Contacts of the strand formed by residues 123 - 135 (chain J) in PDB entry 1FPY
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 THR 123 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112J GLU* 4.9 4.0 - - - +
115J LEU* 3.7 4.4 - - - +
116J ARG* 4.7 7.2 - - - +
121J ALA 3.7 1.4 - - - -
122J ASP* 1.3 98.0 + - - +
124J VAL* 1.3 66.3 + - - +
125J LEU* 4.8 9.8 - - - +
227J THR* 5.0 15.9 - - + -
274J LEU* 3.5 5.5 - - - +
275J ALA* 3.0 40.8 + - - +
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Residues in contact with VAL 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J GLU* 4.0 20.6 + - + +
115J LEU* 3.8 28.9 - - + -
123J THR* 1.3 72.3 - - - +
125J LEU* 1.3 76.8 + - - +
126J PHE* 3.5 23.8 - - + -
227J THR* 3.3 2.4 - - - -
228J MET* 3.0 32.5 + - + -
272J MET* 5.4 1.8 - - + -
273J SER 4.3 2.5 - - - +
274J LEU* 3.6 17.0 - - + -
297J TYR* 4.3 5.4 - - - +
375J LEU* 3.8 24.9 - - + -
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Residues in contact with LEU 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J THR* 4.8 10.1 - - - +
124J VAL* 1.3 89.1 - - - +
126J PHE* 1.3 63.0 + - - +
225J PHE* 3.5 30.3 - - + -
226J ASN 3.9 11.4 - - - +
227J THR* 4.0 10.3 - - + +
271J HIS 4.1 0.2 - - - -
272J MET* 3.0 32.9 - - - +
273J SER* 2.9 34.7 + - - +
275J ALA* 4.8 17.7 - - + -
4480J ADP 4.0 14.8 - - - +
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Residues in contact with PHE 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J VAL* 3.5 18.6 - - + -
125J LEU* 1.3 78.2 - - - +
127J GLY* 1.3 57.9 + - - +
128J PRO* 3.8 2.9 - - + -
225J PHE* 3.1 23.3 - - - -
226J ASN 3.1 16.6 + - - +
228J MET* 3.4 36.1 - - + -
231J LYS* 3.5 21.4 - - + +
270J CYS* 4.7 7.2 - - + -
271J HIS 3.3 4.0 - - - -
272J MET* 3.5 33.9 - - + -
297J TYR* 4.6 0.2 - - - -
371J PHE* 3.3 60.8 - + + -
374J LEU* 4.0 8.7 - - + -
375J LEU* 4.4 2.9 - - + -
4480J ADP 4.4 0.4 - - - -
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Residues in contact with GLY 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J PHE* 1.3 75.7 - - - +
128J PRO* 1.3 62.2 - - - +
129J GLU* 4.1 0.5 + - - +
225J PHE* 3.9 8.5 - - - -
269J HIS 3.7 1.6 - - - +
270J CYS* 4.7 0.2 - - - -
271J HIS* 2.9 45.0 + - - +
4480J ADP 3.2 27.2 + - - +
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Residues in contact with PRO 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126J PHE* 4.5 1.8 - - + -
127J GLY* 1.3 88.7 - - - +
129J GLU* 1.3 62.3 + - - +
130J PRO* 3.2 11.2 - - - +
222J ALA* 5.6 0.3 - - - -
223J THR* 4.3 11.8 + - - +
231J LYS* 3.3 33.9 - - + -
235J ILE* 4.2 7.0 - - + -
268J MET* 3.8 28.0 - - + -
269J HIS 3.1 8.3 - - - +
270J CYS* 4.3 8.1 - - - -
371J PHE* 3.6 27.4 - - + -
4480J ADP 4.3 4.9 + - - -
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Residues in contact with GLU 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J GLY 4.7 2.5 - - - +
128J PRO* 1.3 74.5 - - + +
130J PRO* 1.3 58.2 - - - +
131J GLU* 3.4 3.7 + - - +
220J GLU* 3.5 20.0 - - - +
221J VAL 5.6 0.2 - - - -
222J ALA* 5.8 3.4 - - + +
267J GLY 2.8 25.6 - - - +
268J MET* 3.2 7.3 - - - -
269J HIS* 2.9 21.6 + - + +
271J HIS* 3.4 13.7 + - - -
357J GLU* 2.8 6.2 - - - +
470J MN 1.9 34.0 + - - -
4480J ADP 2.6 54.6 + - - +
