Contacts of the helix formed by residues 260 - 273 (chain F) in PDB entry 1J0B
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 260 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253F PHE* 3.6 23.5 - - + -
258F LYS* 3.6 33.5 + - + +
259F ILE* 1.3 75.7 - - - +
261F GLY* 1.3 64.6 + - - +
262F GLU* 3.0 20.3 + - - +
263F VAL* 3.3 23.1 + - - +
264F ALA 3.3 14.4 + - - -
324F LEU* 3.1 16.4 - - - +
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Residues in contact with GLY 261 (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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138D GLU* 3.7 21.1 - - - -
260F THR* 1.3 73.9 - - - +
262F GLU* 1.3 64.8 + - - +
264F ALA* 3.3 3.8 + - - +
265F GLN* 3.2 26.9 + - - +
324F LEU* 3.6 25.5 - - - +
325F LEU* 5.1 0.2 - - - +
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Residues in contact with GLU 262 (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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138D GLU* 3.8 22.7 - - + +
142D GLU* 3.8 20.6 - - - +
145D LYS* 4.9 7.4 + - - +
153D VAL* 5.8 1.2 - - - +
253F PHE* 4.0 15.1 - - + -
260F THR* 3.0 25.5 + - - +
261F GLY* 1.3 76.2 + - - +
263F VAL* 1.3 62.5 + - - +
265F GLN* 3.3 7.0 + - - +
266F ILE* 3.3 22.2 + - - +
288F TYR* 3.9 26.4 - - + +
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Residues in contact with VAL 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F PHE* 3.2 37.0 - - + -
259F ILE* 5.4 2.0 - - + -
260F THR* 3.3 19.1 + - - +
262F GLU* 1.3 74.0 - - - +
264F ALA* 1.3 59.2 + - - +
266F ILE* 3.6 6.8 - - - +
267F ILE* 3.0 24.2 + - - +
280F PRO* 3.5 35.4 - - + +
284F GLY* 3.8 23.6 - - - +
285F LYS* 3.6 13.7 - - + -
288F TYR* 5.6 1.8 - - + -
321F LEU* 4.7 0.2 - - - -
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Residues in contact with ALA 264 (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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117E ILE* 5.4 1.7 - - - +
260F THR 3.3 9.9 + - - +
261F GLY 3.3 7.8 + - - +
262F GLU 3.3 1.0 - - - -
263F VAL* 1.3 76.8 - - - +
265F GLN* 1.3 63.6 + - - +
267F ILE* 3.4 4.7 + - - +
268F ARG* 3.3 17.0 + - - +
321F LEU* 3.2 31.4 - - + +
324F LEU* 4.0 13.2 - - + -
325F LEU* 3.5 32.8 - - + +
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Residues in contact with GLN 265 (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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134D MET* 4.6 3.5 - - - +
135D LYS* 3.4 47.5 + - + +
138D GLU* 4.9 12.1 - - + +
261F GLY 3.2 10.9 + - - +
262F GLU* 3.5 11.4 - - - +
264F ALA* 1.3 78.5 - - - +
266F ILE* 1.3 59.3 + - - +
268F ARG* 3.4 22.9 + - - +
269F LYS* 3.1 47.8 + - - +
324F LEU 4.8 2.4 - - - +
325F LEU* 3.4 30.7 + - - +
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Residues in contact with ILE 266 (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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262F GLU 3.3 9.5 + - - +
263F VAL* 3.6 14.6 - - - +
265F GLN* 1.3 76.1 - - - +
267F ILE* 1.3 68.8 + - + +
269F LYS* 4.3 9.4 - - + -
270F VAL* 3.0 38.7 + - + +
278F LEU* 4.6 5.2 - - + -
284F GLY* 3.5 23.8 - - - +
287F PHE* 4.0 15.0 - - + -
288F TYR* 3.2 47.1 - - + +
291F VAL* 4.0 17.9 - - + -
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Residues in contact with ILE 267 (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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117E ILE* 4.6 12.6 - - + -
