Contacts of the strand formed by residues 123 - 135 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B GLU* 5.1 3.4 - - - +
115B LEU* 3.9 4.7 - - - +
116B ARG* 5.0 4.9 - - - +
121B ALA 3.8 0.4 - - - -
122B ASP* 1.3 97.9 + - + +
124B VAL* 1.3 61.9 + - - +
125B LEU* 4.6 13.7 - - - +
227B THR* 4.7 15.3 - - + -
274B LEU* 3.7 6.1 - - - +
275B ALA* 3.1 39.7 + - - +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU* 3.4 23.7 + - + +
115B LEU* 3.7 20.6 - - + -
123B THR* 1.3 73.7 - - - +
125B LEU* 1.3 64.6 + - - +
126B PHE* 3.9 14.6 - - + -
227B THR* 3.2 8.1 - - - -
228B MET* 3.0 32.2 + - + -
272B MET* 6.0 1.1 - - + -
273B SER 3.9 3.8 - - - +
274B LEU* 3.3 21.1 - - + -
297B TYR* 4.7 3.4 - - - +
375B LEU* 3.7 35.2 - - + -
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B THR* 4.2 9.8 + - - +
124B VAL* 1.3 84.5 - - - +
126B PHE* 1.3 65.8 + - - +
225B PHE* 3.6 33.9 - - + -
226B ASN 3.7 1.8 - - - +
227B THR* 4.2 22.2 - - + +
271B HIS 4.4 0.2 - - - -
272B MET* 3.2 25.6 - - - +
273B SER* 2.9 35.1 + - - +
275B ALA* 5.0 14.6 - - + -
1472B ADP 4.1 13.5 - - - +
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B VAL* 3.9 17.5 - - + -
125B LEU* 1.3 79.5 - - - +
127B GLY* 1.3 59.3 + - - +
128B PRO* 3.9 2.0 - - + -
225B PHE* 3.1 5.4 - - - -
226B ASN 2.9 36.5 + - - +
228B MET* 3.5 36.1 - - + -
231B LYS* 3.4 20.9 - - + +
270B CYS* 4.7 7.2 - - + -
271B HIS 3.5 2.2 - - - -
272B MET* 3.5 35.7 - - + -
297B TYR* 4.8 0.2 - - - -
371B PHE* 3.3 60.6 - + + -
374B LEU* 4.1 8.3 - - + -
375B LEU* 4.6 3.4 - - + -
1472B ADP 4.4 0.2 - - - -
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PHE* 1.3 76.4 - - - +
128B PRO* 1.3 66.2 - - - +
225B PHE* 3.9 3.8 - - - -
269B HIS 3.7 0.3 - - - +
270B CYS* 4.6 0.4 - - - -
271B HIS* 2.9 47.9 + - - -
1472B ADP 3.9 27.9 - - - +
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Residues in contact with PRO 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PHE* 5.1 0.2 - - + -
127B GLY* 1.3 88.4 - - - +
129B GLU* 1.3 60.3 + - - +
130B PRO* 3.2 8.5 - - - +
222B ALA* 5.9 0.7 - - - -
223B THR* 4.7 9.9 + - - +
231B LYS* 3.3 29.4 - - + -
235B ILE* 3.9 16.2 - - + -
268B MET* 3.8 26.5 - - + -
269B HIS 3.1 8.7 - - - +
270B CYS* 4.4 5.2 - - - -
371B PHE* 3.4 30.3 - - + -
1472B ADP 4.4 5.5 + - - -
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PRO* 1.3 76.1 - - - +
130B PRO* 1.3 62.2 - - - +
131B GLU* 3.5 5.1 + - - +
220B GLU* 3.6 10.2 - - - +
221B VAL 5.9 0.7 - - - -
222B ALA* 5.9 4.0 - - + +
267B GLY 3.2 13.7 - - - +
268B MET* 3.4 6.7 - - - +
269B HIS* 2.7 29.7 + - + +
271B HIS* 3.1 16.5 + - + -
357B GLU* 2.5 10.6 - - - +
470B MN 2.0 36.6 + - - -
1472B ADP 2.6 61.6 + - - +
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Residues in contact with PRO 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PRO* 3.2 19.1 - - + +
