Contacts of the helix formed by residues 79 - 90 (chain B) in PDB entry 4L57
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 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77B ILE 3.3 1.0 + - - -
78B PRO* 1.3 69.8 - - - +
80B ALA* 1.3 57.2 + - - +
81B LEU 3.5 2.0 - - - -
82B ASP* 3.6 12.6 + - - +
83B ALA* 3.0 31.0 + - - +
183B TRP* 3.8 11.0 - - - +
184B SER 5.9 0.2 - - - -
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Residues in contact with ALA 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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14B VAL 3.3 25.8 - - - +
15B LEU* 3.8 18.4 - - + +
77B ILE* 3.1 19.2 + - + +
78B PRO 3.1 2.0 + - - -
79B GLY* 1.3 75.2 - - - +
81B LEU* 1.3 62.8 + - + +
83B ALA* 3.3 1.6 + - - +
84B VAL* 2.9 34.3 + - - +
183B TRP* 3.4 19.2 - - + +
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Residues in contact with LEU 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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15B LEU* 5.0 7.0 - - + +
76B PRO* 3.9 31.2 - - + -
77B ILE 4.5 0.4 + - - -
79B GLY 3.5 0.2 - - - -
80B ALA* 1.3 75.9 - - + +
82B ASP* 1.3 70.5 + - - +
84B VAL* 3.4 2.2 + - - +
85B ARG* 3.0 32.4 + - + +
115B TRP* 4.0 23.3 - - + -
119B HIS* 3.9 26.0 - - + +
120B LEU* 3.7 34.6 - - + +
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Residues in contact with ASP 82 (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 GLY* 3.6 13.8 + - - +
80B ALA 3.3 0.4 - - - -
81B LEU* 1.3 81.9 - - - +
83B ALA* 1.3 62.0 + - - +
85B ARG* 3.4 20.2 + - - +
86B GLU* 3.0 41.6 + - - +
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Residues in contact with ALA 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 GLY 3.0 19.9 + - - +
80B ALA 3.3 2.4 + - - +
82B ASP* 1.3 77.0 - - - +
84B VAL* 1.3 56.9 + - - +
86B GLU* 3.3 12.8 + - - +
87B MET* 2.8 31.5 + - - +
183B TRP* 3.4 37.0 - - + +
187B TRP* 3.9 16.7 - - - +
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Residues in contact with VAL 84 (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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9B VAL* 4.2 19.3 - - + -
15B LEU* 3.5 28.0 - - + -
80B ALA 2.9 19.1 + - - +
81B LEU* 4.0 4.3 - - - +
83B ALA* 1.3 76.7 - - - +
85B ARG* 1.3 61.7 + - - +
87B MET* 3.7 7.4 - - + +
88B ASN* 3.0 23.6 + - - +
95B VAL* 4.4 11.6 - - + +
97B ILE* 5.5 1.8 - - + -
120B LEU* 4.5 12.8 - - + -
124B PHE* 3.3 31.9 - - + -
183B TRP* 4.8 7.9 - - + -
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Residues in contact with ARG 85 (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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81B LEU* 3.0 26.5 + - - +
82B ASP* 3.5 18.3 + - - +
84B VAL* 1.3 77.9 - - - +
86B GLU* 1.3 62.3 + - + +
88B ASN* 3.8 2.3 - - - +
89B ASP* 3.0 34.5 + - - +
120B LEU* 4.2 15.9 - - + +
124B PHE* 4.4 13.7 - - + -
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Residues in contact with GLU 86 (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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82B ASP* 3.0 35.3 + - - +
83B ALA* 3.7 5.0 - - - +
85B ARG* 1.3 73.6 - - + +
87B MET* 1.3 67.9 + - - +
89B ASP* 3.1 15.9 + - - +
90B LEU* 3.2 19.0 + - + +
187B TRP* 3.8 11.6 + - + -
188B ARG* 3.1 33.7 + - - +
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Residues in contact with MET 87 (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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7B VAL* 3.8 24.5 - - + -
9B VAL* 4.2 8.1 - - + -
83B ALA 2.8 24.1 + - - +
84B VAL* 3.7 7.6 - - - +
86B GLU* 1.3 72.2 - - - +
88B ASN* 1.3 61.1 + - - +
90B LEU* 3.0 15.8 + - - +
93B THR* 3.5 16.7 - - + +
95B VAL* 3.7 22.2 - - + -
143B ILE* 4.3 12.6 - - + -
183B TRP* 3.8 28.7 - - + -
187B TRP* 3.7 33.5 - - + -
191B LEU* 3.9 20.4 - - + -
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Residues in contact with ASN 88 (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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84B VAL 3.0 18.6 + - - +
85B ARG 3.8 4.0 - - - +
86B GLU 3.2 0.2 - - - -
87B MET* 1.3 75.8 - - - +
89B ASP* 1.3 69.2 + - - +
90B LEU 3.7 0.9 + - - +
93B THR 4.2 12.0 - - - +
94B GLN* 4.9 10.4 + - - +
95B VAL* 3.8 31.7 + - + +
123B GLN* 6.3 1.2 - - - +
124B PHE* 3.7 28.0 - - + -
127B ARG* 5.0 6.9 + - - +
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Residues in contact with ASP 89 (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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85B ARG* 3.0 21.2 + - - +
86B GLU* 3.1 10.7 + - - +
88B ASN* 1.3 89.7 + - - +
90B LEU* 1.3 64.1 + - - +
91B PRO* 3.5 4.3 - - - +
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Residues in contact with LEU 90 (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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86B GLU* 3.2 15.1 + - + +
87B MET* 3.0 13.4 + - - +
88B ASN 4.3 1.0 - - - +
89B ASP* 1.3 80.3 - - - +
91B PRO* 1.3 79.4 - - + +
92B ASP 3.4 1.4 + - - -
93B THR* 3.4 26.9 + - - +
94B GLN* 5.5 0.2 + - - -
187B TRP* 3.9 29.2 - - + -
188B ARG* 4.8 19.3 - - + +
191B LEU* 4.3 5.4 - - + -
195B ARG* 4.1 17.9 - - - +
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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