Contacts of the strand formed by residues 81 - 87 (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 81 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530A PRO* 3.7 24.3 + - - +
531A GLY* 5.0 0.2 - - - -
75G TRP* 3.5 14.7 - - - -
76G ASP* 3.0 28.7 + - - +
79G LYS* 3.3 12.1 - - - +
80G GLN* 1.3 80.9 - - - +
82G PHE* 1.3 74.6 + - - +
83G VAL* 3.3 3.0 + - - +
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Residues in contact with PHE 82 (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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531A GLY 6.3 0.2 - - - -
532A SER* 3.9 10.1 - - - -
535A ILE* 4.0 15.9 - - + -
50G VAL* 4.2 12.6 - - + -
73G PRO* 4.0 21.8 - - + -
74G LEU 3.2 16.4 - - - +
75G TRP* 3.7 30.1 - + + -
81G SER* 1.3 82.7 + - - +
83G VAL* 1.3 62.3 + - - +
84G GLY 4.9 2.9 - - - +
129G LEU* 4.2 18.8 - - + +
156G ILE* 4.1 16.8 - - + -
161G GLY 3.7 22.7 - - - -
163G THR* 3.1 30.7 - - - -
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Residues in contact with VAL 83 (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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53G THR* 3.6 23.8 - - + -
74G LEU* 2.8 22.9 + - + +
76G ASP* 3.5 26.9 - - + +
79G LYS* 4.0 25.4 - - + +
81G SER* 3.3 3.8 + - - +
82G PHE* 1.3 73.5 - - - +
84G GLY* 1.3 60.2 + - - +
118G ARG* 3.3 29.3 + - - +
128G PRO* 4.6 1.7 - - - +
129G LEU* 3.3 19.1 + - - +
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Residues in contact with GLY 84 (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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73G PRO* 3.8 0.5 - - - +
74G LEU* 2.9 26.9 + - - +
82G PHE* 3.5 3.0 - - - +
83G VAL* 1.3 83.8 - - - +
85G MET* 1.3 68.2 + - - +
118G ARG* 3.7 13.9 - - - -
129G LEU* 3.7 21.3 - - - +
401G AMP 4.7 2.5 - - - -
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Residues in contact with MET 85 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71G ALA* 4.7 5.2 - - + -
72G ALA 3.4 29.8 - - - +
73G PRO* 3.5 20.9 - - + -
74G LEU* 3.5 11.4 - - - +
84G GLY* 1.3 77.5 - - - +
86G LEU* 1.3 63.0 + - - +
87G THR* 4.2 16.8 - - + -
90G ASP* 4.0 2.4 - - - +
118G ARG* 4.3 3.0 + - - +
129G LEU* 4.1 5.8 - - + +
152G ARG* 4.6 10.3 - - + -
154G PRO* 3.5 39.0 - - + -
166G ILE* 4.8 4.9 - - - -
401G AMP 3.8 54.4 + - + +
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Residues in contact with LEU 86 (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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51G PHE* 4.0 22.4 - - + -
57G VAL* 6.2 0.9 - - + -
60G ALA* 4.3 9.0 - - + -
61G PHE* 3.5 26.7 - - + -
64G LEU* 4.9 7.5 - - + +
70G ARG 4.1 0.2 - - - +
71G ALA* 3.3 4.3 - - - -
72G ALA 3.0 39.6 + - - +
74G LEU* 3.9 24.7 - - + -
85G MET* 1.3 74.1 - - - +
87G THR* 1.3 76.6 + - - +
90G ASP* 3.3 17.0 - - + +
114G ILE* 4.1 17.3 - - + -
117G TRP* 6.0 1.6 - - + -
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Residues in contact with THR 87 (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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61G PHE* 4.2 2.4 - - - -
64G LEU* 5.3 4.3 - - - -
70G ARG 3.5 13.7 - - - -
71G ALA* 4.4 1.1 - - + -
85G MET* 4.3 11.0 - - + -
86G LEU* 1.3 90.6 - - - +
88G ILE* 1.3 64.0 + - - +
89G THR* 3.0 11.5 + - - -
90G ASP* 2.7 18.8 + - - +
91G PHE 3.9 1.7 + - - -
152G ARG* 3.9 31.9 - - + -
401G AMP 3.0 46.8 + - + +
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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