Contacts of the strand formed by residues 123 - 135 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C GLU* 5.1 3.6 - - - +
115C LEU* 3.9 4.0 - - - +
116C ARG* 5.0 4.5 - - - +
121C ALA 3.8 0.2 - - - -
122C ASP* 1.3 97.6 + - + +
124C VAL* 1.3 62.6 + - - +
125C LEU* 4.2 13.3 + - - +
227C THR* 4.7 15.3 - - + -
274C LEU* 3.7 5.7 - - - +
275C ALA* 3.1 40.8 + - - +
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Residues in contact with VAL 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C GLU* 3.4 24.4 + - + +
115C LEU* 3.7 19.5 - - + -
123C THR* 1.3 74.7 - - - +
125C LEU* 1.3 64.0 + - - +
126C PHE* 3.9 15.3 - - + -
227C THR* 3.2 8.0 - - - -
228C MET* 3.0 32.0 + - + -
272C MET* 6.0 1.1 - - + -
273C SER 3.9 3.4 - - - +
274C LEU* 3.3 20.9 - - + -
297C TYR* 4.7 3.8 - - - +
375C LEU* 3.7 35.2 - - + -
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C THR* 4.2 9.2 - - - +
124C VAL* 1.3 85.6 - - - +
126C PHE* 1.3 64.7 + - - +
225C PHE* 3.6 32.8 - - + -
226C ASN 3.7 2.0 - - - +
227C THR* 4.2 22.4 - - + +
272C MET* 3.2 25.8 - - - +
273C SER* 2.9 34.0 + - - +
275C ALA* 5.0 14.8 - - + -
1473C ADP 4.1 13.0 - - - +
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Residues in contact with PHE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C VAL* 3.9 16.4 - - + -
125C LEU* 1.3 78.8 - - - +
127C GLY* 1.3 57.8 + - - +
128C PRO* 3.9 2.2 - - + -
225C PHE* 3.1 5.9 - - - -
226C ASN 2.9 36.8 + - - +
228C MET* 3.5 36.1 - - + -
231C LYS* 3.4 21.0 - - + +
270C CYS* 4.7 7.6 - - + -
271C HIS 3.5 2.5 - - - -
272C MET* 3.5 37.0 - - + -
297C TYR* 5.0 0.2 - - - -
371C PHE* 3.3 60.6 - + + -
374C LEU* 4.1 8.3 - - + -
375C LEU* 4.6 3.4 - - + -
1473C ADP 4.4 0.2 - - - -
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Residues in contact with GLY 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PHE* 1.3 75.3 - - - +
128C PRO* 1.3 66.1 - - - +
225C PHE* 3.9 3.6 - - - -
269C HIS 3.7 0.3 - - - +
270C CYS* 4.6 0.4 - - - -
271C HIS* 2.9 47.4 + - - -
1473C ADP 3.9 29.2 - - - +
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Residues in contact with PRO 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PHE* 4.8 0.9 - - + -
127C GLY* 1.3 88.4 - - - +
129C GLU* 1.3 59.4 + - - +
130C PRO* 3.2 8.7 - - - +
222C ALA* 5.9 0.3 - - - -
223C THR* 4.7 10.0 + - - +
231C LYS* 3.3 30.1 - - + -
235C ILE* 3.9 15.7 - - + -
268C MET* 3.8 26.7 - - + -
269C HIS 3.1 8.1 - - - +
270C CYS* 4.4 5.6 - - - -
371C PHE* 3.4 29.6 - - + -
1473C ADP 4.4 5.9 + - - +
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Residues in contact with GLU 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C PRO* 1.3 77.1 - - - +
130C PRO* 1.3 62.1 - - - +
131C GLU* 3.5 4.7 + - - +
220C GLU* 3.6 10.1 - - - +
221C VAL 5.9 0.4 - - - -
222C ALA* 5.9 4.0 - - + +
267C GLY 3.2 14.6 - - - +
268C MET* 3.4 6.1 - - - +
269C HIS* 2.7 28.8 + - + +
271C HIS* 3.1 16.1 + - + -
357C GLU* 2.5 10.3 - - - +
470C MN 2.0 37.4 + - - -
1473C ADP 2.6 61.1 + - - +
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Residues in contact with PRO 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C PRO* 3.2 18.4 - - + +
