Contacts of the strand formed by residues 299 - 304 (chain C) in PDB entry 3HU1
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 ALA 299 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224C LEU* 3.8 9.2 - - - +
264C ALA* 4.2 0.4 - - - -
265C PHE* 3.2 21.5 - - + +
293C ALA* 3.3 36.8 - - + +
296C ASN 3.5 6.7 - - - +
298C PRO* 1.3 74.3 - - - +
300C ILE* 1.3 63.2 + - - +
340C HIS 3.1 7.1 + - - -
341C VAL* 3.5 8.7 - - + -
342C ILE 3.2 22.9 + - - -
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Residues in contact with ILE 300 (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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220C VAL* 3.8 19.7 - - + -
221C GLU* 4.3 2.2 - - - +
224C LEU* 3.7 15.9 - - + -
258C VAL* 3.9 8.1 - - + -
262C THR* 3.8 36.6 - - + +
264C ALA* 3.8 10.5 - - + -
265C PHE 2.8 9.4 + - - +
266C PHE* 3.5 26.5 - - + -
267C PHE* 2.8 33.6 + - - +
299C ALA* 1.3 76.6 - - - +
301C ILE* 1.3 62.8 + - - +
302C PHE 4.0 0.2 - - - -
342C ILE 3.4 9.2 - - - +
344C MET* 4.0 26.5 - - + -
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Residues in contact with ILE 301 (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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267C PHE* 3.4 11.2 - - + +
269C ILE* 3.7 29.4 - - + -
289C ALA 4.2 2.0 - - - +
290C PHE* 3.9 41.3 - - + -
293C ALA* 3.6 33.9 - - + -
300C ILE* 1.3 74.1 - - - +
302C PHE* 1.3 58.1 + - - +
303C ILE* 4.3 4.7 - - + -
341C VAL* 3.8 17.0 - - + -
342C ILE 3.0 7.4 + - - +
343C VAL* 3.3 17.8 - - + +
344C MET 2.7 34.5 + - - +
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Residues in contact with PHE 302 (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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243C LEU* 4.3 10.8 - - + -
251C LYS 4.5 1.8 - - - -
254C ILE 5.4 0.2 - - - -
255C ALA* 3.5 35.9 - - + -
258C VAL* 5.9 0.4 - - + -
266C PHE* 3.5 30.7 - + + -
267C PHE 2.8 11.3 + - - +
268C LEU* 3.6 6.3 - - + +
269C ILE* 2.7 34.8 + - - +
300C ILE 4.0 1.0 - - - -
301C ILE* 1.3 72.1 - - - +
303C ILE* 1.3 63.7 + - - +
304C ASP* 3.7 23.3 + - + -
344C MET* 3.2 46.9 - - + -
345C ALA 4.3 2.2 - - - -
346C ALA* 3.7 35.2 - - + -
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Residues in contact with ILE 303 (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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269C ILE* 3.4 29.6 - - + +
271C GLY 5.2 1.6 - - - +
286C LEU* 5.3 0.7 - - + -
290C PHE* 4.8 5.8 - - + -
301C ILE* 4.3 1.3 - - + -
302C PHE* 1.3 73.8 - - - +
304C ASP* 1.3 63.1 + - - +
305C GLU 3.8 0.6 + - - -
306C LEU* 3.8 29.9 + - + +
309C ILE* 3.9 18.2 - - + -
328C LEU* 3.8 28.5 - - + -
343C VAL* 3.8 24.2 - - + -
344C MET 2.8 12.0 + - - +
345C ALA* 3.1 8.4 - - + +
346C ALA 3.1 23.4 + - - +
363C PHE* 4.2 10.3 - - + -
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Residues in contact with ASP 304 (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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251C LYS* 5.2 0.2 - - - +
252C THR* 3.0 40.5 + - - +
255C ALA* 5.4 0.2 - - - -
256C ARG* 3.9 5.4 + - - -
268C LEU* 4.2 3.6 - - + -
269C ILE 2.8 9.4 + - - +
270C ASN* 3.7 19.4 - - - +
271C GLY* 2.7 32.6 + - - -
272C PRO* 4.4 0.2 - - - +
302C PHE* 3.7 19.3 + - + -
303C ILE* 1.3 71.3 - - - +
305C GLU* 1.3 81.3 + - - +
346C ALA* 3.6 17.7 - - - +
801C MG 4.2 1.9 - - - -
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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