 1.3 63.6 + - - +
151A LYS* 3.5 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PHE* 3.1 27.5 + - - -
147A PHE 3.3 8.8 + - - +
148A ARG 5.0 0.3 - - - +
149A ARG* 1.3 76.1 - - - +
151A LYS* 1.3 69.1 + - - +
152A ILE* 3.2 35.0 + - - +
155A PHE* 3.7 20.9 - - - +
156A ASP* 3.5 17.7 - - - +
----------------------------------------------------------
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