Contacts of the strand formed by residues 147 - 155 (chain A) in PDB entry 1JG0
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 HIS 147 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 5.4 2.2 + - - -
62A PHE* 3.8 26.5 - + - -
94A TYR* 3.2 55.4 - + - -
98A TRP* 4.9 0.9 + + - -
132A ALA* 4.4 2.1 - - - +
146A CYS* 1.3 75.2 - - + +
148A ALA* 1.3 58.2 + - - +
149A PHE 3.6 3.0 + - - -
150A PHE* 5.5 1.4 - - - -
163A LEU* 3.4 30.5 - - + -
164A TYR 3.9 2.5 - - - -
165A GLN* 4.3 7.8 - - + +
177A ASN* 4.6 9.1 + - - +
180A SER* 6.3 1.1 - - - -
181A TYR* 2.4 43.9 + + + +
303A UMP 3.9 20.7 + + - -
304A DDT 6.1 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A SER* 3.6 1.7 + - - -
132A ALA* 3.0 27.5 + - - -
133A TRP* 3.5 38.4 + - + +
145A PRO* 4.2 9.6 - - + +
146A CYS 2.9 11.3 + - - +
147A HIS* 1.3 72.0 - - - +
149A PHE* 1.3 65.7 + - + +
150A PHE* 5.6 0.9 - - - -
164A TYR* 3.3 8.1 + - + +
166A ARG* 5.3 2.2 - - + -
149B PHE* 4.5 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE* 3.6 41.1 - - + -
130A VAL 3.6 6.7 - - - -
131A SER* 4.1 18.2 - - - -
147A HIS 3.6 2.6 + - - -
148A ALA* 1.3 83.1 - - + +
150A PHE* 1.3 76.6 + - - +
151A GLN* 4.5 0.9 - - + -
162A GLN 5.3 0.2 - - - -
163A LEU* 3.4 2.8 - - - +
164A TYR* 2.8 43.8 + - + -
133B TRP* 4.2 18.6 - + + -
148B ALA* 4.2 15.0 - - + -
149B PHE* 4.7 22.2 - + + -
164B TYR* 3.5 42.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 150 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A TRP* 3.8 34.1 - + - -
112A ILE* 4.8 3.1 - - + -
129A ILE* 3.5 4.2 - - - +
130A VAL* 3.0 73.5 + - + +
132A ALA* 6.2 0.9 - - + -
147A HIS 5.5 2.0 - - - -
148A ALA 5.6 0.2 - - - -
149A PHE* 1.3 83.7 - - - +
151A GLN* 1.3 62.2 + - - +
152A PHE* 3.7 34.0 - + - -
161A CYS* 4.0 12.8 - - - -
162A GLN 3.1 14.1 - - - +
163A LEU* 4.0 10.1 - - + -
181A TYR* 3.7 18.2 - + + -
184A LEU* 3.7 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 151 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ARG* 3.2 20.2 - - - +
128A ILE 3.3 13.5 - - - +
129A ILE* 3.9 11.0 - - + +
149A PHE* 4.5 2.2 - - + -
150A PHE* 1.3 75.8 - - - +
152A PHE* 1.3 75.5 + - - +
161A CYS* 3.2 4.3 - - - -
162A GLN 2.8 30.9 + - - -
30B PHE* 3.4 17.7 - - + -
164B TYR* 2.7 47.9 + - - +
166B ARG* 3.1 33.8 + - - +
204B GLY* 3.7 4.0 - - - -
205B ASP* 4.2 2.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.6 30.3 - - + -
119A LEU* 4.1 5.4 - - + -
125A SER 4.9 3.5 - - - +
126A ARG 6.0 0.2 - - - -
128A ILE* 2.9 40.9 + - + +
130A VAL* 4.6 4.3 - - + -
150A PHE* 3.7 36.3 - + - -
151A GLN* 1.3 88.1 - - - +
153A TYR* 1.3 63.8 + - - +
159A LEU* 3.8 25.4 - - + -
160A SER 3.3 13.7 - - - +
161A CYS* 3.9 17.0 - - + -
184A LEU* 4.7 7.2 - - + -
185A VAL* 4.7 7.4 - - + -
188A MET* 4.0 28.5 - - + -
30B PHE* 4.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 153 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PRO 5.2 2.0 - - - -
125A SER 5.7 3.1 - - - -
128A ILE* 5.5 1.3 - - - -
152A PHE* 1.3 77.4 - - - +
154A VAL* 1.3 74.1 + - - +
155A ALA* 3.5 29.7 - - + +
158A LYS 5.4 0.2 - - - -
159A LEU* 3.6 1.0 - - - +
160A SER* 2.8 40.9 + - - -
16B THR* 4.5 3.1 + - - -
18B LYS* 4.0 11.2 - - - -
28B SER* 2.8 38.4 + - - -
29B ILE* 4.0 3.5 + - - -
30B PHE* 3.4 54.7 - + + -
205B ASP* 3.5 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.5 28.5 - - + -
123A PRO* 3.7 36.2 + - + +
124A ASP* 4.1 2.4 - - - +
153A TYR* 1.3 83.7 - - - +
155A ALA* 1.3 62.9 + - - +
157A GLY* 4.4 6.1 - - - +
158A LYS 3.4 13.7 - - - +
159A LEU* 4.1 7.2 - - + -
194A LEU* 4.2 27.1 - - + -
18B LYS* 2.7 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A TYR* 3.5 28.4 - - + +
154A VAL* 1.3 75.3 - - - +
156A ASP* 1.3 74.1 + - - +
157A GLY 3.1 1.8 - - - -
158A LYS* 2.8 27.1 + - + +
16B THR* 4.1 22.0 - - + +
18B LYS* 4.6 5.2 - - - +
----------------------------------------------------------
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