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Residues in contact with PRO 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J PRO 3.2 11.0 - - - +
129J GLU* 1.3 81.4 - - - +
131J GLU* 1.3 64.8 + - - +
132J PHE* 3.9 0.9 - - - -
220J GLU* 4.0 4.9 - - + +
221J VAL 4.1 15.9 - - - +
223J THR* 5.0 1.8 - - - +
235J ILE* 3.9 15.5 - - + -
238J TYR* 2.9 47.3 + - + -
239J LYS* 6.2 0.9 - - + -
255J PHE* 4.8 6.3 - - + -
267J GLY 3.9 2.5 - - - +
268J MET* 3.7 36.6 - - + -
363J PRO* 4.7 4.0 - - + -
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Residues in contact with GLU 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J GLU 4.4 0.9 - - - +
130J PRO* 1.3 72.1 - - - +
132J PHE* 1.3 65.3 + - - +
212J GLU* 3.1 17.4 - - + +
218J GLN* 4.6 3.1 - - - +
219J ASN 3.8 5.2 - - - +
220J GLU* 3.0 25.6 - - + +
255J PHE* 3.4 14.9 - - - -
266J SER* 3.7 15.7 - - - -
267J GLY 3.0 28.0 + - - +
269J HIS* 5.3 1.3 - - - -
363J PRO* 3.5 11.8 - - - +
469J MN 2.3 30.4 + - - -
5909J PPQ 2.4 44.1 + - - +
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Residues in contact with PHE 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J PRO 3.9 3.8 - - - -
131J GLU* 1.3 79.5 - - - +
133J PHE* 1.3 74.3 + - - +
134J LEU* 3.9 17.9 - - + -
192J ARG* 5.5 0.7 - - + -
195J MET* 4.0 20.4 - - - -
218J GLN* 3.2 6.6 - - - +
219J ASN* 2.7 68.3 + - + -
220J GLU* 4.2 2.9 - - - -
221J VAL* 4.3 7.6 - - + -
238J TYR* 3.5 19.3 - + - -
242J VAL* 3.9 26.2 - - + -
254J THR 3.5 16.6 - - - +
255J PHE* 3.7 26.2 - + + -
266J SER* 4.0 6.4 - - - -
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Residues in contact with PHE 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J PHE* 1.3 76.5 - - - +
134J LEU* 1.3 65.7 + - - +
135J PHE* 3.3 22.4 - + + -
214J ALA* 3.6 9.4 - - + -
215J THR 3.6 2.9 - - - -
216J ALA 3.5 17.7 - - - -
217J GLY 3.3 4.0 - - - -
218J GLN* 3.4 32.3 - - + -
252J THR 3.9 0.5 - - - +
253J ALA* 3.3 7.4 - - - +
254J THR* 3.2 31.5 + - + +
256J MET 4.9 0.7 - - - -
259J PRO* 3.3 27.1 - - + -
260J MET* 3.1 30.7 - - + -
264J ASN 3.4 21.8 - - - -
266J SER* 3.3 25.8 - - - -
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Residues in contact with LEU 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J PHE* 3.9 22.0 - - + -
133J PHE* 1.3 75.3 - - - +
135J PHE* 1.3 63.5 + - - +
153J ASP* 3.1 23.0 - - - +
188J ALA* 4.9 4.5 - - + -
191J ILE* 4.4 28.3 - - + -
192J ARG* 5.6 1.6 - - + -
195J MET* 4.5 6.7 - - + -
216J ALA 3.6 6.9 - - - +
217J GLY* 2.8 17.8 + - - +
219J ASN* 4.2 13.9 - - - +
246J ALA* 3.8 17.5 - - + -
251J LYS* 4.0 19.4 + - + -
252J THR 3.8 1.6 - - - +
253J ALA* 3.5 31.4 - - + +
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Residues in contact with PHE 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D PHE* 6.4 0.2 - + - -
466D TYR* 3.8 23.8 - + - -
133J PHE* 3.3 28.5 - + + -
134J LEU* 1.3 71.7 - - - +
136J ASP* 1.3 61.5 + - - +
137J ASP 4.1 6.5 - - - +
138J ILE* 5.0 3.1 - - + -
151J ILE* 3.6 33.2 - - + -
152J ASP 3.4 8.5 - - - +
153J ASP* 3.3 15.7 - - + -
216J ALA* 3.2 32.3 - - + -
251J LYS* 3.5 10.0 - - - +
252J THR* 3.0 38.0 + - + -
254J THR* 3.4 24.7 - - + -
259J PRO* 4.2 16.2 - - + -
260J MET* 4.2 4.0 - - + -
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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