129C GLU* 1.3 84.2 - - - +
131C GLU* 1.3 60.9 + - - +
132C PHE* 4.3 0.2 - - - -
220C GLU* 3.7 8.1 - - - +
221C VAL 4.9 3.4 - - - +
222C ALA* 6.2 0.2 - - - -
223C THR* 5.4 2.9 - - - +
235C ILE* 3.8 18.8 - - + -
238C TYR* 2.9 58.5 + - + +
239C LYS* 6.5 0.2 - - + -
255C PHE* 4.8 3.6 - - + -
267C GLY 3.7 5.2 - - - +
268C MET* 3.8 21.1 - - + -
363C PRO* 4.4 10.8 - - + -
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Residues in contact with GLU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C GLU 4.2 2.7 - - - +
130C PRO* 1.3 73.9 - - - +
132C PHE* 1.3 65.0 + - - +
212C GLU* 2.9 18.4 - - + +
218C GLN* 4.5 3.4 - - - +
219C ASN 3.8 5.2 - - - +
220C GLU* 3.3 22.7 - - + +
255C PHE* 3.5 6.4 - - - -
266C SER* 3.5 16.1 - - - +
267C GLY* 2.9 29.4 + - - +
269C HIS* 5.7 4.0 + - - -
363C PRO* 3.4 18.0 - - - +
469C MN 2.0 34.3 + - - -
474C TL 2.7 30.8 - - - -
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Residues in contact with PHE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C PRO 4.3 0.2 - - - -
131C GLU* 1.3 79.6 - - - +
133C PHE* 1.3 65.2 + - - +
134C LEU* 3.9 24.5 - - + -
192C ARG* 5.4 1.6 - - + -
195C MET* 3.8 24.0 - - + -
218C GLN* 3.2 7.1 - - - +
219C ASN* 2.8 66.0 + - + -
220C GLU* 4.0 6.3 - - - -
221C VAL* 4.2 7.9 - - + -
238C TYR* 3.6 24.2 - + - -
242C VAL* 3.8 27.4 - - + -
254C THR 3.4 15.7 - - - +
255C PHE* 3.6 21.3 - + + -
266C SER* 3.8 4.5 + - - -
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Residues in contact with PHE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C PHE* 1.3 76.4 - - - +
134C LEU* 1.3 62.9 + - - +
135C PHE* 3.7 22.9 - + + -
214C ALA* 3.5 15.0 - - + -
215C THR 3.7 3.6 - - - -
216C ALA 3.7 11.7 - - - -
217C GLY 3.3 3.6 - - - -
218C GLN* 3.5 32.1 - - + -
252C THR 3.8 0.9 - - - +
253C ALA* 3.2 8.3 - - - +
254C THR* 3.0 38.3 + - + +
256C MET 4.8 2.7 - - - -
259C PRO* 3.5 28.0 - - + -
260C MET* 3.4 24.0 - - + -
264C ASN 3.5 21.1 - - - -
266C SER* 3.4 27.8 - - - -
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C PHE* 3.9 19.7 - - + -
133C PHE* 1.3 73.4 - - - +
135C PHE* 1.3 61.4 + - - +
153C ASP* 3.4 12.7 - - - +
188C ALA* 4.6 11.0 - - + -
191C ILE* 4.0 29.8 - - + -
192C ARG* 5.7 1.6 - - + -
195C MET* 4.1 8.5 - - + -
216C ALA 3.5 13.3 - - - +
217C GLY* 2.8 16.6 + - - +
219C ASN* 3.9 17.3 - - - +
246C ALA* 3.8 17.5 - - + -
251C LYS* 4.0 16.0 - - + -
252C THR 3.6 2.5 - - - +
253C ALA* 3.6 28.3 - - + -
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Residues in contact with PHE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C PHE* 3.7 25.6 - + + -
134C LEU* 1.3 73.5 - - - +
136C ASP* 1.3 61.2 + - - +
137C ASP 4.2 4.9 - - - +
138C ILE* 4.8 5.2 - - + -
151C ILE* 3.6 40.6 - - + -
152C ASP 3.6 6.3 - - - +
153C ASP* 3.4 14.4 - - + -
216C ALA* 3.1 32.3 - - + -
251C LYS* 3.3 10.1 - - - +
252C THR* 2.9 40.3 + - + -
254C THR* 3.9 20.4 - - + -
259C PRO* 4.2 15.5 - - + -
260C MET* 4.6 3.1 - - + -
462I PHE* 5.9 0.2 - + - -
466I TYR* 3.8 24.0 - + - -
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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