Contacts of the strand formed by residues 45 - 52 (chain G) in PDB entry 40ER
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 SER 45 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A TYR 3.4 3.7 + - - +
344A LEU* 3.6 9.4 - - - -
229B LEU* 3.6 12.8 - - - +
230B LEU* 3.2 37.5 + - - +
231B PRO 2.9 22.8 + - - -
232B GLU* 4.1 0.2 - - - -
233B PRO* 3.7 16.5 - - - +
263B TYR* 3.3 8.3 + - - +
265B THR* 5.3 2.4 + - - -
43G PRO* 4.4 0.7 - - - -
44G THR* 1.3 81.2 - - - +
46G SER* 1.3 64.2 + - - +
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Residues in contact with SER 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ALA* 3.3 14.4 - - - -
230B LEU* 3.8 11.0 - - - +
263B TYR 3.2 4.7 + - - -
264B VAL* 3.6 20.4 - - - +
265B THR* 3.0 25.1 + - - -
42G ILE* 5.0 0.3 - - - +
43G PRO* 4.1 24.7 + - - +
45G SER* 1.3 76.7 + - - +
47G LYS* 1.3 64.8 + - - +
164G LEU 4.3 1.6 + - - -
165G TYR* 4.2 17.8 - - - +
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Residues in contact with LYS 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A TRP* 6.2 1.8 - - - -
217B LEU* 3.8 23.5 + - + +
227B PRO 4.1 16.1 + - - -
228B ALA* 2.6 29.1 + - - +
230B LEU* 3.6 20.5 - - + +
264B VAL* 6.2 0.2 - - - -
265B THR 3.7 3.6 - - - +
267B LEU* 3.9 19.1 - - + -
46G SER* 1.3 77.5 - - - +
48G LEU* 1.3 69.1 + - - +
49G VAL* 4.8 3.1 - - + -
67G ASN* 3.2 44.0 + - + +
69G VAL* 4.7 11.0 - - + +
165G TYR* 5.5 3.6 - - - -
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Residues in contact with LEU 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264B VAL* 5.8 3.1 - - + -
265B THR 3.0 11.6 + - - +
266B THR* 3.4 19.0 - - + +
267B LEU* 2.7 35.0 + - - +
47G LYS* 1.3 78.8 - - - +
49G VAL* 1.3 66.3 + - - +
50G VAL* 4.5 5.2 - - + -
69G VAL* 5.3 2.9 - - - -
71G ALA 5.0 1.6 - - - +
73G PRO* 3.7 23.1 - - + -
163G THR* 3.2 45.3 - - + +
164G LEU 4.4 11.2 - - - +
165G TYR* 5.6 1.3 - - - -
166G ILE* 3.7 26.5 - - + +
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Residues in contact with VAL 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B LEU* 3.5 22.0 - - + +
269B TYR* 4.9 2.7 - - + -
47G LYS* 4.8 2.5 - - + -
48G LEU* 1.3 79.8 - - - +
50G VAL* 1.3 63.5 + - - +
51G PHE* 4.2 17.9 - - + -
63G ALA 5.6 0.2 - - - +
67G ASN* 3.6 37.2 - - + +
69G VAL* 3.5 30.2 - - + +
71G ALA 4.5 1.5 + - - +
72G ALA* 3.1 27.7 - - + +
73G PRO* 3.2 13.0 - - - +
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Residues in contact with VAL 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535A ILE* 3.7 20.2 - - + -
266B THR* 4.4 15.0 - - + -
267B LEU 2.9 21.1 + - - +
268B LEU* 3.5 22.0 - - + +
269B TYR* 3.2 24.3 + - - -
48G LEU* 4.5 4.9 - - + -
49G VAL* 1.3 79.5 - - - +
51G PHE* 1.3 69.2 + - - +
72G ALA* 4.3 0.9 - - - -
73G PRO* 3.4 32.5 - - + +
75G TRP* 5.2 2.5 - - + -
82G PHE* 4.2 14.1 - - + -
163G THR* 5.6 0.2 - - - -
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Residues in contact with PHE 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B LEU* 4.8 2.7 - - - -
269B TYR* 3.7 27.4 - + + -
49G VAL* 4.2 16.2 - - + -
50G VAL* 1.3 83.8 - - - +
52G ASP* 1.3 60.8 + - - +
55G LEU* 3.8 18.2 - - + -
60G ALA* 3.3 38.1 - - + -
63G ALA* 3.7 14.4 - - + -
64G LEU* 4.1 13.9 - - + -
72G ALA* 3.7 22.7 - - + -
73G PRO 3.2 7.3 + - - -
74G LEU* 3.5 10.5 - - + +
75G TRP* 2.9 25.8 + - - -
86G LEU* 4.0 16.2 - - + -
114G ILE* 3.9 16.8 - - + -
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Residues in contact with ASP 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B LEU* 4.5 4.9 - - + +
269B TYR 3.3 21.2 + - - +
270B LYS* 3.4 24.3 - - + +
271B PRO* 4.0 5.8 - - + -
51G PHE* 1.3 74.6 - - - +
53G THR* 1.3 76.2 + - - +
54G SER* 2.8 28.5 + - - +
55G LEU* 3.0 24.5 + - - +
75G TRP* 3.0 19.0 - - + +
77G SER* 3.6 28.7 + - - -
114G ILE* 3.5 6.3 - - - +
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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