Contacts of the helix formed by residues 73 - 87 (chain B) in PDB entry 4R54
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 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ALA* 1.3 80.2 - - - +
74B SER* 1.3 66.3 + - - -
75B SER* 3.2 3.6 - - - -
76B THR 3.1 12.6 + - - -
77B SER* 3.3 10.0 + - - -
95B THR* 3.4 12.8 - - - +
403B NAP 3.5 26.9 - - - -
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY* 1.3 71.0 - - - -
75B SER* 1.3 55.9 + - - +
77B SER* 3.4 2.9 + - - -
78B ALA* 3.0 29.4 + - - +
95B THR* 3.6 18.7 - - - +
96B SER* 4.2 8.8 + - - -
97B TYR* 3.4 35.8 + - - +
403B NAP 4.2 2.8 + - - -
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Residues in contact with SER 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLY 3.1 0.8 + - - -
74B SER* 1.3 81.3 - - - +
76B THR* 1.3 62.1 + - - +
78B ALA* 3.5 6.4 + - - +
79B LYS* 3.2 45.1 + - - +
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Residues in contact with THR 76 (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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8B VAL* 4.1 13.0 - - + -
57B THR* 4.4 1.6 - - + -
70B PHE* 4.0 2.8 - - + -
72B ALA* 3.1 37.0 + - + -
73B GLY 3.1 9.0 + - - -
75B SER* 1.3 79.4 - - - +
77B SER* 1.3 57.3 + - - +
79B LYS* 4.8 2.9 - - - +
80B TYR* 3.0 45.2 + - + +
402B NAP 3.3 40.1 + - + +
403B NAP 3.9 0.2 - - + -
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 3.3 23.9 - - - +
72B ALA 5.1 0.9 + - - -
73B GLY 3.3 4.3 + - - -
74B SER 3.9 3.6 - - - -
76B THR* 1.3 74.3 - - - +
78B ALA* 1.3 67.0 + - - +
81B ALA* 3.0 28.8 + - - +
82B PRO* 3.5 0.9 - - - +
93B ASP* 2.6 41.2 + - - -
95B THR* 3.4 17.9 - - - +
97B TYR* 4.9 0.7 - - - -
98B PHE* 3.6 9.3 - - - -
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER 3.0 18.1 + - - +
75B SER* 3.6 9.6 - - - +
77B SER* 1.3 78.3 - - - +
79B LYS* 1.3 62.4 + - + +
82B PRO* 3.5 16.1 - - - +
97B TYR* 3.4 45.1 - - + +
98B PHE* 4.3 2.0 - - - -
358B LYS* 4.6 18.8 + - + +
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 3.2 36.8 + - - +
76B THR* 4.8 1.6 - - - +
78B ALA* 1.3 85.0 - - + +
80B TYR* 1.3 91.9 + - + +
81B ALA 3.8 0.4 - - - -
82B PRO* 3.9 2.4 - - - +
83B TYR* 3.3 27.2 - - - -
358B LYS* 4.7 22.5 + - + -
402B NAP 4.9 11.2 + - - -
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Residues in contact with TYR 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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57B THR* 3.7 32.2 + - + -
58B THR* 3.5 38.5 - - - -
59B GLU* 3.5 29.3 + - + -
62B PHE* 4.1 14.4 - - + -
70B PHE* 4.1 6.5 - - + -
76B THR* 3.0 26.9 + - + +
79B LYS* 1.3 108.5 + - + +
81B ALA* 1.3 65.8 + - - +
82B PRO* 3.3 3.1 - - - -
83B TYR* 3.2 8.7 + - - +
84B ALA* 3.0 20.3 + - - +
402B NAP 5.0 6.3 - - - -
403B NAP 5.5 1.3 - - - -
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 3.8 21.5 - - + -
77B SER* 3.0 21.2 + - - +
80B TYR* 1.3 75.2 - - - +
82B PRO* 1.3 68.1 - - + +
84B ALA* 3.2 4.5 + - - +
85B VAL* 3.0 28.4 + - - +
91B VAL* 4.1 17.4 - - + +
93B ASP* 5.8 0.2 - - - -
98B PHE* 3.9 16.4 - - + -
122B ILE* 4.4 4.9 - - + -
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Residues in contact with PRO 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B SER 3.5 1.3 - - - +
78B ALA 3.5 23.1 - - - +
79B LYS 3.9 3.6 - - - +
80B TYR 3.5 3.8 - - - -
81B ALA* 1.3 94.6 - - + +
83B TYR* 1.3 57.0 + - + +
85B VAL* 3.4 9.7 + - + +
86B LYS* 2.9 25.8 + - - +
98B PHE* 4.3 9.0 - - + -
122B ILE* 5.2 0.7 - - + -
353B LEU* 4.0 4.0 - - + +
355B PHE* 3.9 22.7 - - + +
356B GLU 3.2 28.3 - - - +
357B LEU* 3.7 16.8 - - + +
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU* 3.8 56.3 - - + +
62B PHE* 4.8 4.2 - - + +
79B LYS 3.3 26.0 - - - -
80B TYR* 3.2 9.2 + - - +
82B PRO* 1.3 74.5 - - + +
84B ALA* 1.3 61.2 + - - +
86B LYS* 3.2 17.5 + - + +
87B ALA* 2.8 29.9 + - - +
357B LEU* 3.6 36.4 + - + +
358B LYS 3.1 36.1 + - - -
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 3.7 40.4 - - + -
70B PHE* 4.5 0.9 - - + -
80B TYR 3.0 11.7 + - - +
81B ALA* 3.2 10.5 + - - +
83B TYR* 1.3 76.8 - - - +
85B VAL* 1.3 56.5 + - - +
87B ALA* 2.9 16.3 + - - -
88B GLY 3.2 0.2 + - - -
89B VAL* 3.0 29.0 + - + +
91B VAL* 3.7 18.8 - - + -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA 3.0 19.2 + - - +
82B PRO* 3.6 7.4 - - + +
83B TYR 3.3 0.2 - - - -
84B ALA* 1.3 74.5 - - - +
86B LYS* 1.3 63.4 - - - +
88B GLY* 3.1 13.9 + - - -
89B VAL 3.7 8.2 - - - +
91B VAL* 4.1 4.5 - - + -
120B ASN 3.9 18.2 - - - +
121B GLY* 3.7 14.4 - - - +
122B ILE* 3.6 31.9 - - + -
350B THR* 4.2 21.2 + - - +
352B GLU 5.3 1.3 - - - +
353B LEU* 4.1 17.5 - - + +
355B PHE* 4.5 6.5 - - + -
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO 2.9 14.7 + - - +
83B TYR* 3.3 22.2 - - + +
85B VAL* 1.3 77.2 - - - +
87B ALA* 1.3 56.9 + - - +
88B GLY* 3.1 4.4 + - - -
353B LEU* 4.0 27.9 - - + +
357B LEU* 3.4 31.9 - - + -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLU 6.1 0.7 - - - +
62B PHE* 3.6 32.0 - - + +
63B GLU* 3.6 31.6 - - - +
64B GLY 5.0 3.8 + - - -
65B VAL 4.8 1.9 - - - +
83B TYR 2.8 13.0 + - - +
84B ALA 2.9 9.3 + - - +
86B LYS* 1.3 74.3 - - - +
88B GLY* 1.3 59.4 + - - +
89B VAL* 3.4 0.9 + - - +
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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