Contacts of the strand formed by residues 123 - 135 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112H GLU* 5.1 3.4 - - - +
115H LEU* 3.9 3.9 - - - +
116H ARG* 5.0 4.7 - - - +
121H ALA 3.8 0.6 - - - -
122H ASP* 1.3 98.5 + - + +
124H VAL* 1.3 62.8 + - - +
125H LEU* 4.2 13.7 + - - +
227H THR* 4.7 15.3 - - + -
274H LEU* 3.7 5.9 - - - +
275H ALA* 3.1 40.4 + - - +
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Residues in contact with VAL 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H GLU* 3.4 24.1 + - + +
115H LEU* 3.7 19.7 - - + -
123H THR* 1.3 73.6 - - - +
125H LEU* 1.3 65.0 + - - +
126H PHE* 3.9 14.8 - - + -
227H THR* 3.2 8.3 - - - -
228H MET* 3.0 31.2 + - + -
272H MET* 6.0 1.1 - - + -
273H SER 3.9 2.9 - - - +
274H LEU* 3.3 21.3 - - + -
297H TYR* 4.7 3.6 - - + +
375H LEU* 3.7 35.0 - - + -
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Residues in contact with LEU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H THR* 4.2 8.9 - - - +
124H VAL* 1.3 85.5 - - - +
126H PHE* 1.3 65.2 + - - +
225H PHE* 3.6 33.2 - - + -
226H ASN 3.7 1.6 - - - +
227H THR* 4.2 21.8 - - + +
271H HIS 4.4 0.4 - - - -
272H MET* 3.2 25.8 - - - +
273H SER* 2.9 35.9 + - - +
275H ALA* 5.0 14.6 - - + -
1478H ADP 4.1 13.2 - - - +
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Residues in contact with PHE 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H VAL* 3.9 17.5 - - + -
125H LEU* 1.3 78.6 - - - +
127H GLY* 1.3 59.3 + - - +
128H PRO* 3.9 1.8 - - + -
225H PHE* 3.1 6.1 - - - -
226H ASN 2.9 37.6 + - - +
228H MET* 3.5 36.3 - - + -
231H LYS* 3.4 21.2 - - + +
270H CYS* 4.7 6.7 - - + -
271H HIS 3.5 2.2 - - - -
272H MET* 3.5 35.7 - - + -
297H TYR* 4.8 0.2 - - - -
371H PHE* 3.3 59.7 - + + -
374H LEU* 4.1 8.7 - - + -
375H LEU* 4.6 2.9 - - + -
1478H ADP 4.4 0.2 - - - -
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Residues in contact with GLY 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H PHE* 1.3 75.1 - - - +
128H PRO* 1.3 67.4 - - - +
225H PHE* 3.9 2.9 - - - -
269H HIS 3.7 0.5 - - - +
270H CYS* 4.6 0.4 - - - -
271H HIS* 2.9 46.9 + - - -
1478H ADP 3.9 28.9 - - - +
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Residues in contact with PRO 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H PHE* 4.8 0.9 - - + -
127H GLY* 1.3 88.4 - - - +
129H GLU* 1.3 60.4 + - - +
130H PRO* 3.2 9.4 - - - +
222H ALA* 5.9 0.2 - - - -
223H THR* 4.7 10.0 + - - +
231H LYS* 3.3 29.2 - - + -
235H ILE* 3.9 16.8 - - + -
268H MET* 3.8 26.2 - - + -
269H HIS 3.1 8.7 - - - +
270H CYS* 4.4 5.4 - - - -
371H PHE* 3.4 30.1 - - + -
1478H ADP 4.4 5.7 + - - -
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Residues in contact with GLU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H PRO* 1.3 75.6 - - - +
130H PRO* 1.3 62.7 - - - +
131H GLU* 3.5 5.2 + - - +
220H GLU* 3.6 10.4 - - - +
221H VAL 5.9 0.2 - - - -
222H ALA* 5.9 4.3 - - + +
267H GLY 3.2 14.4 - - - +
268H MET* 3.4 7.0 - - - +
269H HIS* 2.7 29.7 + - + +
271H HIS* 3.1 16.3 + - + -
357H GLU* 2.5 9.9 - - - +
470H MN 2.0 37.2 + - - -
1478H ADP 2.6 61.3 + - - +
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Residues in contact with PRO 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H PRO* 3.2 17.7 - - + +