129B GLU* 1.3 83.7 - - - +
131B GLU* 1.3 60.0 + - - +
132B PHE* 4.3 0.2 - - - -
220B GLU* 3.7 8.3 - - - +
221B VAL 4.9 3.8 - - - +
223B THR* 5.4 2.9 - - - +
235B ILE* 3.8 18.2 - - + -
238B TYR* 2.9 57.6 + - + +
239B LYS* 6.5 0.2 - - + -
255B PHE* 4.8 3.6 - - + -
267B GLY 3.7 5.8 - - - +
268B MET* 3.8 21.7 - - + -
363B PRO* 4.4 10.8 - - + -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU 4.2 3.1 - - - +
130B PRO* 1.3 73.7 - - - +
132B PHE* 1.3 64.2 + - - +
212B GLU* 2.9 18.0 - - + +
218B GLN* 4.5 3.6 - - - +
219B ASN 3.8 4.9 - - - +
220B GLU* 3.3 22.0 - - + +
255B PHE* 3.5 6.5 - - - -
266B SER* 3.5 16.2 - - - +
267B GLY* 2.9 28.3 + - - +
269B HIS* 5.7 3.3 + - - -
363B PRO* 3.4 18.9 - - - +
469B MN 2.0 35.1 + - - -
474B TL 2.7 30.5 - - - -
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Residues in contact with PHE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PRO 4.3 0.2 - - - -
131B GLU* 1.3 79.5 - - - +
133B PHE* 1.3 66.3 + - - +
134B LEU* 3.9 24.7 - - + -
192B ARG* 5.4 1.1 - - + -
195B MET* 3.8 24.2 - - + -
218B GLN* 3.2 7.1 - - - +
219B ASN* 2.8 65.9 + - + -
220B GLU* 4.0 6.3 - - - -
221B VAL* 4.2 7.9 - - + -
238B TYR* 3.6 23.6 - + - -
242B VAL* 3.8 27.6 - - + -
254B THR 3.4 16.4 - - - +
255B PHE* 3.6 23.1 - + + -
266B SER* 3.8 5.1 + - - -
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE* 1.3 76.5 - - - +
134B LEU* 1.3 63.4 + - - +
135B PHE* 3.7 23.6 - + + -
214B ALA* 3.5 14.8 - - + -
215B THR 3.7 3.4 - - - -
216B ALA 3.7 12.1 - - - -
217B GLY 3.3 2.9 - - - -
218B GLN* 3.5 32.1 - - + -
252B THR 3.8 0.7 - - - +
253B ALA* 3.2 8.0 - - - +
254B THR* 3.0 38.3 + - + +
256B MET 4.8 2.7 - - - -
259B PRO* 3.5 28.9 - - + -
260B MET* 3.4 23.6 - - + -
264B ASN 3.5 21.1 - - - -
266B SER* 3.4 27.4 - - - -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE* 3.9 20.0 - - + -
133B PHE* 1.3 73.2 - - - +
135B PHE* 1.3 61.2 + - - +
153B ASP* 3.4 13.3 - - - +
188B ALA* 4.5 10.1 - - + -
191B ILE* 4.0 30.1 - - + -
192B ARG* 5.7 1.6 - - + -
195B MET* 4.1 8.7 - - + -
216B ALA 3.5 13.5 - - - +
217B GLY* 2.8 17.1 + - - +
219B ASN* 3.9 18.2 - - - +
246B ALA* 3.8 17.3 - - + -
251B LYS* 4.0 15.8 + - + -
252B THR 3.6 2.2 - - - +
253B ALA* 3.6 28.0 - - + -
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Residues in contact with PHE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.7 25.8 - + + -
134B LEU* 1.3 72.8 - - - +
136B ASP* 1.3 60.5 + - - +
137B ASP 4.2 4.5 - - - +
138B ILE* 4.8 5.4 - - + -
151B ILE* 3.6 39.9 - - + -
152B ASP 3.6 7.6 - - - +
153B ASP* 3.4 14.4 - - + -
216B ALA* 3.1 33.0 - - + -
251B LYS* 3.3 9.7 - - - +
252B THR* 2.9 40.3 + - + +
254B THR* 3.9 20.9 - - + -
259B PRO* 4.2 15.5 - - + -
260B MET* 4.6 2.5 - - + -
462H PHE* 5.9 0.2 - + - -
466H 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