Contacts of the strand formed by residues 123 - 135 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I GLU* 4.9 4.3 - - - +
115I LEU* 3.7 5.3 - - - +
116I ARG* 4.7 7.0 - - - +
121I ALA 3.7 1.0 - - - -
122I ASP* 1.3 97.5 + - - +
124I VAL* 1.3 65.3 + - - +
125I LEU* 4.2 10.2 + - - +
227I THR* 5.0 16.8 - - + -
274I LEU* 3.5 5.0 - - - +
275I ALA* 3.0 40.1 + - - +
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Residues in contact with VAL 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112I GLU* 4.0 20.0 + - + +
115I LEU* 3.8 29.4 - - + -
123I THR* 1.3 71.8 - - - +
125I LEU* 1.3 78.3 + - - +
126I PHE* 3.5 23.8 - - + -
227I THR* 3.3 2.8 - - - -
228I MET* 3.0 32.3 + - + -
272I MET* 5.4 1.1 - - + -
273I SER 4.3 2.5 - - - +
274I LEU* 3.6 16.4 - - + -
297I TYR* 4.3 5.8 - - + +
375I LEU* 3.8 23.8 - - + -
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Residues in contact with LEU 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123I THR* 4.8 9.4 - - - +
124I VAL* 1.3 90.5 - - - +
126I PHE* 1.3 62.5 + - - +
225I PHE* 3.5 29.4 - - + -
226I ASN 3.9 11.2 - - - +
227I THR* 4.0 10.3 - - + +
271I HIS 4.1 0.2 - - - -
272I MET* 3.0 33.1 - - - +
273I SER* 2.9 34.0 + - - +
275I ALA* 4.8 17.9 - - + -
4479I ADP 4.0 16.6 - - + +
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Residues in contact with PHE 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I VAL* 3.5 19.1 - - + -
125I LEU* 1.3 79.4 - - - +
127I GLY* 1.3 59.4 + - - +
128I PRO* 3.8 2.2 - - + -
225I PHE* 3.1 23.1 - - - -
226I ASN 3.1 16.2 + - - +
228I MET* 3.4 36.1 - - + -
231I LYS* 3.5 21.5 - - + +
270I CYS* 4.7 7.4 - - - -
271I HIS 3.3 3.6 - - - -
272I MET* 3.5 33.2 - - + -
371I PHE* 3.3 60.8 - + + -
374I LEU* 4.0 8.5 - - + -
375I LEU* 4.4 3.6 - - + -
4479I ADP 4.4 0.2 - - - -
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Residues in contact with GLY 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I PHE* 1.3 75.7 - - - +
128I PRO* 1.3 63.2 - - - +
129I GLU* 4.7 0.7 - - - +
225I PHE* 3.9 9.6 - - - -
269I HIS 3.7 1.6 - - - +
270I CYS* 4.7 0.4 - - - -
271I HIS* 2.9 43.5 + - - +
4479I ADP 3.2 27.5 + - - +
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Residues in contact with PRO 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I PHE* 4.5 1.1 - - + -
127I GLY* 1.3 90.2 - - - +
129I GLU* 1.3 62.2 + - - +
130I PRO* 3.2 10.9 - - - +
222I ALA* 5.6 0.3 - - - -
223I THR* 4.3 12.0 + - - +
231I LYS* 3.3 34.3 - - + -
235I ILE* 4.2 7.4 - - + -
268I MET* 3.8 28.3 - - + -
269I HIS 3.1 7.9 - - - +
270I CYS* 4.3 8.5 - - - -
371I PHE* 3.6 26.9 - - + -
4479I ADP 4.3 4.7 + - - +
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Residues in contact with GLU 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I GLY 4.7 2.7 - - - +
128I PRO* 1.3 73.6 - - + +
130I PRO* 1.3 57.9 - - - +
131I GLU* 3.4 3.7 + - - +
220I GLU* 3.5 20.0 - - - +
222I ALA* 5.8 3.1 - - + +
267I GLY 2.8 25.8 - - - +
268I MET* 3.2 7.5 - - - -
269I HIS* 2.9 21.2 + - + +
271I HIS* 3.4 13.3 + - - -
357I GLU* 2.8 6.8 - - - +
470I MN 1.9 33.7 + - - -
4479I ADP 2.6 54.4 + - - +
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Residues in contact with PRO 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I PRO 3.2 10.8 - - - +