118E MET* 3.8 18.1 - - + +
263F VAL* 3.0 21.5 - - + +
264F ALA 3.4 9.3 + - - +
265F GLN 3.2 0.4 - - - -
266F ILE* 1.3 85.6 - - + +
268F ARG* 1.3 58.1 + - - +
270F VAL* 3.9 0.7 - - - +
271F GLY* 3.0 26.3 + - - -
276F ILE 4.5 1.4 - - - +
277F ILE* 5.4 0.2 - - + -
278F LEU* 3.5 43.2 + - + +
279F ASP* 3.5 22.9 - - - +
280F PRO* 3.6 12.8 - - + -
284F GLY* 4.8 0.2 - - - -
314F THR* 5.3 4.0 - - + +
321F LEU* 4.0 17.5 - - + -
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Residues in contact with ARG 268 (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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132D GLU* 3.9 24.5 + - - +
135D LYS* 6.5 0.7 - - - -
116E LYS 3.1 16.2 + - - -
117E ILE* 2.6 32.7 + - + +
118E MET* 3.4 29.1 - - - +
119E GLY* 3.4 10.7 - - - +
264F ALA 3.3 9.8 + - - +
265F GLN* 3.4 24.7 + - - +
267F ILE* 1.3 80.8 - - - +
269F LYS* 1.3 52.3 + - + +
272F THR* 2.4 46.7 + - + +
273F ARG* 6.2 0.9 - - - +
322F LEU* 5.4 2.0 - - - +
325F LEU* 3.8 35.5 + - + +
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Residues in contact with LYS 269 (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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135D LYS* 4.4 13.3 + - - +
139D GLU* 4.1 24.9 + - - +
30F ILE* 4.6 8.7 - - + +
33F GLU* 4.2 11.6 + - - +
265F GLN* 3.1 38.5 + - - +
266F ILE* 3.9 11.0 - - + +
267F ILE 3.2 0.2 - - - -
268F ARG* 1.3 76.5 - - + +
270F VAL* 1.3 63.0 + - + +
271F GLY 3.2 1.3 - - - -
272F THR* 3.6 4.0 - - - -
273F ARG* 2.9 78.9 + - - +
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Residues in contact with VAL 270 (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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27F LEU* 5.1 3.1 - - + -
30F ILE* 4.8 6.1 - - + -
40F ILE* 6.0 1.3 - - + -
266F ILE* 3.0 23.0 + - + +
267F ILE 4.4 0.4 - - - +
269F LYS* 1.3 77.2 - - + +
271F GLY* 1.3 59.5 + - - +
274F GLU* 3.3 21.4 + - + +
275F GLY 3.1 8.7 + - - -
276F ILE* 3.0 36.6 + - + +
278F LEU* 3.8 33.0 - - + -
287F PHE* 3.8 36.6 - - + -
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Residues in contact with GLY 271 (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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89E LEU* 3.0 22.4 - - - +
118E MET* 3.6 14.8 - - - -
267F ILE 3.0 17.5 + - - -
268F ARG 3.9 0.2 - - - -
269F LYS 3.2 0.2 - - - -
270F VAL* 1.3 79.8 - - - +
272F THR* 1.3 56.6 + - - +
275F GLY* 3.0 21.5 - - - -
276F ILE 3.0 15.5 - - - -
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Residues in contact with THR 272 (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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89E LEU* 4.2 4.9 - - + -
92E LYS* 3.3 27.8 - - + +
93E LYS* 2.8 30.5 + - - -
118E MET* 3.1 35.4 - - + +
268F ARG* 2.4 36.0 + - + +
269F LYS* 3.6 5.4 - - - -
271F GLY* 1.3 78.4 - - - +
273F ARG* 1.3 71.6 + - - -
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Residues in contact with ARG 273 (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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135D LYS* 3.4 29.2 - - - +
92E LYS 5.2 1.1 - - - +
93E LYS* 3.3 12.2 - - - +
29F ASN* 2.4 49.3 + - + +
30F ILE* 4.9 4.3 - - + -
33F GLU* 2.8 35.9 + - - -
268F ARG* 6.2 1.0 - - - +
269F LYS* 2.9 62.6 + - - +
272F THR* 1.3 87.7 + - - +
274F GLU* 1.3 64.7 + - + +
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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