Contacts of the helix formed by residues 78 - 88 (chain B) in PDB entry 4BLU
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 LEU 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B THR* 3.4 42.0 - - + +
68B ILE* 4.8 5.8 - - + -
74B LEU* 3.9 19.3 - - + -
75B PRO* 3.0 23.2 + - + +
77B GLU* 1.3 83.1 - - + +
79B GLU* 1.3 58.1 + - - +
80B ALA 3.4 2.0 - - - -
81B TYR* 3.5 12.7 + - + +
82B ILE* 2.9 33.4 + - + +
256B VAL* 4.9 7.4 - - + -
259B TRP* 3.7 32.3 - - + -
260B LEU* 4.0 18.6 - - + -
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Residues in contact with GLU 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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74B LEU* 3.7 34.5 - - - +
75B PRO 3.9 0.9 - - - +
76B ALA* 3.3 29.2 + - + +
77B GLU 3.6 0.2 - - - -
78B LEU* 1.3 76.8 - - - +
80B ALA* 1.3 65.2 + - - +
82B ILE* 4.2 0.6 - - - +
83B ASN* 2.9 44.5 + - - +
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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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23B SER* 5.0 3.4 - - - +
27B GLU* 4.1 32.3 - - + +
76B ALA 4.9 0.6 + - - -
77B GLU 5.1 2.1 + - - +
78B LEU 3.4 0.6 - - - -
79B GLU* 1.3 81.0 - - - +
81B TYR* 1.3 62.3 + - - +
83B ASN* 3.5 6.4 + - - +
84B VAL* 3.3 24.3 + - - +
107B LEU* 4.2 18.7 - - + +
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Residues in contact with TYR 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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16B VAL* 3.5 18.9 - - - +
19B HIS* 3.5 22.7 - - + -
20B THR* 3.8 26.0 - - - -
23B SER* 3.7 25.5 + - - +
65B ILE* 3.6 15.8 - - + +
68B ILE* 4.3 10.1 - - + -
77B GLU 5.6 0.2 + - - -
78B LEU* 3.5 14.9 + - + +
79B GLU 3.3 0.2 - - - -
80B ALA* 1.3 78.5 - - - +
82B ILE* 1.3 79.2 + - + +
84B VAL* 3.0 17.4 + - - +
85B VAL* 3.1 23.9 + - + +
97B TYR* 2.7 28.1 + + - -
103B ILE* 3.9 20.0 - - + -
107B LEU* 5.4 0.7 - - - -
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Residues in contact with ILE 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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65B ILE* 3.6 30.5 - - + -
68B ILE* 4.1 7.9 - - + -
69B TRP* 3.5 35.2 - - + +
74B LEU* 3.7 32.1 - - + -
78B LEU* 2.9 27.0 + - + +
79B GLU 4.2 1.1 - - - +
81B TYR* 1.3 86.8 - - + +
83B ASN* 1.3 59.0 + - - +
85B VAL* 3.1 5.0 + - + +
86B LYS* 2.8 42.1 + - + +
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Residues in contact with ASN 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 GLU* 2.9 36.9 + - - +
80B ALA* 3.8 7.0 - - - +
82B ILE* 1.3 77.8 - - - +
84B VAL* 1.3 61.2 + - + +
86B LYS* 3.4 19.1 + - - +
87B HIS* 3.1 22.2 + - - +
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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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80B ALA 3.3 15.4 + - - +
81B TYR* 3.0 9.8 + - - +
83B ASN* 1.3 73.6 - - - +
85B VAL* 1.3 64.5 + - - +
87B HIS* 3.2 14.2 + - - +
88B PHE* 3.2 36.4 - - + -
98B PRO* 4.2 4.0 - - + -
102B LEU 4.2 8.5 - - - +
103B ILE* 4.2 24.9 - - + +
106B LEU* 4.0 22.2 - - + -
107B LEU* 4.0 24.5 - - + -
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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
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65B ILE* 4.1 23.3 - - + -
69B TRP* 4.1 17.0 - - + -
81B TYR* 3.1 36.6 + - + +
82B ILE* 3.1 11.5 + - + +
84B VAL* 1.3 74.4 - - - +
86B LYS* 1.3 62.3 + - - +
88B PHE* 3.2 5.9 + - - +
89B ASN* 2.9 37.5 + - - +
94B LEU* 4.4 4.5 - - + -
97B TYR* 4.2 19.7 - - + -
98B PRO* 4.3 14.1 - - + -
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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
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110A GLU* 5.3 10.9 + - - +
69B TRP* 3.6 48.0 + - + -
70B GLN* 5.3 5.5 + - - +
82B ILE* 2.8 27.8 + - + +
83B ASN* 3.8 20.1 + - - +
85B VAL* 1.3 76.7 - - - +
87B HIS* 1.3 63.5 + - - +
89B ASN 2.9 22.2 + - - +
90B ARG* 3.4 7.7 + - - +
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Residues in contact with HIS 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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87A HIS* 3.2 30.2 - + - -
105A ARG* 4.3 11.4 + - - -
106A LEU* 4.8 3.4 - - + -
83B ASN 3.1 14.2 + - - +
84B VAL 3.2 8.9 + - - +
86B LYS* 1.3 78.0 - - - +
88B PHE* 1.3 76.5 + + - +
89B ASN 3.3 0.6 + - - -
90B ARG* 3.0 57.5 + - - +
106B LEU* 3.5 27.4 - - + -
1294B EDO 3.7 6.9 + - - +
1295B SO4 2.6 30.4 + - - -
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Residues in contact with PHE 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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105A ARG* 6.0 0.9 - - - +
47B ARG* 3.8 33.9 - - + -
84B VAL* 3.2 39.7 + - + -
85B VAL 3.2 6.3 + - - +
86B LYS 3.1 0.8 - - - -
87B HIS* 1.3 99.1 - + - +
89B ASN* 1.3 72.4 + - - +
90B ARG 3.9 1.3 - - - -
96B TYR* 3.5 30.3 - - + +
98B PRO* 3.9 27.6 - - + -
102B LEU* 3.7 25.4 - - + -
105B ARG* 6.1 0.2 - - - -
106B LEU* 4.0 12.6 - - + -
1295B SO4 3.7 19.3 - - - -
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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