Contacts of the helix formed by residues 72 - 83 (chain B) in PDB entry 4DTZ
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 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B ASN* 3.4 11.7 + - - +
71B LEU* 1.3 78.7 - - - +
73B GLN* 1.3 79.5 + - - +
74B ALA* 3.4 1.6 + - - +
75B PRO* 3.3 18.2 - - - +
76B LYS* 3.0 16.0 + - - +
332B SER* 3.8 25.6 + - - -
352B GLU* 5.2 3.8 - - - -
354B MET* 4.2 13.6 - - - +
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Residues in contact with GLN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 5.4 5.1 - - - +
47B ARG* 2.8 50.8 + - - +
51B TYR* 5.4 5.1 + - - -
72B SER* 1.3 90.7 + - - +
74B ALA* 1.3 63.1 + - - +
76B LYS* 3.5 10.0 + - + +
77B PHE* 3.0 38.7 + - + -
188B LEU* 3.2 28.4 - - + +
354B MET* 5.7 3.2 - - - -
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B SER* 4.5 1.1 + - - +
73B GLN* 1.3 79.0 - - - +
75B PRO* 1.3 74.6 - - + +
77B PHE* 3.0 7.9 + - - +
78B VAL* 2.9 27.2 + - - +
184B ALA* 4.8 1.4 - - - +
185B MET* 4.0 30.7 - - + -
188B LEU* 4.0 14.4 - - + -
437B LEU* 4.3 9.2 - - + -
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Residues in contact with PRO 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS* 5.8 1.3 - - - +
70B ASN 5.3 1.8 - - - +
71B LEU* 4.6 20.4 - - + -
72B SER* 3.3 30.3 - - - +
74B ALA* 1.3 95.5 - - + +
76B LYS* 1.3 62.2 + - - +
78B VAL* 3.1 8.7 + - + -
79B ARG* 2.9 25.3 + - - +
87B PHE* 4.4 28.0 - - + +
88B THR* 3.6 10.3 - - + +
437B LEU* 5.4 1.7 - - + -
500B HEM 5.5 4.7 - - - +
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 3.8 35.2 - - + +
72B SER 3.0 14.4 + - - +
73B GLN* 3.6 11.0 - - + +
74B ALA 3.4 0.2 - - - -
75B PRO* 1.3 78.2 - - - +
77B PHE* 1.3 65.3 + - + +
79B ARG* 3.4 19.3 - - + +
80B ASP* 4.0 7.8 + - - +
90B TRP* 4.5 15.7 - - - -
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN* 3.0 29.6 + - + -
74B ALA 3.0 7.8 + - - +
76B LYS* 1.3 76.7 - - + +
78B VAL* 1.3 66.1 + - - +
79B ARG 3.2 0.2 - - - -
80B ASP* 3.1 33.0 + - - +
184B ALA* 3.7 30.1 - - + +
187B LYS* 3.6 38.6 - - + +
188B LEU* 3.5 28.9 - - + -
205B PHE* 4.3 6.2 - - - -
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ALA 2.9 18.6 + - - +
75B PRO* 3.1 9.6 + - + +
77B PHE* 1.3 78.1 - - - +
79B ARG* 1.4 51.3 + - - +
80B ASP 3.0 0.4 - - - -
81B PHE* 2.9 29.4 + - + -
82B ALA* 2.8 39.2 + - + -
87B PHE* 4.7 9.4 - - + -
88B THR* 3.9 15.9 - - + -
181B LEU* 4.2 20.9 - - + -
184B ALA* 4.1 14.1 - - + -
185B MET* 5.6 1.8 - - - -
263B ALA* 5.7 2.7 - - + -
264B ALA* 6.3 1.1 - - + -
437B LEU* 4.7 15.5 - - + -
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LEU* 4.2 8.5 - - - -
75B PRO 2.9 13.0 + - - +
76B LYS* 3.4 18.6 - - - +
77B PHE 3.2 0.2 - - - -
78B VAL* 1.4 76.2 - - - +
80B ASP* 1.4 60.0 + - - +
83B GLY* 2.9 41.9 + - - +
84B ASP* 4.1 10.8 + - - +
88B THR* 2.8 45.0 + - - +
89B SER* 3.5 3.4 - - - +
90B TRP* 3.9 11.3 - - - +
93B GLU* 2.7 43.0 + - - -
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Residues in contact with ASP 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS 4.2 5.9 - - - +
77B PHE* 3.1 26.4 + - - +
78B VAL 3.0 1.6 - - - -
79B ARG* 1.4 79.6 - - - +
81B PHE* 1.4 57.5 + - - +
187B LYS* 4.0 15.9 + - - -
205B PHE* 3.7 21.1 - - + -
206B GLN* 6.2 0.2 - - - +
209B ILE* 3.8 17.4 - - + +
256B TYR* 5.3 3.8 + - - -
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Residues in contact with PHE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B VAL* 2.9 35.7 + - + -
80B ASP* 1.4 75.2 - - - +
82B ALA* 1.3 62.9 + - + +
83B GLY 3.4 1.8 - - - -
177B MET* 4.9 1.3 - - + -
180B ALA* 3.6 29.4 - - + -
181B LEU* 3.7 33.2 - - + -
184B ALA* 4.5 1.8 - - + -
205B PHE* 3.9 13.7 - + - -
209B ILE* 3.7 17.5 - - + -
212B MET* 3.7 33.9 - - + -
213B ASN* 4.8 2.2 - - - +
256B TYR* 3.4 19.9 - - - -
259B ILE* 3.8 24.5 - - + +
263B ALA* 3.8 24.5 - - + -
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 2.8 28.5 + - + +
81B PHE* 1.3 77.9 - - + +
83B GLY* 1.3 65.9 + - - +
85B GLY* 3.0 17.0 + - - -
87B PHE* 5.9 0.4 - - + -
88B THR* 3.5 12.5 + - + +
256B TYR* 3.4 15.9 - - - +
259B ILE* 4.3 11.4 - - + -
260B THR* 3.6 22.5 + - + +
263B ALA* 5.9 0.9 - - + -
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ARG* 2.9 36.0 + - - +
81B PHE 3.4 2.6 - - - -
82B ALA* 1.3 77.9 - - - +
84B ASP* 1.4 57.6 + - - -
88B THR* 2.6 26.9 + - - +
256B TYR* 3.6 22.2 - - - -
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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