Contacts of the strand formed by residues 123 - 135 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112F GLU* 4.9 4.5 - - - +
115F LEU* 3.7 4.9 - - - +
116F ARG* 4.7 6.7 - - - +
121F ALA 3.7 1.2 - - - -
122F ASP* 1.3 99.1 + - + +
124F VAL* 1.3 66.0 + - - +
125F LEU* 4.2 9.8 + - - +
227F THR* 5.0 15.5 - - + -
274F LEU* 3.5 5.5 - - - +
275F ALA* 3.0 39.4 + - - +
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Residues in contact with VAL 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F GLU* 4.0 19.1 + - + +
115F LEU* 3.8 29.2 - - + -
123F THR* 1.3 71.8 - - - +
125F LEU* 1.3 77.4 + - - +
126F PHE* 3.5 23.8 - - + -
227F THR* 3.3 2.8 - - - -
228F MET* 3.0 32.5 + - + -
272F MET* 5.4 1.1 - - + -
273F SER 4.3 2.2 - - - +
274F LEU* 3.6 17.3 - - + -
297F TYR* 4.3 5.4 - - - +
375F LEU* 3.8 23.8 - - + -
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Residues in contact with LEU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F THR* 4.2 10.1 - - - +
124F VAL* 1.3 89.4 - - - +
126F PHE* 1.3 62.6 + - - +
225F PHE* 3.5 30.7 - - + -
226F ASN 3.9 10.5 - - - +
227F THR* 4.0 10.3 - - + +
271F HIS 4.1 0.2 - - - -
272F MET* 3.0 32.6 - - - +
273F SER* 2.9 34.3 + - - +
275F ALA* 4.8 17.0 - - + -
4476F ADP 4.0 15.0 - - - +
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Residues in contact with PHE 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F VAL* 3.5 19.1 - - + -
125F LEU* 1.3 79.4 - - - +
127F GLY* 1.3 58.5 + - - +
128F PRO* 3.8 2.7 - - + -
225F PHE* 3.1 23.6 - - - -
226F ASN 3.1 17.5 + - - +
228F MET* 3.4 36.1 - - + -
231F LYS* 3.5 20.6 - - + +
270F CYS* 4.7 7.9 - - + -
271F HIS 3.3 2.9 - - - -
272F MET* 3.5 33.9 - - + -
371F PHE* 3.3 62.4 - + + -
374F LEU* 4.0 8.3 - - + -
375F LEU* 4.4 3.1 - - + -
4476F ADP 4.4 0.2 - - - -
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Residues in contact with GLY 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F PHE* 1.3 76.1 - - - +
128F PRO* 1.3 63.2 - - - +
129F GLU* 4.1 0.9 + - - +
225F PHE* 3.9 9.2 - - - -
269F HIS 3.7 1.6 - - - +
270F CYS* 4.7 0.4 - - - -
271F HIS* 2.9 44.0 + - - +
4476F ADP 3.2 27.8 + - - +
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Residues in contact with PRO 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F PHE* 4.5 1.1 - - + -
127F GLY* 1.3 89.5 - - - +
129F GLU* 1.3 63.0 + - - +
130F PRO* 3.2 10.9 - - - +
222F ALA* 5.6 0.3 - - - -
223F THR* 4.3 12.0 + - - +
231F LYS* 3.3 34.5 - - + -
235F ILE* 4.2 7.8 - - + +
268F MET* 3.8 28.0 - - + -
269F HIS 3.1 7.9 - - - +
270F CYS* 4.3 7.6 - - - -
371F PHE* 3.6 26.5 - - + -
4476F ADP 4.3 4.9 + - - +
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Residues in contact with GLU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F GLY 4.7 2.9 - - - +
128F PRO* 1.3 73.1 - - + +
130F PRO* 1.3 58.9 - - - +
131F GLU* 3.4 3.8 + - - +
220F GLU* 3.5 19.5 - - - +
221F VAL 5.6 0.2 - - - -
222F ALA* 5.8 2.7 - - + +
267F GLY 2.8 26.0 - - - +
268F MET* 3.2 7.1 - - - -
269F HIS* 2.9 22.1 + - + +
271F HIS* 3.4 13.3 + - - -
357F GLU* 2.8 6.8 - - - +
470F MN 1.9 33.5 + - - -
4476F ADP 2.6 55.7 + - - +
