Contacts of the strand formed by residues 147 - 154 (chain A) in PDB entry 1J3R
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A THR 3.6 2.3 - - - +
74A LEU* 2.9 38.9 + - + +
102A ALA* 4.2 16.8 - - + -
104A LYS 3.3 16.4 - - - -
105A GLY* 4.3 2.9 - - - -
106A LYS* 3.8 17.5 - - - +
107A GLY* 3.8 11.9 - - - -
108A GLY 4.0 2.2 - - - -
123A MET* 3.7 40.6 - - + -
139A THR* 3.3 31.6 - - + -
140A ILE 3.6 23.3 - - - -
141A ASN* 3.7 21.3 - - + +
145A LYS 3.4 0.4 + - - -
146A PRO* 1.3 72.0 - - - +
148A ILE* 1.3 63.4 + - - +
149A PHE* 3.8 11.1 - + - -
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Residues in contact with ILE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE 4.5 2.2 - - - +
14A GLU 3.5 24.5 - - - +
15A THR 3.9 14.6 - - - +
16A GLY* 3.6 24.5 - - - +
71A THR* 5.2 1.6 - - - -
72A THR 3.4 9.4 - - - +
73A VAL* 4.2 11.9 - - + -
102A ALA* 3.7 1.4 - - - -
103A LEU* 2.8 41.2 + - + -
104A LYS* 2.7 43.6 + - + +
146A PRO* 4.3 16.8 - - + +
147A PHE* 1.3 80.2 - - - +
149A PHE* 1.3 64.3 + - - +
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Residues in contact with PHE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR* 3.1 8.9 - - - -
72A THR* 3.0 69.3 + - + -
74A LEU* 4.6 2.5 - - + -
86A THR* 4.8 0.9 - - + -
100A TYR* 3.2 34.1 - + + -
101A PHE 3.4 13.7 - - - +
102A ALA* 3.8 10.8 - - + -
103A LEU* 4.1 4.3 - - - +
123A MET* 4.6 4.9 - - + -
139A THR* 3.1 39.5 - - + -
147A PHE* 3.8 26.0 - + + -
148A ILE* 1.3 79.5 - - - +
150A LEU* 1.3 66.7 + - - +
151A ALA* 4.7 4.0 - - + -
600A 6PG 3.6 10.1 - - - -
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Residues in contact with LEU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 4.3 4.9 - - + -
18A ILE* 4.4 1.6 - - + -
69A PHE* 4.5 5.4 - - + -
70A ALA* 3.5 26.2 - - - +
71A THR* 3.8 19.1 - - + -
99A VAL 3.8 0.5 - - - +
100A TYR* 3.3 4.7 - - - +
101A PHE* 2.7 48.2 + - + +
103A LEU* 4.3 9.3 - - + +
149A PHE* 1.3 75.9 - - - +
151A ALA* 1.3 61.2 + - - +
152A LEU* 3.8 22.8 - - + +
99B VAL* 6.3 1.8 - - + -
101B PHE* 3.9 35.9 - - + -
128B ILE* 4.3 17.7 - - + -
150B LEU* 6.0 1.3 - - + -
152B LEU* 6.1 0.4 - - + -
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Residues in contact with ALA 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE* 3.2 6.6 - - - +
70A ALA 2.7 38.8 + - - +
98A GLU* 3.3 23.1 - - - +
99A VAL 3.3 4.7 - - - -
100A TYR* 4.0 22.7 - - + -
149A PHE* 4.8 2.9 - - + -
150A LEU* 1.3 76.3 - - - +
152A LEU* 1.3 60.8 + - - +
153A TYR* 3.9 2.5 - - + -
600A 6PG 4.1 14.4 - - - -
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 5.7 5.6 - - + -
68A ASN 3.5 6.1 - - - +
69A PHE* 4.1 8.1 - - + -
98A GLU* 3.4 2.8 - - - +
99A VAL* 2.8 38.9 + - + +
101A PHE* 5.4 4.0 - - + -
150A LEU* 3.8 26.9 - - + +
151A ALA* 1.3 80.3 - - - +
153A TYR* 1.3 63.8 + - - +
67B LEU* 3.7 7.6 - - + +
99B VAL* 3.8 29.8 - - + -
101B PHE* 6.6 0.2 - - + -
150B LEU* 5.9 0.4 - - + -
152B LEU* 3.3 59.0 - - + -
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Residues in contact with TYR 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA* 4.2 1.0 - - - +
59A GLU* 3.2 24.6 + - - +
67A LEU* 3.7 7.4 - - - +
68A ASN* 2.8 66.4 + - + +
69A PHE* 4.0 5.4 + - - -
70A ALA* 3.9 10.0 - - - +
91A HIS* 4.5 3.1 - - - +
97A ALA 4.3 0.4 - - - +
98A GLU* 3.5 27.8 - - + +
151A ALA 3.9 10.3 - - - -
152A LEU* 1.3 80.0 - - - +
154A PRO* 1.3 83.5 - - + +
157A ALA* 4.9 4.5 - - + -
158A GLY 5.9 0.7 - - - -
159A HIS* 4.4 7.0 - + - -
201A FE 3.8 13.9 - - - -
600A 6PG 2.7 38.6 + - - -
67B LEU* 4.5 0.7 - - - -
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Residues in contact with PRO 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLY 6.2 1.8 - - - +
66A ASP 3.5 11.2 - - - +
67A LEU* 4.1 3.1 - - + -
68A ASN* 4.4 0.2 + - - -
96A ARG* 3.9 10.8 - - + +
97A ALA 3.2 20.2 - - - +
153A TYR* 1.3 95.2 - - + +
155A ALA* 1.3 62.5 + - - +
156A ASP* 3.1 21.9 + - - +
157A ALA* 3.1 20.9 + - + +
158A GLY 4.7 0.5 + - - -
65B GLY* 3.7 26.7 - - - +
67B LEU* 4.1 17.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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