Contacts of the helix formed by residues 261 - 271 (chain C) in PDB entry 3HB8
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 HIS 261 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C ASP* 4.4 16.5 + - - -
220C GLY* 4.2 17.5 - - - -
221C LEU* 4.7 16.0 - - + +
257C ILE* 4.0 10.5 - - + +
258C TYR* 2.8 36.5 + + + +
260C ASN* 1.3 102.2 + - - +
262C ILE* 1.3 70.7 + - - +
264C PRO* 3.5 13.6 - - + +
265C LEU* 2.8 30.0 + - + +
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Residues in contact with ILE 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 3.8 24.0 - - + +
56C LEU* 3.9 20.0 - - + -
257C ILE* 4.5 5.8 - - + -
258C TYR 4.3 6.5 - - - +
259C LEU* 2.9 43.2 + - + +
260C ASN 3.7 0.6 - - - -
261C HIS* 1.3 81.6 - - - +
263C GLU* 1.3 70.0 + - + +
265C LEU* 3.0 3.9 + - - +
266C LYS* 2.9 50.4 + - - +
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Residues in contact with GLU 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C ILE* 1.3 84.3 - - + +
264C PRO* 1.3 74.2 - - + +
266C LYS* 2.9 41.8 + - - +
267C ILE* 3.0 21.8 + - + +
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Residues in contact with PRO 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C ASN 4.1 15.5 - - - +
261C HIS* 3.3 19.7 - - + +
262C ILE 3.5 0.4 - - - +
263C GLU* 1.3 96.4 - - + +
265C LEU* 1.3 59.4 + - - +
267C ILE* 3.3 29.1 - - + +
268C GLN* 3.4 6.8 + - - +
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Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C TYR* 4.7 4.5 - - - +
37C ILE* 3.9 43.3 - - + -
41C LEU* 5.3 2.7 - - + -
219C MET 5.1 2.2 - - - +
220C GLY* 4.7 16.8 - - - +
257C ILE* 3.4 35.7 - - + -
261C HIS* 2.8 22.5 + - + +
262C ILE* 3.4 3.4 - - - +
264C PRO* 1.3 72.6 - - - +
266C LYS* 1.3 68.0 + - - +
267C ILE 3.1 1.8 - - - -
268C GLN* 3.0 27.4 + - - +
269C LEU* 2.9 26.4 + - - +
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Residues in contact with LYS 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 4.1 25.8 - - + +
262C ILE* 2.9 42.7 + - - +
263C GLU* 2.9 34.9 + - - +
265C LEU* 1.3 75.5 - - - +
267C ILE* 1.3 63.1 + - + +
269C LEU* 3.2 26.7 + - + +
270C GLN* 3.6 11.6 + - - +
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Residues in contact with ILE 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C GLU* 3.0 19.9 + - + +
264C PRO* 3.3 18.2 - - + +
266C LYS* 1.3 77.9 - - + +
268C GLN* 1.3 62.4 + - - +
270C GLN* 3.3 20.3 + - - +
271C ARG* 3.7 27.3 + - + +
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Residues in contact with GLN 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C TYR* 3.7 27.2 + - - -
34C LEU* 4.4 6.5 - - + +
74C LEU* 5.4 1.0 - - - +
76C THR* 2.7 44.2 + - - +
77C LYS* 3.7 31.5 - - - +
220C GLY 5.7 0.7 - - - +
224C PRO* 6.1 0.2 - - - +
264C PRO 3.4 6.0 + - - +
265C LEU* 3.0 30.1 + - + +
267C ILE* 1.3 81.0 - - - +
269C LEU* 1.3 57.4 + - - +
271C ARG* 2.9 38.5 + - - +
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Residues in contact with LEU 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 3.4 52.5 - - + +
37C ILE* 3.9 15.9 - - + -
38C GLN* 3.5 34.3 - - + +
41C LEU* 3.7 26.7 - - + -
265C LEU 2.9 16.5 + - - +
266C LYS* 3.2 14.3 + - + +
268C GLN* 1.3 76.8 - - - +
270C GLN* 1.3 62.7 + - + +
271C ARG 3.4 6.2 + - - +
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Residues in contact with GLN 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C LYS 3.6 10.3 + - - +
267C ILE* 3.3 14.1 + - - +
268C GLN 3.1 1.0 - - - -
269C LEU* 1.3 78.4 - - + +
271C ARG* 1.3 65.3 + - - +
272C GLU* 3.6 2.4 + - - +
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Residues in contact with ARG 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C LEU* 4.5 1.7 - - - +
76C THR* 3.3 32.0 + - + +
77C LYS* 5.1 0.8 - - - +
267C ILE* 3.7 23.5 + - + +
268C GLN* 2.9 28.1 + - - +
269C LEU 3.7 7.1 - - - +
270C GLN* 1.3 80.9 - - - +
272C GLU* 1.3 60.7 + - - +
273C PRO* 3.4 10.4 - - - +
304C HIS* 3.0 42.4 + - + +
305C PRO* 2.6 30.6 + - - -
306C THR* 3.6 15.6 + - - +
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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