129I GLU* 1.3 80.8 - - - +
131I GLU* 1.3 64.5 + - - +
132I PHE* 3.9 1.2 - - - -
220I GLU* 4.0 4.7 - - + +
221I VAL 4.1 16.2 - - - +
223I THR* 5.0 1.6 - - - +
235I ILE* 3.9 15.7 - - + -
238I TYR* 2.9 47.8 + - + -
239I LYS* 6.2 0.9 - - + -
255I PHE* 4.8 6.1 - - + -
267I GLY 3.9 2.7 - - - +
268I MET* 3.7 35.4 - - + -
363I PRO* 4.7 4.5 - - + -
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Residues in contact with GLU 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I GLU 4.4 0.9 - - - +
130I PRO* 1.3 71.9 - - - +
132I PHE* 1.3 64.5 + - - +
212I GLU* 3.1 16.5 - - + +
218I GLN* 4.8 2.9 - - - +
219I ASN 3.8 5.4 - - - +
220I GLU* 3.0 26.7 - - + +
255I PHE* 3.4 15.4 - - - -
266I SER* 3.7 16.3 - - - -
267I GLY 3.0 28.1 + - - +
269I HIS* 4.8 1.7 - - - -
363I PRO* 3.5 11.3 - - - +
469I MN 2.3 30.1 + - - -
5908I PPQ 2.4 43.1 + - - +
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Residues in contact with PHE 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I PRO 3.9 3.6 - - - -
131I GLU* 1.3 79.3 - - - +
133I PHE* 1.3 74.3 + - - +
134I LEU* 3.9 17.5 - - + -
192I ARG* 5.5 0.4 - - + -
195I MET* 4.0 20.9 - - - -
218I GLN* 3.2 6.4 - - - +
219I ASN* 2.7 68.4 + - + -
220I GLU* 4.2 2.2 - - - -
221I VAL* 4.3 8.3 - - + -
238I TYR* 3.5 19.3 - - - -
242I VAL* 3.9 25.8 - - + -
253I ALA* 4.8 0.2 - - + -
254I THR 3.5 17.3 - - - +
255I PHE* 3.7 26.2 - + + -
266I SER* 4.0 6.0 - - - -
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Residues in contact with PHE 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I PHE* 1.3 77.4 - - - +
134I LEU* 1.3 65.3 + - - +
135I PHE* 3.3 22.2 - + + -
214I ALA* 3.6 9.9 - - + -
215I THR 3.6 2.2 - - - -
216I ALA 3.5 17.5 - - - -
217I GLY 3.3 3.6 - - - -
218I GLN* 3.4 31.6 - - + -
252I THR 3.9 0.3 - - - +
253I ALA* 3.3 6.8 - - - +
254I THR* 3.2 32.9 + - + -
256I MET 4.9 0.4 - - - -
259I PRO* 3.3 27.1 - - + -
260I MET* 3.1 30.1 - - + -
264I ASN 3.4 21.8 - - - -
266I SER* 3.3 24.5 - - - -
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Residues in contact with LEU 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I PHE* 3.9 21.5 - - + -
133I PHE* 1.3 75.2 - - - +
135I PHE* 1.3 63.6 + - - +
153I ASP* 3.1 22.6 - - - +
188I ALA* 4.9 4.5 - - + -
191I ILE* 4.4 27.6 - - + -
192I ARG* 5.6 1.8 - - + -
195I MET* 4.5 6.5 - - + -
216I ALA 3.6 7.1 + - - +
217I GLY* 2.8 17.5 + - - +
219I ASN* 4.2 14.8 - - - +
246I ALA* 3.8 17.5 - - + -
251I LYS* 3.9 20.7 + - + -
252I THR 3.8 1.3 - - - +
253I ALA* 3.5 31.4 - - + +
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Residues in contact with PHE 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462C PHE* 6.3 0.2 - + - -
466C TYR* 3.9 23.3 - + - -
133I PHE* 3.3 28.3 - + + -
134I LEU* 1.3 71.9 - - - +
136I ASP* 1.3 61.1 + - - +
137I ASP 4.1 6.3 - - - +
138I ILE* 5.0 2.9 - - + -
151I ILE* 3.6 32.5 - - + -
152I ASP 3.4 8.5 - - - +
153I ASP* 3.3 16.6 - - + -
216I ALA* 3.2 32.3 - - + -
251I LYS* 3.5 10.2 - - - +
252I THR* 3.0 39.0 + - + -
254I THR* 3.4 24.7 - - + -
259I PRO* 4.2 16.4 - - + -
260I MET* 4.2 3.1 - - + -
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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