Contacts of the strand formed by residues 123 - 135 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A GLU* 4.9 4.7 - - - +
115A LEU* 3.7 4.9 - - - +
116A ARG* 4.7 7.2 - - - +
121A ALA 3.7 0.8 - - - -
122A ASP* 1.3 98.6 + - - +
124A VAL* 1.3 65.2 + - - +
125A LEU* 4.2 9.8 + - - +
227A THR* 5.0 17.3 - - + -
274A LEU* 3.5 5.4 - - - +
275A ALA* 3.0 39.5 + - - +
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Residues in contact with VAL 124 (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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112A GLU* 4.0 19.7 + - + +
115A LEU* 3.8 28.9 - - + -
123A THR* 1.3 72.2 - - - +
125A LEU* 1.3 77.8 + - - +
126A PHE* 3.5 24.7 - - + -
227A THR* 3.3 2.3 - - - -
228A MET* 3.0 32.1 + - + -
272A MET* 5.4 1.3 - - + -
273A SER 4.3 2.7 - - - +
274A LEU* 3.6 16.2 - - + -
297A TYR* 4.3 5.2 - - - +
375A LEU* 3.8 24.0 - - + -
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Residues in contact with LEU 125 (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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123A THR* 4.8 9.9 - - - +
124A VAL* 1.3 89.2 - - - +
126A PHE* 1.3 61.8 + - - +
225A PHE* 3.5 31.2 - - + -
226A ASN 3.9 11.0 - - - +
227A THR* 4.0 11.0 - - + +
271A HIS 4.1 0.2 - - - -
272A MET* 3.0 32.9 - - - +
273A SER* 2.9 36.0 + - - +
275A ALA* 4.8 17.3 - - + -
4471A ADP 4.0 14.8 - - - +
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Residues in contact with PHE 126 (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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124A VAL* 3.5 19.5 - - + -
125A LEU* 1.3 79.8 - - - +
127A GLY* 1.3 58.0 + - - +
128A PRO* 3.8 2.7 - - + -
225A PHE* 3.1 23.3 - - - -
226A ASN 3.1 16.5 + - - +
228A MET* 3.4 36.3 - - + -
231A LYS* 3.5 21.4 - - + +
270A CYS* 4.7 7.4 - - + -
271A HIS 3.3 3.6 - - - -
272A MET* 3.5 33.4 - - + -
371A PHE* 3.3 61.9 - + + -
374A LEU* 4.0 9.2 - - + -
375A LEU* 4.4 3.4 - - + -
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Residues in contact with GLY 127 (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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126A PHE* 1.3 76.3 - - - +
128A PRO* 1.3 63.2 - - - +
129A GLU* 4.1 0.7 + - - +
225A PHE* 3.9 9.2 - - - -
269A HIS 3.7 1.4 - - - +
270A CYS* 4.7 0.4 - - - -
271A HIS* 2.9 43.4 + - - +
4471A ADP 3.2 28.1 + - - +
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Residues in contact with PRO 128 (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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126A PHE* 4.5 1.1 - - + -
127A GLY* 1.3 88.8 - - - +
129A GLU* 1.3 61.6 + - - +
130A PRO* 3.2 10.7 - - - +
222A ALA* 5.6 0.5 - - - -
223A THR* 4.3 12.0 + - - +
231A LYS* 3.3 35.0 - - + -
235A ILE* 4.2 7.2 - - + -
268A MET* 3.8 28.3 - - + -
269A HIS 3.1 7.9 - - - +
270A CYS* 4.3 8.1 - - - -
371A PHE* 3.6 26.2 - - + -
4471A ADP 4.3 4.9 + - - +
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Residues in contact with GLU 129 (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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127A GLY 4.7 2.7 - - - +
128A PRO* 1.3 73.9 - - + +
130A PRO* 1.3 57.9 - - - +
131A GLU* 3.4 3.9 + - - +
220A GLU* 3.5 19.7 - - - +
221A VAL 5.6 0.2 - - - -
222A ALA* 5.8 3.6 - - + +
267A GLY 2.8 26.0 - - - +
268A MET* 3.2 6.9 - - - -
269A HIS* 2.9 22.1 + - + +
271A HIS* 3.4 13.4 + - - -
357A GLU* 2.8 6.8 - - - +
470A MN 1.9 33.2 + - - -
4471A ADP 2.6 54.5 + - - +
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Residues in contact with PRO 130 (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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128A PRO 3.2 10.5 - - - +
