Contacts of the helix formed by residues 272 - 280 (chain B) in PDB entry 5HJS
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 PRO 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B PHE* 5.3 0.4 - - + -
94B THR* 3.7 35.4 - - + +
95B GLU* 6.3 0.4 - - + -
98B ILE* 3.6 31.0 - - + -
270B LYS 3.9 2.4 - - - +
271B LEU* 1.3 87.4 - - + +
273B PRO* 1.4 77.5 - - + +
274B LEU 3.5 0.9 - - - -
275B LEU* 3.3 13.0 + - + -
276B SER* 2.9 18.7 + - - -
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Residues in contact with PRO 273 (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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98B ILE* 5.9 0.2 - - + -
271B LEU 4.6 0.4 - - - +
272B PRO* 1.4 85.9 - - + +
274B LEU* 1.4 58.6 + - - +
276B SER* 3.3 5.3 + - - -
277B GLU* 2.9 29.3 + - - +
4D ILE* 3.5 20.3 - - + +
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Residues in contact with LEU 274 (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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98B ILE* 4.5 33.5 - - + +
101B VAL* 3.8 37.5 - - + -
102B GLN* 4.6 4.0 - - + +
272B PRO* 3.5 2.0 - - - +
273B PRO* 1.4 77.0 - - - +
275B LEU* 1.3 63.1 + - + +
277B GLU* 3.4 17.3 + - - +
278B ILE* 3.2 25.9 + - + +
4D ILE* 3.6 32.6 - - + +
5D LEU* 4.1 13.7 - - + +
8D LEU* 4.1 16.2 - - + -
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Residues in contact with LEU 275 (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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94B THR* 3.6 30.1 - - + +
97B ALA* 3.8 15.9 - - + -
98B ILE* 3.8 20.0 - - + -
101B VAL* 4.1 24.7 - - + -
271B LEU* 4.1 11.2 - - + -
272B PRO* 3.3 24.7 + - + +
274B LEU* 1.3 77.3 - - + +
276B SER* 1.4 59.1 + - - +
278B ILE* 3.5 5.4 + - + +
279B TRP* 2.9 64.7 + - + +
301B 668 4.4 2.7 - - + -
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Residues in contact with SER 276 (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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265B ARG* 5.3 0.9 + - - -
271B LEU* 3.8 14.2 - - - +
272B PRO 2.9 17.7 + - - -
273B PRO* 3.7 6.7 - - - -
275B LEU* 1.4 75.5 - - - +
277B GLU* 1.3 58.0 + - - +
280B ASP* 2.7 50.5 + - - +
282B HIS* 3.2 21.0 + - - -
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Residues in contact with GLU 277 (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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127B LYS* 3.4 4.0 + - - -
273B PRO 2.9 16.5 + - - +
274B LEU* 3.4 9.6 - - - +
276B SER* 1.3 78.9 - - - +
278B ILE* 1.3 61.6 + - - +
280B ASP 4.6 0.7 - - - +
282B HIS* 4.1 14.5 + - - -
1D ARG 3.7 7.3 - - - +
2D HIS* 3.3 44.6 + - + -
3D LYS* 3.3 6.1 + - - +
4D ILE* 2.8 34.5 + - - +
5D LEU* 2.8 38.3 + - - +
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Residues in contact with ILE 278 (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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101B VAL* 4.0 24.9 - - + -
126B LEU 5.5 0.2 - - - +
127B LYS* 2.9 43.3 + - - +
130B ALA* 3.9 21.8 - - + -
274B LEU* 3.2 26.2 + - + +
275B LEU* 3.6 9.2 - - + +
277B GLU* 1.3 80.3 - - - +
279B TRP* 1.4 91.2 + - + +
2D HIS* 4.3 5.6 - - + -
5D LEU* 3.9 28.7 - - + -
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Residues in contact with TRP 279 (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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97B ALA* 4.7 1.1 - - + -
127B LYS* 4.6 7.9 + - - -
131B ILE* 3.9 20.9 - - + +
134B MET* 3.6 39.9 - - + -
257B HIS* 3.3 29.7 - + + -
261B VAL* 3.9 22.9 - - + +
271B LEU* 4.1 11.4 - - + -
275B LEU* 2.9 51.8 + - + +
278B ILE* 1.4 104.9 - - + +
280B ASP* 1.3 65.9 + - - +
281B VAL* 3.8 5.9 + - - +
301B 668 3.2 30.3 - - + -
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Residues in contact with ASP 280 (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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127B LYS* 4.8 5.0 + - - -
261B VAL* 3.3 21.8 - - - +
265B ARG* 3.9 30.6 + - - +
271B LEU* 4.0 14.6 + - - +
276B SER* 2.7 49.4 + - - +
277B GLU 4.6 2.6 - - - +
279B TRP* 1.3 76.0 - - - +
281B VAL* 1.3 60.7 + - - +
282B HIS* 3.4 25.3 + - + -
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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