Contacts of the helix formed by residues 100 - 113 (chain B) in PDB entry 5BZZ
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 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B TYR* 3.7 32.7 - - + +
89B PRO 4.1 3.6 - - - +
90B PHE* 3.4 35.0 - - + -
96B PRO* 3.9 7.2 - - + -
97B GLN* 3.1 32.7 + - - +
99B GLU* 1.3 76.7 - - - +
101B ILE* 1.3 65.7 + - - +
102B LYS 3.5 0.2 - - - -
103B PRO* 3.4 13.3 - - - +
104B PHE* 3.5 9.5 + - - +
134B MET* 4.5 4.0 - - + -
233C ARG* 3.8 15.2 - - + +
234C ARG 3.1 31.2 - - - +
235C GLU* 4.5 3.4 - - + -
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Residues in contact with ILE 101 (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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96B PRO* 3.6 33.4 - - + -
97B GLN 4.0 1.1 - - - +
98B LEU* 3.2 30.8 + - + +
100B LEU* 1.3 78.5 - - - +
102B LYS* 1.3 59.3 + - - +
104B PHE* 3.2 6.4 + - - +
105B CYS* 3.0 25.9 + - - -
133B VAL* 5.0 3.8 - - + -
134B MET* 4.2 13.2 - - + -
137B ALA* 3.7 21.3 - - + -
174B TYR* 3.9 25.1 - - + +
178B TYR* 3.5 33.4 - - + -
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Residues in contact with LYS 102 (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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98B LEU 4.6 1.7 + - - +
99B GLU* 4.3 2.4 + - - +
101B ILE* 1.3 77.4 - - - +
103B PRO* 1.3 68.1 - - + +
105B CYS* 3.3 2.5 + - - +
106B GLU* 2.9 59.5 + - + +
141B HIS* 5.4 3.2 - - + -
178B TYR* 3.6 31.4 + - + +
187B ASP* 5.4 8.0 + - - -
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Residues in contact with PRO 103 (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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88B TYR* 3.5 9.7 + - + +
99B GLU 3.1 24.7 - - - +
100B LEU 3.4 10.1 - - - +
102B LYS* 1.3 92.2 - - + +
104B PHE* 1.3 57.9 + - - +
106B GLU* 4.0 10.8 - - + +
107B ASP* 2.9 30.1 + - - +
235C GLU* 3.6 32.8 - - + +
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Residues in contact with PHE 104 (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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68B TYR* 3.6 32.1 - + + -
70B LEU* 4.2 9.0 - - + -
88B TYR* 3.6 32.9 - + + -
100B LEU 3.5 5.1 + - - +
101B ILE 3.2 10.5 + - - +
102B LYS 3.2 0.4 - - - -
103B PRO* 1.3 78.2 - - - +
105B CYS* 1.3 68.0 + - - +
107B ASP* 3.2 2.6 + - - +
108B LEU* 2.8 52.0 + - + +
122B ILE* 4.0 22.2 - - + -
134B MET* 3.2 63.0 - - + -
135B ILE* 4.7 0.9 - - - -
138B TYR* 4.6 0.9 - - + -
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Residues in contact with CYS 105 (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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101B ILE* 3.0 21.8 + - - -
102B LYS 3.5 7.2 - - - +
104B PHE* 1.3 82.8 - - - +
106B GLU* 1.3 52.3 + - - +
108B LEU* 3.2 2.1 + - - +
109B ASP* 2.7 38.0 + - - +
137B ALA* 3.9 5.2 - - - -
138B TYR* 3.6 40.3 - - + -
141B HIS* 3.6 32.5 - - + +
178B TYR* 3.9 12.3 - - - +
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Residues in contact with GLU 106 (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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102B LYS* 2.9 55.1 + - + +
103B PRO* 4.0 8.3 - - + +
105B CYS* 1.3 73.0 - - - +
107B ASP* 1.3 65.9 + - - +
109B ASP* 3.7 6.4 - - - +
110B GLN* 3.1 24.3 + - - +
141B HIS* 4.2 17.1 - - + +
