Contacts of the helix formed by residues 82 - 91 (chain B) in PDB entry 4C48
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 THR 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B HIS* 4.1 1.8 - - - -
73B VAL 4.1 11.7 - - - +
74B ASN* 4.5 14.8 + - + +
75B ALA 3.8 7.5 + - - +
76B TYR* 5.1 2.9 - - - +
80B GLY 4.3 3.8 + - - -
81B SER* 1.3 74.6 - - - +
83B PRO* 1.3 79.6 - - + +
84B LEU* 3.1 21.5 - - + +
85B HIS* 3.1 36.4 + - - +
86B LEU* 3.4 8.7 + - - +
104B ALA* 5.7 1.1 - - + -
105B ASP 5.1 2.0 - - - +
108B ALA* 3.6 25.3 - - + +
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Residues in contact with PRO 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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51B LEU* 3.7 30.5 - - + +
52B HIS* 3.4 26.2 - - + +
55B ALA* 3.4 20.7 - - + +
72B ASP 5.5 0.2 - - - +
73B VAL 3.9 7.0 - - - +
75B ALA* 3.3 17.0 - - + +
82B THR* 1.3 93.0 - - + +
84B LEU* 1.3 56.2 + - - +
86B LEU* 3.1 4.9 + - + +
87B ALA* 2.9 26.5 + - - +
99B LEU* 3.7 20.0 - - + -
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Residues in contact with LEU 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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73B VAL 5.5 0.2 + - - -
82B THR* 3.1 16.5 - - + +
83B PRO* 1.3 76.2 - - - +
85B HIS* 1.3 57.7 + - - +
87B ALA* 4.6 1.6 - - - -
88B ALA* 2.9 31.4 + - - +
96B VAL* 3.5 36.1 - - + +
99B LEU* 4.0 10.5 - - + +
100B LEU* 4.3 10.8 - - + -
104B ALA* 4.2 20.6 - - + +
105B ASP 3.4 25.8 - - - +
106B VAL* 3.7 19.3 - - + -
116B PRO* 3.7 23.1 - - + -
132B LEU* 4.3 4.3 - - + -
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Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLY 4.6 0.9 - - - -
81B SER* 4.4 5.4 - - - -
82B THR* 3.1 37.4 + - - +
84B LEU* 1.3 77.1 - - - +
86B LEU* 1.3 64.3 + - + +
88B ALA* 3.2 6.0 + - - +
89B HIS* 3.0 24.9 + - - +
108B ALA 3.0 31.2 - - - -
109B LYS 4.4 0.2 - - - -
110B ASP* 3.7 21.6 + - + -
114B ILE* 2.7 32.2 + - + -
115B THR 3.9 2.6 - - - -
116B PRO* 3.5 13.6 - - + +
119B LEU* 3.7 32.7 - - + +
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Residues in contact with LEU 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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809A TRP 5.5 1.1 - - - +
48B TRP* 3.5 32.5 - - + -
52B HIS* 3.2 42.0 - - + +
55B ALA 3.8 11.9 - - - +
56B TYR* 3.8 17.5 - - + +
81B SER* 3.9 22.9 - - - +
82B THR 3.4 6.0 + - - +
83B PRO* 3.1 9.2 + - + +
85B HIS* 1.3 83.9 - - + +
87B ALA* 1.3 64.7 + - - +
89B HIS* 3.3 2.2 + - - -
90B PHE* 3.1 35.8 + - + +
119B LEU* 6.3 0.2 - - + -
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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
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55B ALA* 3.7 11.6 + - + +
83B PRO 2.9 16.8 + - - +
84B LEU* 4.2 5.2 - - - +
86B LEU* 1.3 77.0 - - - +
88B ALA* 1.3 64.7 + - - +
89B HIS 3.4 0.3 + - - -
91B GLY* 3.4 4.0 + - - -
92B HIS* 3.3 31.4 + - + +
95B ILE* 4.1 26.2 - - + -
96B VAL* 4.4 18.8 - - + +
99B LEU* 4.8 1.8 - - + -
128B ILE* 4.5 1.6 - - - +
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Residues in contact with ALA 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 LEU 2.9 21.7 + - - +
85B HIS 3.4 5.2 - - - +
86B LEU 3.2 0.2 - - - -
87B ALA* 1.3 80.4 - - - +
89B HIS* 1.3 61.6 + - - +
91B GLY 4.0 1.0 + - - -
96B VAL* 5.0 3.1 - - + +
116B PRO* 3.4 33.2 - - + +
119B LEU* 4.8 0.7 - - + -
120B ALA* 3.5 24.8 - - + +
125B HIS* 3.9 7.1 + - - -
128B ILE* 4.3 13.7 - - + +
132B LEU* 4.6 4.9 - - + -
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Residues in contact with HIS 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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808A ARG* 5.3 16.9 + - - -
85B HIS 3.0 10.8 + - - +
86B LEU* 3.3 6.3 + - - +
88B ALA* 1.3 73.7 - - - +
90B PHE* 1.3 91.3 + + + +
91B GLY 3.1 4.5 - - - -
119B LEU* 3.2 38.1 + - + +
122B ASN* 6.0 1.1 - - + +
123B ARG* 3.6 28.1 - - + +
125B HIS* 3.0 24.8 + - - -
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Residues in contact with PHE 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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810A GLU* 5.5 3.4 - - + -
56B TYR* 3.1 63.0 - + - -
86B LEU* 3.1 30.7 + - + +
87B ALA 3.5 0.4 + - - -
89B HIS* 1.3 103.8 - + + +
91B GLY* 1.3 62.2 + - - +
92B HIS* 3.5 30.7 - + + +
125B HIS* 3.8 5.9 + - - -
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Residues in contact with GLY 91 (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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87B ALA 3.4 2.4 + - - -
89B HIS 3.0 6.3 + - - -
90B PHE* 1.3 80.8 - - - +
92B HIS* 1.3 62.7 + - - +
93B LEU* 3.2 11.2 + - - +
94B GLU* 5.5 0.2 - - - +
125B HIS* 3.3 23.9 - - - -
127B GLU* 4.6 3.8 - - - +
128B ILE* 3.5 16.1 - - - +
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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