129A GLU* 1.3 81.3 - - - +
131A GLU* 1.3 64.4 + - - +
132A PHE* 3.9 1.2 - - - -
220A GLU* 4.0 5.0 - - + +
221A VAL 4.1 16.4 - - - +
222A ALA* 5.7 0.2 - - - -
223A THR* 5.0 1.6 - - - +
235A ILE* 3.9 15.7 - - + -
238A TYR* 2.9 47.6 + - + -
239A LYS* 6.2 0.9 - - + -
255A PHE* 4.8 6.1 - - + -
267A GLY 3.9 2.9 - - - +
268A MET* 3.7 35.4 - - + -
363A PRO* 4.7 4.3 - - + -
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Residues in contact with GLU 131 (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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129A GLU 4.4 1.6 - - - +
130A PRO* 1.3 72.7 - - - +
132A PHE* 1.3 65.2 + - - +
212A GLU* 3.1 16.3 - - + +
218A GLN* 4.8 2.9 - - - +
219A ASN 3.8 4.9 - - - +
220A GLU* 3.0 26.0 - - + +
255A PHE* 3.4 15.4 - - - -
266A SER* 3.7 15.9 - - - -
267A GLY 3.0 28.5 + - - +
269A HIS* 4.8 2.2 - - - -
363A PRO* 3.5 11.3 - - - +
469A MN 2.3 30.8 + - - -
5900A PPQ 2.4 42.5 + - - +
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Residues in contact with PHE 132 (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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130A PRO 3.9 3.8 - - - -
131A GLU* 1.3 79.7 - - - +
133A PHE* 1.3 74.7 + - - +
134A LEU* 3.9 17.0 - - + -
192A ARG* 5.5 0.9 - - + -
195A MET* 4.0 21.1 - - - -
218A GLN* 3.2 6.3 - - - +
219A ASN* 2.7 68.4 + - + +
220A GLU* 4.2 2.7 - - - -
221A VAL* 4.3 7.4 - - + -
238A TYR* 3.5 20.0 - - - -
242A VAL* 3.9 25.4 - - + -
253A ALA* 4.8 0.2 - - + -
254A THR 3.5 17.0 - - - +
255A PHE* 3.7 25.8 - + + -
266A SER* 4.0 6.0 - - - -
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Residues in contact with PHE 133 (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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132A PHE* 1.3 77.3 - - - +
134A LEU* 1.3 64.4 + - - +
135A PHE* 3.3 22.4 - + + -
214A ALA* 3.6 9.4 - - + -
215A THR 3.6 2.5 - - - -
216A ALA 3.5 17.5 - - - -
217A GLY 3.3 4.0 - - - -
218A GLN* 3.4 33.2 - - + -
252A THR 3.9 0.3 - - - +
253A ALA* 3.3 6.8 - - - +
254A THR* 3.2 32.2 + - + -
256A MET 4.9 0.4 - - - -
259A PRO* 3.3 26.9 - - + -
260A MET* 3.1 30.3 - - + -
264A ASN 3.4 22.2 - - - -
266A SER* 3.3 26.0 - - - -
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Residues in contact with LEU 134 (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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132A PHE* 3.9 22.0 - - + -
133A PHE* 1.3 75.7 - - - +
135A PHE* 1.3 63.3 + - - +
153A ASP* 3.1 22.7 - - - +
188A ALA* 4.9 4.3 - - + -
191A ILE* 4.4 28.5 - - + -
192A ARG* 5.6 1.3 - - + -
195A MET* 4.5 6.7 - - + -
216A ALA 3.6 7.1 - - - +
217A GLY* 2.8 17.5 + - - +
219A ASN* 4.2 15.3 - - - +
246A ALA* 3.8 16.8 - - + -
251A LYS* 3.9 20.8 + - + -
252A THR 3.8 1.6 - - - +
253A ALA* 3.5 31.9 - - + +
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Residues in contact with PHE 135 (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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133A PHE* 3.3 28.3 - + + -
134A LEU* 1.3 72.3 - - - +
136A ASP* 1.3 61.3 + - - +
137A ASP 4.1 6.3 - - - +
138A ILE* 5.0 2.5 - - + -
151A ILE* 3.6 31.0 - - + -
152A ASP 3.4 8.3 - - - +
153A ASP* 3.3 15.9 - - + -
216A ALA* 3.2 31.4 - - + -
251A LYS* 3.5 10.2 - - - +
252A THR* 3.0 39.4 + - + -
254A THR* 3.4 24.9 - - + -
259A PRO* 4.2 16.2 - - + -
260A MET* 4.2 3.8 - - + -
462G PHE* 6.3 0.4 - + - -
466G TYR* 3.8 23.8 - + - -
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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