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Residues in contact with PRO 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F PRO 3.2 10.8 - - - +
129F GLU* 1.3 81.9 - - - +
131F GLU* 1.3 64.5 + - - +
132F PHE* 3.9 1.4 - - - -
220F GLU* 4.0 5.1 - - + +
221F VAL 4.1 15.7 - - - +
222F ALA* 5.7 0.2 - - - -
223F THR* 5.0 2.2 - - - +
235F ILE* 3.9 15.5 - - + -
238F TYR* 2.9 47.8 + - + -
239F LYS* 6.2 0.7 - - + -
255F PHE* 4.8 6.1 - - + -
267F GLY 3.9 2.7 - - - +
268F MET* 3.7 35.4 - - + -
363F PRO* 4.7 4.3 - - + -
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Residues in contact with GLU 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F GLU 4.4 1.3 - - - +
130F PRO* 1.3 71.6 - - - +
132F PHE* 1.3 65.3 + - - +
212F GLU* 3.1 15.5 - - + +
218F GLN* 4.8 2.9 - - - +
219F ASN 3.8 4.7 - - - +
220F GLU* 3.0 26.5 - - + +
255F PHE* 3.4 15.2 - - - -
266F SER* 3.7 15.3 - - - -
267F GLY 3.0 28.3 + - - +
269F HIS* 4.8 2.0 - - - -
363F PRO* 3.5 11.1 - - - +
469F MN 2.3 30.7 + - - +
5905F PPQ 2.4 43.9 + - - +
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Residues in contact with PHE 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F PRO 3.9 4.0 - - - -
131F GLU* 1.3 80.9 - - - +
133F PHE* 1.3 75.4 + - - +
134F LEU* 3.9 17.9 - - + -
192F ARG* 5.5 0.2 - - + -
195F MET* 4.0 21.1 - - - -
218F GLN* 3.2 6.3 - - - +
219F ASN* 2.7 68.6 + - + -
220F GLU* 4.2 2.9 - - - -
221F VAL* 4.3 7.6 - - + -
238F TYR* 3.5 20.0 - + - -
242F VAL* 3.9 25.4 - - + -
254F THR 3.5 16.4 - - - +
255F PHE* 3.7 25.8 - + + -
266F SER* 4.0 5.6 - - - -
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Residues in contact with PHE 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F PHE* 1.3 78.0 - - - +
134F LEU* 1.3 64.9 + - - +
135F PHE* 3.3 22.7 - + + -
214F ALA* 3.6 9.6 - - + -
215F THR 3.6 2.5 - - - -
216F ALA 3.5 18.2 - - - -
217F GLY 3.3 3.6 - - - -
218F GLN* 3.4 32.8 - - + -
252F THR 3.9 0.5 - - - +
253F ALA* 3.3 7.3 - - - +
254F THR* 3.2 32.5 + - + +
256F MET 4.9 0.4 - - - -
259F PRO* 3.3 26.9 - - + -
260F MET* 3.1 29.4 - - + -
264F ASN 3.4 21.8 - - - -
266F SER* 3.3 25.4 - - - -
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Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F PHE* 3.9 21.5 - - + -
133F PHE* 1.3 75.0 - - - +
135F PHE* 1.3 62.4 + - - +
153F ASP* 3.1 22.8 - - - +
188F ALA* 4.9 4.7 - - + -
191F ILE* 4.4 28.0 - - + -
192F ARG* 5.6 1.6 - - + -
195F MET* 4.5 7.4 - - + -
216F ALA 3.6 6.8 - - - +
217F GLY* 2.8 17.7 + - - +
219F ASN* 4.2 14.4 - - - +
246F ALA* 3.8 17.3 - - + -
251F LYS* 3.9 20.1 + - + -
252F THR 3.8 1.6 - - - +
253F ALA* 3.5 31.0 - - + +
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Residues in contact with PHE 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F PHE* 3.3 28.0 - + + -
134F LEU* 1.3 71.9 - - - +
136F ASP* 1.3 60.7 + - - +
137F ASP 4.1 6.5 - - - +
138F ILE* 5.0 3.1 - - + -
151F ILE* 3.6 32.5 - - + -
152F ASP 3.4 8.3 - - - +
153F ASP* 3.3 16.2 - - + -
216F ALA* 3.2 31.9 - - + -
251F LYS* 3.5 9.7 - - - +
252F THR* 3.0 38.9 + - + -
254F THR* 3.4 24.9 - - + -
259F PRO* 4.2 16.8 - - + -
260F MET* 4.2 4.0 - - + -
462L PHE* 6.3 0.2 - + - -
466L 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