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Residues in contact with ASP 107 (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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66B LYS* 2.8 21.9 + - - -
68B TYR* 2.7 31.8 + - + -
86B ALA* 4.1 4.2 - - - +
88B TYR* 2.6 28.6 + - + +
103B PRO 2.9 20.3 + - - +
104B PHE 3.3 4.7 - - - +
106B GLU* 1.3 75.6 - - - +
108B LEU* 1.3 62.7 + - - +
110B GLN* 3.2 7.5 + - - +
111B TRP* 3.2 17.8 + - - +
236C ASP* 4.1 6.9 - - - +
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Residues in contact with LEU 108 (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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32B ILE* 5.3 3.8 - - + -
68B TYR* 3.3 22.0 - - + +
104B PHE* 2.8 39.5 + - + +
105B CYS 3.5 4.3 - - - +
107B ASP* 1.3 72.4 - - - +
109B ASP* 1.3 63.7 + - - +
111B TRP* 3.3 2.7 + - + +
112B LEU* 3.1 35.9 + - + +
120B ALA* 3.3 33.9 - - + -
122B ILE* 4.5 9.6 - - + -
135B ILE* 5.8 1.3 - - - -
138B TYR* 3.4 39.5 - - + -
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Residues in contact with ASP 109 (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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105B CYS 2.7 22.2 + - - +
106B GLU* 3.7 9.4 - - - +
108B LEU* 1.3 74.8 - - - +
110B GLN* 1.3 56.4 + - - +
112B LEU* 3.8 1.0 - - - +
113B SER* 2.8 39.9 + - - -
138B TYR* 2.8 31.1 + - + -
141B HIS* 4.1 13.0 + - - +
142B ARG* 3.1 28.1 + - - -
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Residues in contact with GLN 110 (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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106B GLU 3.1 15.6 + - - +
107B ASP* 3.6 6.1 - - - +
109B ASP* 1.3 79.5 - - - +
111B TRP* 1.3 62.6 + - - +
113B SER* 3.2 19.0 + - - -
114B GLU* 3.3 29.7 + - - +
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Residues in contact with TRP 111 (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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63B ASN 4.8 4.0 - - - -
64B HIS* 3.6 16.4 - - - -
65B TYR 3.3 28.0 - - - -
66B LYS* 3.3 34.5 - - + +
68B TYR* 3.6 19.7 - + - +
107B ASP 3.2 4.1 + - - +
108B LEU 3.3 2.4 + - - +
110B GLN* 1.3 81.2 - - - +
112B LEU* 1.3 73.9 + - + +
114B GLU* 3.4 17.1 + - - +
118B HIS* 2.7 65.4 + + - -
119B VAL 2.7 29.5 + - - +
120B ALA* 4.2 7.2 - - + -
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Residues in contact with LEU 112 (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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31B ASN* 3.6 34.5 + - + +
32B ILE* 4.0 15.7 - - + -
108B LEU* 3.1 39.0 + - + +
109B ASP 4.0 2.2 - - - +
111B TRP* 1.3 80.7 - - + +
113B SER* 1.3 56.6 + - - +
114B GLU 3.3 0.9 - - - -
115B ASP 3.1 19.8 - - - +
118B HIS* 3.5 26.4 - - - +
119B VAL 3.9 2.5 - - - -
120B ALA 3.7 12.6 - - - +
138B TYR* 3.9 27.6 - - + +
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Residues in contact with SER 113 (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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109B ASP* 2.8 29.1 + - - -
110B GLN* 3.2 20.0 + - - -
111B TRP 3.3 0.2 - - - -
112B LEU* 1.3 75.3 - - - +
114B GLU* 1.3 62.2 + - - +
115B ASP 3.5 1.1 - - - -
142B ARG* 5.9 3.6 - - - -
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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