Contacts of the strand formed by residues 82 - 90 (chain M) in PDB entry 3HOU
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 GLY 82 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M VAL* 4.8 1.7 - - - +
31M SER* 3.2 14.2 - - - -
33M ALA 3.5 8.3 - - - -
35M ILE* 4.1 1.3 - - - -
58M LEU* 3.8 14.2 - - - +
81M PHE* 1.3 78.9 - - - +
83M HIS* 1.3 63.4 + - - +
240M PRO* 3.7 4.3 - - - +
241M VAL* 2.8 32.5 + - - -
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Residues in contact with HIS 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ASP* 4.7 2.9 - - - -
27M VAL* 4.1 7.2 - - + -
28M ARG* 3.7 24.0 - - + +
31M SER* 3.0 29.5 + - - +
33M ALA 3.1 12.0 + - - -
34M LYS* 2.6 42.8 + - - +
35M ILE* 3.2 5.3 - - - +
82M GLY* 1.3 75.7 - - - +
84M ILE* 1.3 67.2 + - - +
85M ASP* 3.6 28.4 + - - -
238M CYS* 3.3 27.1 - - - -
239M LEU 3.1 12.8 - - - +
241M VAL* 3.6 5.1 - - - +
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Residues in contact with ILE 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M LYS 4.6 2.5 - - - -
35M ILE* 3.8 11.7 - - + +
53M LEU* 6.6 0.2 - - + -
83M HIS* 1.3 83.4 - - - +
85M ASP* 1.3 69.0 + - - +
86M LEU* 3.2 24.3 + - + -
238M CYS* 3.6 1.5 - - - -
239M LEU* 2.9 36.5 + - + +
241M VAL* 3.8 17.9 - - + -
266M LEU* 4.7 14.4 - - + +
269M ILE* 4.6 14.6 - - + -
270M LEU* 3.2 36.8 - - + +
273M ASN* 4.6 8.3 - - - +
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Residues in contact with ASP 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D ASP* 3.5 34.3 - - - +
205D ASP* 4.0 24.7 - - - +
28M ARG* 3.6 20.6 + - - +
34M LYS 5.6 0.9 - - - +
83M HIS* 3.6 24.4 + - - -
84M ILE* 1.3 72.2 - - - +
86M LEU* 1.3 66.4 + - - +
237M THR* 4.3 4.0 - - - -
238M CYS* 4.1 3.7 - - - +
273M ASN* 3.4 13.9 + - - -
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Residues in contact with LEU 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ASP* 5.6 0.2 - - - +
84M ILE* 3.5 26.0 - - + +
85M ASP* 1.3 80.2 - - - +
87M ALA* 1.3 64.3 + - - +
88M LYS 3.4 11.9 - - - +
90M VAL* 3.5 32.3 - - + -
236M LEU* 3.8 19.1 - - + +
237M THR* 3.1 23.2 + - - +
239M LEU* 4.1 20.4 - - + +
269M ILE* 4.6 8.7 - - + -
273M ASN* 3.4 11.7 - - - +
296M LEU* 4.6 3.8 - - + -
300M VAL* 4.6 10.1 - - + -
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Residues in contact with ALA 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M LEU* 1.3 74.9 - - - +
88M LYS* 1.3 69.6 + - - +
89M PRO* 4.8 0.2 - - - +
273M ASN* 2.7 23.0 + - - +
276M LEU* 3.2 35.7 - - + -
277M GLU* 4.1 11.2 - - + +
280M GLU* 4.0 12.4 - - - +
296M LEU* 4.3 0.4 - - - +
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Residues in contact with LYS 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M LEU* 3.4 9.7 - - - +
87M ALA* 1.3 90.9 - - - +
89M PRO* 1.3 76.0 - - + +
90M VAL* 3.3 16.3 + - - +
205M GLU* 3.1 34.7 + - - +
237M THR* 5.8 0.2 - - - -
276M LEU* 4.1 7.2 - - + +
280M GLU* 3.1 27.3 + - - +
289M ILE* 5.3 5.9 - - + +
293M GLU* 2.9 44.9 + - + +
296M LEU* 4.5 2.7 - - - +
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Residues in contact with PRO 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87M ALA 4.8 0.4 - - - +
88M LYS* 1.3 87.5 - - + +
90M VAL* 1.3 59.0 + - - +
204M THR* 2.7 44.0 + - + +
205M GLU* 3.6 30.1 - - + +
208M LEU* 4.0 15.5 - - + -
235M ILE* 3.5 16.6 - - + -
236M LEU 3.4 10.8 - - - +
237M THR* 4.3 9.8 - - - +
293M GLU* 4.2 4.0 - - - +
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Residues in contact with VAL 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M LEU* 3.5 28.3 - - + -
88M LYS 3.4 12.8 - - - +
89M PRO* 1.3 74.9 - - - +
91M PHE* 1.3 67.8 + - - +
204M THR* 4.1 2.9 - - - -
235M ILE* 3.6 3.8 - - - -
236M LEU* 2.9 35.4 + - + +
293M GLU* 4.9 6.3 - - + +
296M LEU* 4.4 11.7 - - + -
297M GLN* 2.7 44.2 - - + +
300M VAL* 4.1 11.2 - - + -
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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