129H GLU* 1.3 83.5 - - - +
131H GLU* 1.3 61.1 + - - +
132H PHE* 4.3 0.2 - - - -
220H GLU* 3.7 8.0 - - - +
221H VAL 4.9 3.6 - - - +
222H ALA* 6.2 0.2 - - - -
223H THR* 5.4 3.1 - - - +
235H ILE* 3.8 17.7 - - + -
238H TYR* 2.9 58.5 + - + -
239H LYS* 6.5 0.2 - - + -
255H PHE* 4.8 3.8 - - + -
267H GLY 3.7 4.9 - - - +
268H MET* 3.8 21.8 - - + -
363H PRO* 4.4 10.8 - - + -
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Residues in contact with GLU 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H GLU 4.2 2.7 - - - +
130H PRO* 1.3 73.9 - - - +
132H PHE* 1.3 64.9 + - - +
212H GLU* 2.9 19.2 - - + +
218H GLN* 4.5 3.8 - - - +
219H ASN 3.8 5.6 - - - +
220H GLU* 3.3 22.2 - - + +
255H PHE* 3.5 6.1 - - - -
266H SER* 3.5 16.8 - - - +
267H GLY* 2.9 27.2 + - - +
269H HIS* 5.7 3.8 + - - -
363H PRO* 3.4 18.8 - - - +
469H MN 2.0 34.3 + - - -
474H TL 2.7 30.6 - - - -
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Residues in contact with PHE 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H PRO 4.3 0.4 - - - -
131H GLU* 1.3 79.7 - - - +
133H PHE* 1.3 65.4 + - - +
134H LEU* 3.9 25.1 - - + -
192H ARG* 5.4 1.3 - - + -
195H MET* 3.8 23.3 - - + -
218H GLN* 3.2 7.6 - - - +
219H ASN* 2.8 65.7 + - + -
220H GLU* 4.0 6.5 - - - -
221H VAL* 4.2 7.6 - - + -
238H TYR* 3.6 24.2 - + - -
242H VAL* 3.8 26.9 - - + -
253H ALA* 4.7 0.2 - - + -
254H THR 3.4 15.3 - - - +
255H PHE* 3.6 22.9 - + + -
266H SER* 3.8 4.4 + - - -
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Residues in contact with PHE 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H PHE* 1.3 75.4 - - - +
134H LEU* 1.3 62.4 + - - +
135H PHE* 3.7 23.3 - + + -
214H ALA* 3.5 15.3 - - + -
215H THR 3.7 4.0 - - - -
216H ALA 3.7 11.7 - - - -
217H GLY 3.3 3.4 - - - -
218H GLN* 3.5 32.3 - - + -
252H THR 3.8 0.9 - - - +
253H ALA* 3.2 7.8 - - - +
254H THR* 3.0 38.8 + - + +
256H MET 4.8 2.5 - - - -
259H PRO* 3.5 27.4 - - + -
260H MET* 3.4 23.8 - - + -
264H ASN 3.5 21.5 - - - -
266H SER* 3.4 27.4 - - - -
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Residues in contact with LEU 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H PHE* 3.9 20.2 - - + -
133H PHE* 1.3 74.2 - - - +
135H PHE* 1.3 61.8 + - - +
153H ASP* 3.4 12.9 - - - +
188H ALA* 4.6 10.3 - - + -
191H ILE* 4.0 30.5 - - + -
192H ARG* 5.7 1.3 - - + -
195H MET* 4.1 8.3 - - + -
216H ALA 3.5 13.3 - - - +
217H GLY* 2.8 16.3 + - - +
219H ASN* 3.9 17.5 - - - +
246H ALA* 3.8 17.7 - - + -
251H LYS* 4.0 15.6 + - + -
252H THR 3.6 1.6 - - - +
253H ALA* 3.6 27.8 - - + -
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Residues in contact with PHE 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B PHE* 5.9 0.2 - + - -
466B TYR* 3.8 23.8 - + - -
133H PHE* 3.7 25.6 - + + -
134H LEU* 1.3 72.8 - - - +
136H ASP* 1.3 61.0 + - - +
137H ASP 4.2 4.9 - - - +
138H ILE* 4.8 5.2 - - + -
151H ILE* 3.6 40.8 - - + -
152H ASP 3.6 6.7 - - - +
153H ASP* 3.4 14.4 - - + -
216H ALA* 3.1 32.8 - - + -
251H LYS* 3.3 9.9 - - - +
252H THR* 2.9 40.9 + - + -
254H THR* 3.9 20.6 - - + -
259H PRO* 4.2 15.9 - - + -
260H MET* 4.6 2.9 - - + -
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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