Contacts of the helix formed by residues 103 - 117 (chain B) in PDB entry 4BEJ
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 ASP 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B TYR* 4.5 1.4 - - - +
102B THR* 1.3 79.9 + - - +
104B PHE* 1.3 62.2 + - - +
105B ASP* 3.0 15.2 + - - +
106B GLU* 2.8 57.2 + - + +
107B ILE* 3.4 11.2 + - - +
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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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46B VAL* 5.5 1.3 - - + -
48B ARG* 3.3 56.8 - - + +
49B ASP 4.9 8.0 - - - +
50B LEU* 4.5 17.9 - - + -
89B GLU* 3.6 47.3 - - + -
90B TRP* 3.9 7.2 - - - -
102B THR 4.3 9.9 - - - -
103B ASP* 1.3 71.1 + - - +
105B ASP* 1.3 64.0 + - - +
106B GLU 3.2 0.2 - - - -
107B ILE* 3.4 28.0 + - + +
108B ARG* 3.2 21.8 + - - +
134B ILE* 4.1 24.0 - - + -
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Residues in contact with ASP 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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103B ASP* 3.0 14.3 + - - +
104B PHE* 1.3 78.2 - - - +
106B GLU* 1.3 58.7 + - - +
108B ARG* 2.7 43.2 + - - +
109B GLN* 3.1 30.5 + - - +
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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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99B LYS* 4.0 16.1 + - - +
101B TYR* 3.4 27.7 - - + -
103B ASP* 2.8 28.9 + - - +
105B ASP* 1.3 79.2 - - - +
107B ILE* 1.3 59.1 + - - +
109B GLN* 3.3 7.6 + - + +
110B GLU* 2.9 29.6 + - - +
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Residues in contact with ILE 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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50B LEU* 4.8 7.2 - - + -
91B GLY* 4.1 9.4 - - - +
93B PHE* 3.5 25.7 - - + -
101B TYR* 3.5 36.8 - - + +
103B ASP 3.7 6.7 - - - +
104B PHE* 3.4 40.4 + - + +
105B ASP 3.4 0.2 - - - -
106B GLU* 1.3 77.3 - - - +
108B ARG* 1.3 61.5 + - - +
110B GLU 3.2 1.4 + - - -
111B ILE* 3.1 26.4 + - + +
132B LEU* 3.7 20.9 - - + -
134B ILE* 4.0 13.7 - - + -
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Residues in contact with ARG 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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49B ASP* 4.7 11.2 - - - +
50B LEU* 3.4 23.1 - - - +
51B LEU 4.1 12.1 - - - -
52B PRO* 4.0 24.2 - - + +
53B ARG 5.2 2.2 - - - +
104B PHE 3.2 13.0 + - - +
105B ASP* 2.7 48.9 + - - +
107B ILE* 1.3 80.5 - - - +
109B GLN* 1.3 86.8 + - - +
111B ILE* 3.3 5.7 + - - +
112B GLU* 3.1 25.0 + - - +
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Residues in contact with GLN 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 ASP* 3.1 29.1 + - - +
106B GLU* 3.7 9.2 - - + +
107B ILE 3.3 0.2 - - - -
108B ARG* 1.3 102.4 - - - +
110B GLU* 1.3 57.6 + - - +
112B GLU* 3.5 21.9 + - - +
113B ASN* 2.9 53.1 + - - +
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Residues in contact with GLU 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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93B PHE* 3.8 20.9 - - + -
95B HIS* 2.5 39.8 + - + +
96B THR* 4.6 2.4 - - - +
99B LYS* 5.7 1.4 + - - -
101B TYR* 3.8 16.3 + - + +
106B GLU 2.9 17.3 + - - +
107B ILE 3.2 5.6 + - - +
109B GLN* 1.3 74.2 - - - +
111B ILE* 1.3 61.3 + - - +
113B ASN* 4.0 9.1 + - - +
114B GLU* 2.9 29.3 + - - +
117B ARG* 3.3 24.2 + - - -
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Residues in contact with ILE 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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50B LEU* 3.4 31.0 - - + +
51B LEU* 4.8 3.4 - - + -
52B PRO* 3.9 19.1 - - + -
59B THR* 4.9 6.9 - - + +
63B LEU* 4.8 23.3 - - + -
93B PHE* 3.8 17.9 - - + -
107B ILE* 3.1 14.1 + - + +
108B ARG 3.6 5.8 - - - +
110B GLU* 1.3 77.9 - - - +
112B GLU* 1.3 61.2 + - - +
114B GLU* 3.6 4.8 + - - +
115B THR* 3.3 21.0 + - - +
130B ILE* 4.3 12.2 - - + +
132B LEU* 3.6 24.9 - - + -
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Residues in contact with GLU 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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52B PRO* 4.3 26.0 - - + +
54B GLY* 4.9 12.5 - - - -
56B GLY* 5.7 1.9 + - - -
57B ILE 5.5 6.6 + - - +
59B THR* 5.0 4.3 - - + -
108B ARG* 3.1 13.7 + - - +
109B GLN* 3.6 32.0 + - - +
111B ILE* 1.3 80.4 - - - +
113B ASN* 1.3 58.5 + - - +
115B THR* 3.3 9.2 + - - -
116B GLU* 3.2 42.6 + - + +
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Residues in contact with ASN 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 GLN* 2.9 42.2 + - - +
110B GLU* 3.6 14.5 + - - +
111B ILE 3.3 0.2 - - - -
112B GLU* 1.3 76.3 - - - +
114B GLU* 1.3 54.6 + - - +
115B THR 3.1 2.0 - - - -
116B GLU* 3.1 13.8 + - - +
117B ARG* 2.7 54.5 + - - +
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Residues in contact with GLU 114 (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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61B ARG* 2.3 48.0 + - - +
95B HIS* 4.0 32.5 + - + +
110B GLU* 2.9 20.7 + - - +
111B ILE* 4.0 0.9 - - - +
112B GLU 3.5 0.2 - - - -
113B ASN* 1.3 73.3 - - - +
115B THR* 1.3 60.3 + - - +
117B ARG* 3.1 46.3 + - - +
118B ILE 4.0 2.1 + - - -
128B GLU* 5.4 0.7 - - - +
130B ILE* 3.5 29.2 - - + -
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Residues in contact with THR 115 (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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58B VAL 4.0 4.7 - - - +
59B THR* 3.7 23.4 - - - +
60B ARG* 3.1 51.3 + - + +
61B ARG* 4.5 12.7 + - - +
111B ILE* 3.3 12.5 + - - +
112B GLU 3.3 10.3 + - - -
113B ASN 3.1 0.4 - - - -
114B GLU* 1.3 76.5 - - - +
116B GLU* 1.3 65.0 - - + +
118B ILE* 3.1 23.9 - - - +
130B ILE* 4.6 6.8 - - - +
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Residues in contact with GLU 116 (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 ILE* 4.6 20.6 - - + +
60B ARG* 5.0 7.5 + - - +
112B GLU* 3.2 30.9 + - + +
113B ASN* 3.4 15.3 - - - +
115B THR* 1.3 81.8 - - + +
117B ARG* 1.3 62.6 + - - +
118B ILE 3.2 10.4 + - - +
119B SER* 5.2 0.3 - - - -
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Residues in contact with ARG 117 (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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95B HIS* 4.8 5.5 + - - -
110B GLU* 3.3 26.9 + - - -
113B ASN* 2.7 34.7 + - - +
114B GLU* 3.1 46.6 + - - +
116B GLU* 1.3 72.4 - - - +
118B ILE* 1.3 58.2 + - - +
119B SER 3.5 2.9 + - - -
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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