Contacts of the helix formed by residues 81 - 91 (chain G) in PDB entry 3DV0
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 GLN 81 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78G THR* 3.1 13.4 + - - +
80G GLY* 1.3 82.6 - - - +
82G GLU* 1.3 67.3 + - - +
83G ALA* 2.7 5.9 + - - -
84G SER* 3.1 8.8 + - - +
85G GLN* 3.0 43.9 + - + +
103G ARG* 3.9 11.8 - - - +
200G GLN* 3.3 30.1 + - - +
202G ASN* 3.2 28.9 + - - +
235G GLY 5.2 0.7 - - - -
265G CYS* 4.2 18.9 - - + -
266G PHE 4.7 0.2 - - - +
267G ARG* 3.3 25.4 - - + +
1370G TPW 4.5 0.9 + - - -
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Residues in contact with GLU 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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53G MET* 3.5 46.3 - - + +
56G THR* 4.1 15.4 - - + +
57G ARG* 2.8 47.1 + - + +
78G THR 3.8 3.9 + - - +
79G ALA* 3.6 10.6 + - - -
80G GLY* 2.8 21.1 + - - -
81G GLN* 1.3 79.0 + - - +
83G ALA* 1.3 57.6 + - - +
85G GLN* 4.8 0.4 + - - -
86G ILE* 2.9 43.5 + - - +
87G ALA 3.7 0.3 + - - -
295G PRO* 4.4 7.5 - - + +
296G LEU* 5.2 3.8 - - + -
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Residues in contact with ALA 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 MET* 4.2 8.9 - - - -
81G GLN 2.7 5.7 + - - -
82G GLU* 1.3 71.3 - - - +
84G SER* 1.3 60.2 + - - +
85G GLN 3.0 3.8 - - - -
87G ALA* 2.9 38.3 + - - +
235G GLY 3.3 17.0 - - - +
236G MET 3.7 10.5 - - - +
237G ASP 4.1 1.1 - - - +
238G PRO* 3.9 13.7 - - + -
241G VAL* 4.0 2.2 - - + +
295G PRO* 3.7 26.6 - - + +
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Residues in contact with SER 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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81G GLN* 3.1 8.1 + - - +
83G ALA* 1.3 79.0 - - - +
85G GLN* 1.3 52.7 + - - +
88G SER* 2.7 29.4 + - - -
170G TYR* 3.9 8.1 - - - -
198G VAL* 5.2 1.6 - - - +
200G GLN* 3.1 18.7 + - - +
235G GLY* 3.4 10.4 + - - -
241G VAL* 3.7 12.5 - - - +
263G THR* 3.5 37.2 + - - -
265G CYS* 3.8 12.4 - - - -
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Residues in contact with GLN 85 (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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56G THR* 4.8 1.6 - - - +
78G THR* 3.5 23.9 - - - +
81G GLN* 3.0 40.1 + - - +
82G GLU 4.8 0.2 + - - -
84G SER* 1.3 78.3 - - - +
86G ILE* 1.3 72.4 + - + +
87G ALA 3.4 0.2 - - - -
88G SER* 2.9 17.3 + - - -
89G HIS* 3.1 15.9 + - - +
103G ARG* 3.4 19.0 + - - +
104G ASP* 3.1 22.8 + - - -
106G PRO* 3.9 8.2 - - - +
107G GLN* 3.5 28.7 + - - +
200G GLN* 3.3 15.7 - - - +
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Residues in contact with ILE 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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49G LEU* 3.8 13.0 - - + -
52G ARG* 3.8 25.2 + - + +
53G MET* 3.7 21.1 - - + -
56G THR* 3.3 42.0 - - + +
82G GLU* 2.9 23.8 + - - +
85G GLN* 1.3 88.0 - - + +
87G ALA* 1.3 55.4 + - - +
89G HIS* 3.4 7.9 + - - +
90G PHE* 3.0 25.1 + - - +
106G PRO* 4.1 11.9 - - + -
107G GLN 5.3 0.4 - - - +
110G TRP* 3.7 15.7 - - + +
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Residues in contact with ALA 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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49G LEU* 3.8 20.6 - - + -
53G MET* 5.5 0.4 - - - -
82G GLU 3.7 0.6 + - - +
83G ALA* 2.9 18.7 + - - +
86G ILE* 1.3 76.8 - - - +
88G SER* 1.3 63.1 + - - +
90G PHE* 3.2 13.8 + - - +
91G ALA 3.5 5.5 + - - -
238G PRO* 3.3 37.7 - - + +
241G VAL* 4.4 4.7 - - + -
242G TYR* 3.7 13.7 - - + +
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Residues in contact with SER 88 (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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83G ALA 3.7 2.8 + - - -
84G SER 2.7 26.1 + - - -
85G GLN 2.9 5.4 + - - -
87G ALA* 1.3 77.2 - - - +
89G HIS* 1.3 64.8 + - - +
91G ALA 3.4 8.1 + - - -
92G LEU* 3.7 7.1 - - - +
168G ILE* 5.8 0.8 - - - +
170G TYR* 2.5 33.4 + - - -
198G VAL* 5.5 3.4 - - - -
241G VAL* 3.8 8.6 - - - +
245G VAL* 3.5 43.4 - - - +
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Residues in contact with HIS 89 (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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52G ARG* 3.8 20.5 + - - -
85G GLN 3.1 14.7 + - - +
86G ILE* 3.6 7.5 + - - +
87G ALA 3.2 0.2 - - - -
88G SER* 1.3 85.4 + - - +
90G PHE* 1.3 63.2 + - - +
92G LEU* 3.0 30.3 + - + +
98G ILE* 3.8 17.9 - - + -
107G GLN* 3.1 33.0 - - + -
110G TRP* 3.4 33.3 + - + +
111G HIS* 3.0 24.5 + + - -
170G TYR* 4.3 1.6 - - - +
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Residues in contact with PHE 90 (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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41G LEU* 4.1 18.2 - - + -
45G GLN* 3.6 39.3 - - + -
48G GLU* 3.9 16.6 - - + -
49G LEU* 3.8 27.4 - - + -
52G ARG* 3.5 38.6 - - - -
86G ILE 3.0 14.1 + - - +
87G ALA* 3.3 12.6 - - - +
88G SER 3.2 0.4 - - - -
89G HIS* 1.3 79.0 - - - +
91G ALA* 1.3 58.4 + - - +
92G LEU 3.2 7.2 + - - +
93G GLU* 5.4 0.7 - - - +
242G TYR* 3.7 23.7 + + + -
246G LYS* 5.7 0.2 - - - -
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Residues in contact with ALA 91 (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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87G ALA 3.5 2.5 + - - +
88G SER 3.4 2.6 + - - +
89G HIS 3.1 1.8 - - - -
90G PHE* 1.3 77.0 - - - +
92G LEU* 1.3 61.7 + - - +
93G GLU* 4.5 2.1 - - - +
242G TYR* 3.6 20.6 - - + +
245G VAL* 3.4 28.4 - - + +
246G LYS* 3.7 35.9 - - + +
249G ARG* 3.4 20.3 - - - +
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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