Contacts of the strand formed by residues 123 - 135 (chain D) in PDB entry 1F1H
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D GLU* 5.1 2.7 - - - +
115D LEU* 3.9 4.6 - - - +
116D ARG* 5.0 4.5 - - - +
121D ALA 3.8 0.4 - - - -
122D ASP* 1.3 99.8 + - + +
124D VAL* 1.3 63.0 + - - +
125D LEU* 4.2 13.3 + - - +
227D THR* 4.7 15.0 - - + -
274D LEU* 3.7 5.7 - - - +
275D ALA* 3.1 41.0 + - - +
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Residues in contact with VAL 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D GLU* 3.4 24.2 + - + +
115D LEU* 3.7 19.5 - - + -
123D THR* 1.3 73.6 - - - +
125D LEU* 1.3 63.4 + - - +
126D PHE* 3.9 14.8 - - + -
227D THR* 3.2 8.5 - - - -
228D MET* 3.0 31.0 + - + -
272D MET* 6.0 1.3 - - + -
273D SER 3.9 4.3 - - - +
274D LEU* 3.3 21.5 - - + -
297D TYR* 4.7 3.1 - - - +
375D LEU* 3.7 36.1 - - + -
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D THR* 4.2 9.8 - - - +
124D VAL* 1.3 83.7 - - - +
126D PHE* 1.3 65.4 + - - +
225D PHE* 3.6 33.4 - - + -
226D ASN 3.7 2.0 - - - +
227D THR* 4.2 22.4 - - + +
271D HIS 4.4 0.2 - - - -
272D MET* 3.2 25.8 - - - +
273D SER* 2.9 35.0 + - - +
275D ALA* 5.0 14.4 - - + -
1474D ADP 4.1 12.3 - - - +
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Residues in contact with PHE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D VAL* 3.9 17.7 - - + -
125D LEU* 1.3 79.4 - - - +
127D GLY* 1.3 59.7 + - - +
128D PRO* 3.9 2.2 - - + -
225D PHE* 3.1 5.8 - - - -
226D ASN 2.9 36.0 + - - +
228D MET* 3.5 36.3 - - + -
231D LYS* 3.4 21.6 - - + +
270D CYS* 4.7 7.6 - - + -
271D HIS 3.5 2.5 - - - -
272D MET* 3.5 36.3 - - + -
371D PHE* 3.3 59.7 - + + -
374D LEU* 4.1 8.5 - - + -
375D LEU* 4.6 3.6 - - + -
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Residues in contact with GLY 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 1.3 76.5 - - - +
128D PRO* 1.3 67.0 - - - +
225D PHE* 3.9 3.6 - - - -
269D HIS 3.7 0.3 - - - +
270D CYS* 4.6 0.2 - - - -
271D HIS* 2.9 46.0 + - - -
1474D ADP 3.9 28.6 - - - +
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Residues in contact with PRO 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D PHE* 4.8 0.9 - - + -
127D GLY* 1.3 87.6 - - - +
129D GLU* 1.3 61.3 + - - +
130D PRO* 3.2 8.3 - - - +
222D ALA* 5.9 0.2 - - - -
223D THR* 4.7 10.2 + - - +
231D LYS* 3.3 29.6 - - + -
235D ILE* 3.9 15.7 - - + -
268D MET* 3.8 26.7 - - + -
269D HIS 3.1 8.5 - - - +
270D CYS* 4.4 5.1 - - - -
371D PHE* 3.4 30.5 - - + -
1474D ADP 4.4 5.9 + - - +
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Residues in contact with GLU 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D PRO* 1.3 76.1 - - - +
130D PRO* 1.3 62.6 - - - +
131D GLU* 3.5 4.5 + - - +
220D GLU* 3.6 10.3 - - - +
221D VAL 5.9 0.4 - - - -
222D ALA* 5.9 4.3 - - + +
267D GLY 3.2 13.9 - - - +
268D MET* 3.4 6.9 - - - +
269D HIS* 2.7 30.1 + - + +
271D HIS* 3.1 16.3 + - + -
357D GLU* 2.5 10.6 - - - +
470D MN 2.0 37.2 + - - -
1474D ADP 2.6 61.6 + - - +
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Residues in contact with PRO 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D PRO* 3.2 18.2 - - + +
