Contacts of the strand formed by residues 147 - 154 (chain B) in PDB entry 1J3Q
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 147 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR 3.7 1.9 - - - +
73B VAL 3.8 0.2 - - - -
74B LEU* 2.9 39.5 + - + +
102B ALA* 4.3 14.6 - - + -
104B LYS 3.2 16.4 - - - -
105B GLY* 4.3 2.2 - - - -
106B LYS* 3.7 19.5 - - - +
107B GLY* 3.8 19.1 - - - -
108B GLY 4.0 2.5 - - - -
123B MET* 3.6 37.9 - - + -
139B THR* 3.5 31.2 - - + -
140B ILE 3.8 13.5 - - - -
141B ASN* 3.4 21.0 - - + +
146B PRO* 1.3 71.8 - - - +
148B ILE* 1.3 61.2 + - - +
149B PHE* 3.8 18.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE 5.3 1.8 - - - +
14B GLU 3.6 24.2 - - - +
15B THR* 3.7 15.5 - - - +
16B GLY* 3.8 22.9 - - - +
71B THR* 5.0 2.7 - - - -
72B THR 3.5 9.0 - - - +
73B VAL* 4.4 19.5 - - + -
102B ALA* 4.0 0.9 - - - -
103B LEU* 2.8 36.0 + - + -
104B LYS* 2.8 40.8 + - + +
146B PRO* 4.5 12.3 - - + +
147B PHE* 1.3 79.2 - - - +
149B PHE* 1.3 69.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 3.1 8.4 - - - -
72B THR* 3.0 65.8 + - + -
74B LEU* 4.5 3.1 - - + -
86B THR* 4.8 3.1 - - + -
100B TYR* 3.4 37.9 - + + -
101B PHE 3.4 16.4 - - - +
102B ALA* 4.0 9.2 - - + -
103B LEU* 4.1 4.5 - - - +
123B MET* 5.7 2.5 - - - -
139B THR* 3.2 38.6 - - + -
147B PHE* 3.8 31.0 - + + -
148B ILE* 1.3 80.6 - - - +
150B LEU* 1.3 62.6 + - - +
151B ALA* 4.8 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 6.3 0.9 - - + -
101A PHE* 4.1 34.8 - - + -
128A ILE* 4.4 21.3 - - + -
150A LEU* 5.9 0.7 - - + -
152A LEU* 5.7 0.9 - - + -
11B LEU* 4.6 2.0 - - + -
18B ILE* 4.6 0.4 - - + -
69B PHE* 4.5 7.2 - - + -
70B ALA* 3.5 28.3 - - - +
71B THR* 4.0 15.0 - - + -
99B VAL 3.9 0.7 - - - +
100B TYR* 3.3 4.3 - - - +
101B PHE* 2.8 46.2 + - + +
103B LEU* 4.4 8.7 - - + +
149B PHE* 1.3 73.7 - - - +
151B ALA* 1.3 61.4 + - - +
152B LEU* 4.1 24.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE* 3.2 5.2 - - - +
70B ALA* 2.8 40.1 + - + +
72B THR* 5.8 1.1 - - - +
98B GLU* 3.6 20.4 - - - +
99B VAL 3.5 5.4 - - - +
100B TYR* 3.7 23.3 - - + +
149B PHE* 4.9 3.8 - - + -
150B LEU* 1.3 73.4 - - - +
152B LEU* 1.3 65.2 + - - +
153B TYR* 4.1 7.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.7 6.5 - - + +
99A VAL* 3.7 36.6 - - + -
150A LEU* 5.5 0.2 - - + -
152A LEU* 3.2 49.6 - - + -
67B LEU* 5.9 4.5 - - + -
68B ASN 3.6 5.8 - - - +
69B PHE* 3.8 13.7 - - + -
98B GLU* 3.1 4.7 - - - +
99B VAL* 2.9 41.5 + - + +
101B PHE* 5.3 5.4 - - + -
150B LEU* 4.1 26.2 - - + +
151B ALA* 1.3 78.4 - - - +
153B TYR* 1.3 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.3 1.3 - - - -
57B ALA* 4.8 1.2 - - - +
59B GLU* 3.2 26.3 + - - +
67B LEU* 3.8 8.5 - - - +
68B ASN* 3.0 58.4 + - + +
69B PHE* 4.3 4.2 + - - -
70B ALA* 4.4 14.6 - - + +
91B HIS* 4.8 5.4 - + + -
97B ALA 4.3 0.4 - - - +
98B GLU* 3.3 35.9 - - + +
151B ALA* 4.1 14.8 - - + -
152B LEU* 1.3 79.1 - - - +
154B PRO* 1.3 88.1 - - + +
157B ALA* 4.8 6.5 - - + -
158B GLY 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLY* 3.7 18.8 - - - +
67A LEU* 4.1 15.9 - - + -
65B GLY 6.2 0.9 - - - +
66B ASP 3.7 8.5 - - - +
67B LEU* 4.2 4.0 - - + -
68B ASN* 4.3 0.3 + - - -
96B ARG* 3.5 34.3 - - + +
97B ALA 3.0 19.5 - - - +
153B TYR* 1.3 95.2 - - + +
155B ALA* 1.3 65.6 + - - +
156B ASP* 3.2 9.6 + - - +
157B ALA* 3.2 15.7 + - + +
158B GLY 4.9 0.2 + - - -
----------------------------------------------------------
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