Contacts of the helix formed by residues 278 - 286 (chain A) in PDB entry 5L0U
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 PHE 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A PHE* 3.4 29.8 - + - -
163A ALA* 3.7 15.7 - - + -
164A TRP* 3.9 27.6 - + - -
165A THR* 3.6 40.2 - - + -
171A PRO* 3.8 20.6 - - + -
181A LEU* 4.0 13.9 - - + -
277A SER* 1.3 72.8 - - - +
279A ARG* 1.3 60.2 + - - +
280A PHE 3.3 0.9 - - - -
281A LYS* 3.1 19.9 + - - +
282A HIS* 2.8 23.8 + - - -
299A GLU* 4.0 11.9 - - - -
404A 660 3.0 33.8 + - - +
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Residues in contact with ARG 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PHE* 3.5 18.8 - - - -
210A ARG 3.0 27.7 + - - +
211A GLY* 3.4 4.4 - - - -
218A ARG* 4.4 0.2 - - - +
259A LEU* 4.3 5.2 - - + -
262A HIS* 5.2 6.0 + - - -
269A PHE 3.5 21.3 - - - -
270A ASN* 3.4 13.6 + - - +
271A PHE 4.2 4.4 + - - +
277A SER* 3.0 29.5 + - - +
278A PHE* 1.3 76.0 - - - +
280A PHE* 1.3 66.7 + - - +
282A HIS* 3.0 18.2 + - - +
283A LEU* 3.4 27.5 + - + +
404A 660 2.9 78.5 + - - +
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASN* 3.3 33.4 + - + +
277A SER 3.4 14.8 + - - +
278A PHE 3.3 0.4 - - - -
279A ARG* 1.3 79.0 - - - +
281A LYS* 1.3 64.7 + - - +
282A HIS 3.1 0.9 + - - -
283A LEU* 3.2 15.5 + - - +
284A PHE* 3.3 40.9 - + - -
290A VAL* 3.9 6.3 - - + -
292A HIS* 3.4 35.9 - + + -
299A GLU* 5.0 0.7 - - - +
301A PHE* 4.3 3.6 - + - -
302A TYR* 3.3 44.2 - + + +
305A LEU* 3.7 23.1 - - + -
311A TYR* 4.3 10.5 - + - -
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A THR* 4.1 15.5 + - - +
166A PHE* 3.6 38.4 - - + +
184A TRP* 3.7 39.2 - - + -
277A SER 5.0 0.2 + - - -
278A PHE* 3.1 36.7 + - - +
280A PHE* 1.3 81.3 - - - +
282A HIS* 1.3 83.1 + - - +
283A LEU 3.5 0.2 + - - -
284A PHE* 3.7 18.6 + - - +
285A LEU* 4.1 1.6 + - - +
299A GLU* 5.1 3.2 + - - +
301A PHE* 3.9 24.6 - - + -
346A ILE* 4.0 11.0 - - + +
350A LEU* 4.1 7.4 - - + -
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Residues in contact with HIS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A THR* 6.0 0.2 - - - -
181A LEU* 4.1 22.1 - - + +
182A GLY 5.6 0.8 + - - -
184A TRP* 3.6 21.9 - + - -
187A PHE* 3.5 42.8 - + - +
191A LEU* 3.6 24.4 - - + +
259A LEU* 3.7 26.1 - - + +
278A PHE 2.8 28.2 + - - -
279A ARG 3.0 6.5 + - - +
281A LYS* 1.3 94.7 - - - +
283A LEU* 1.3 67.4 + - - +
285A LEU 3.1 11.4 + - - -
286A CYS* 3.7 4.2 + - - -
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU* 4.0 16.8 - - + -
262A HIS* 4.1 12.1 - - + -
268A LEU* 3.9 37.2 - - + +
269A PHE 3.6 25.6 - - - +
270A ASN* 3.8 15.9 - - + -
279A ARG* 3.4 33.9 - - + +
280A PHE 3.2 6.4 + - - +
282A HIS* 1.3 76.3 - - - +
284A PHE* 1.3 63.3 + - - +
286A CYS* 3.1 23.0 + - - +
287A GLY 4.2 1.0 + - - -
288A SER 4.2 5.4 + - - +
290A VAL* 3.7 18.2 - - + -
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Residues in contact with PHE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A PHE* 3.3 68.0 - + - -
281A LYS* 4.0 5.6 - - - +
282A HIS 3.2 0.6 - - - -
283A LEU* 1.3 78.2 - - - +
285A LEU* 1.3 58.0 + - - +
286A CYS 3.1 0.2 - - - -
287A GLY* 3.0 18.0 + - - -
288A SER 4.4 5.4 + - - +
290A VAL* 3.7 21.5 - - + -
305A LEU* 4.1 15.5 - - + -
310A HIS* 3.3 26.0 - - + -
311A TYR* 4.0 8.7 - + + -
339A ALA* 5.5 0.7 - - - -
342A GLY* 3.7 26.7 - - - +
343A SER* 3.3 17.7 - - - +
346A ILE* 3.6 29.8 - - + -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A TRP* 3.6 30.3 - - + -
188A ARG* 3.7 34.8 - - + +
191A LEU* 3.5 25.3 - - + +
192A VAL* 4.3 10.2 + - + +
195A ALA* 3.4 14.2 - - - +
281A LYS 4.2 2.2 - - - +
282A HIS 3.1 8.9 + - - +
284A PHE* 1.3 76.8 - - - +
286A CYS* 1.3 58.7 + - - +
287A GLY 3.1 3.2 + - - -
343A SER* 4.0 6.3 + - - +
346A ILE* 3.7 24.2 - - + -
347A ARG* 3.4 38.5 + - + +
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Residues in contact with CYS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LEU* 3.9 11.2 - - - -
195A ALA* 3.3 15.5 - - - +
203A LYS* 2.8 24.9 + - - -
259A LEU 4.0 5.8 - - - -
262A HIS* 4.1 3.6 - - - -
263A CYS* 2.0 58.5 - - + +
268A LEU* 4.1 7.4 - - + -
282A HIS 3.7 3.9 + - - -
283A LEU* 3.1 17.3 + - - +
285A LEU* 1.3 77.0 - - - +
287A GLY* 1.3 53.6 + - - +
288A SER* 3.1 14.4 - - - +
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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