129D GLU* 1.3 85.5 - - - +
131D GLU* 1.3 61.0 + - - +
132D PHE* 4.3 0.2 - - - -
220D GLU* 3.7 8.0 - - - +
221D VAL 4.9 3.4 - - - +
223D THR* 5.4 3.1 - - - +
235D ILE* 3.8 17.9 - - + -
238D TYR* 2.9 59.1 + - + +
239D LYS* 6.5 0.4 - - + -
255D PHE* 4.8 3.1 - - + -
267D GLY 3.7 5.2 - - - +
268D MET* 3.8 21.5 - - + -
363D PRO* 4.4 10.3 - - + -
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLU 4.2 2.5 - - - +
130D PRO* 1.3 73.9 - - - +
132D PHE* 1.3 65.8 + - - +
212D GLU* 2.9 17.9 - - + +
218D GLN* 4.5 3.8 - - - +
219D ASN 3.8 5.4 - - - +
220D GLU* 3.3 22.2 - - + +
255D PHE* 3.5 6.4 - - - -
266D SER* 3.5 16.2 - - - +
267D GLY* 2.9 28.4 + - - +
269D HIS* 5.7 4.0 + - - -
363D PRO* 3.4 18.8 - - - +
469D MN 2.0 34.9 + - - -
474D TL 2.7 30.4 - - - -
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Residues in contact with PHE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D GLU* 1.3 80.4 - - - +
133D PHE* 1.3 64.3 + - - +
134D LEU* 3.9 24.9 - - + -
192D ARG* 5.4 1.3 - - + -
195D MET* 3.8 23.1 - - + -
218D GLN* 3.2 7.3 - - - +
219D ASN* 2.8 64.6 + - + -
220D GLU* 4.0 6.5 - - - -
221D VAL* 4.2 8.3 - - + -
238D TYR* 3.6 24.2 - + - -
242D VAL* 3.8 27.8 - - + -
253D ALA* 4.7 0.2 - - + -
254D THR 3.4 14.8 - - - +
255D PHE* 3.6 22.9 - + + -
266D SER* 3.8 4.7 - - - -
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Residues in contact with PHE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PHE* 1.3 76.9 - - - +
134D LEU* 1.3 62.3 + - - +
135D PHE* 3.7 22.7 - + + -
214D ALA* 3.5 14.8 - - + -
215D THR 3.7 3.8 - - - -
216D ALA 3.7 11.9 - - - -
217D GLY 3.3 3.4 - - - -
218D GLN* 3.5 33.0 - - + -
252D THR 3.8 0.9 - - - +
253D ALA* 3.2 8.0 - - - +
254D THR* 3.0 39.2 + - + +
256D MET 4.8 2.2 - - - -
259D PRO* 3.5 27.8 - - + -
260D MET* 3.4 23.6 - - + -
264D ASN 3.5 21.5 - - - -
266D SER* 3.4 27.4 - - - -
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Residues in contact with LEU 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D PHE* 3.9 18.8 - - + -
133D PHE* 1.3 74.7 - - - +
135D PHE* 1.3 61.7 + - - +
153D ASP* 3.4 12.6 - - - +
188D ALA* 4.5 10.3 - - + -
191D ILE* 4.0 29.8 - - + -
192D ARG* 5.7 1.6 - - + -
195D MET* 4.1 8.7 - - + -
216D ALA 3.5 13.7 - - - +
217D GLY* 2.8 16.4 + - - +
219D ASN* 3.9 17.9 - - + +
246D ALA* 3.8 17.3 - - + -
251D LYS* 4.0 14.7 - - + -
252D THR 3.6 1.8 - - - +
253D ALA* 3.6 28.5 - - + -
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Residues in contact with PHE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D PHE* 3.7 27.4 - + + -
134D LEU* 1.3 72.5 - - - +
136D ASP* 1.3 61.6 + - - +
137D ASP 4.2 5.2 - - - +
138D ILE* 4.8 5.6 - - + -
151D ILE* 3.6 40.2 - - + -
152D ASP 3.6 6.1 - - - +
153D ASP* 3.4 14.8 - - + -
216D ALA* 3.1 31.6 - - + -
251D LYS* 3.3 9.8 - - - +
252D THR* 2.9 40.6 + - + -
254D THR* 3.9 20.6 - - + -
259D PRO* 4.2 15.3 - - + -
260D MET* 4.6 2.7 - - + -
462J PHE* 6.0 0.2 - + - -
466J TYR* 3.9 23.1 - + - -
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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