Contacts of the helix formed by residues 101 - 117 (chain B) in PDB entry 1B3U
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 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B GLU 3.3 4.8 + - - -
100B GLU* 1.3 88.9 + - - +
102B VAL* 1.3 66.5 + - + +
104B ARG* 3.2 30.8 + - - +
105B ASP* 3.0 33.8 + - - -
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 5.8 1.8 - - + -
66B LEU* 3.8 20.3 - - + +
100B GLU* 3.1 27.7 + - + +
101B THR* 1.3 82.0 - - + +
103B VAL* 1.3 69.4 + - + +
105B ASP* 3.9 9.5 - - - +
106B LYS* 3.1 22.7 + - - +
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Residues in contact with VAL 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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62B ASP* 3.6 41.3 - - + +
65B LEU* 4.0 24.7 - - + +
66B LEU* 4.1 8.7 - - + +
69B ALA* 4.6 1.7 - - + +
95B LEU* 3.8 25.6 - - + +
98B VAL* 4.5 9.0 - - + -
100B GLU* 3.1 18.5 + - + +
102B VAL* 1.3 78.9 - - + +
104B ARG* 1.3 66.8 + - - +
106B LYS* 3.2 6.5 + - - +
107B ALA* 3.0 21.5 + - - +
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Residues in contact with ARG 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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95B LEU 3.8 9.6 - - - +
96B ALA* 3.2 27.9 - - - +
98B VAL 3.1 25.3 + - - +
99B GLU 3.0 27.7 + - - -
100B GLU 3.3 3.6 + - - +
101B THR* 3.2 33.4 + - - +
103B VAL* 1.3 78.8 - - - +
105B ASP* 1.3 59.0 + - - +
107B ALA* 3.1 3.6 + - - +
108B VAL* 2.9 33.9 + - - +
140B PHE* 5.4 4.4 - - - -
141B THR* 3.4 34.5 + - - +
144B THR* 4.1 10.9 + - - +
145B SER* 3.5 16.6 + - - +
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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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101B THR* 3.0 30.2 + - - +
102B VAL* 3.9 9.3 - - - +
104B ARG* 1.3 77.8 - - - +
106B LYS* 1.3 62.8 + - - +
108B VAL* 3.4 10.3 + - - +
109B GLU* 3.0 22.5 + - - +
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Residues in contact with LYS 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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66B LEU* 3.5 37.2 - - + +
69B ALA* 3.8 17.7 - - + -
70B GLU* 3.6 41.3 + - - +
102B VAL 3.1 9.8 + - - +
103B VAL 3.2 5.4 + - - +
105B ASP* 1.3 74.6 - - - +
107B ALA* 1.3 64.5 + - - +
109B GLU* 2.8 37.3 + - - +
110B SER* 3.0 23.1 + - - -
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Residues in contact with ALA 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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69B ALA* 4.1 9.1 - - + +
92B LEU* 3.9 30.1 - - + +
95B LEU* 4.0 10.8 - - + -
96B ALA* 3.9 16.6 - - + +
103B VAL 3.0 11.9 + - - +
104B ARG 3.5 8.1 - - - +
106B LYS* 1.3 78.2 - - - +
108B VAL* 1.3 56.1 + - - +
110B SER* 3.1 4.2 + - - +
111B LEU* 2.8 32.9 + - - +
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Residues in contact with VAL 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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96B ALA* 5.0 4.7 - - + -
104B ARG 2.9 20.0 + - - +
105B ASP* 3.6 14.1 - - - +
106B LYS 3.3 0.2 - - - -
107B ALA* 1.3 75.6 - - - +
109B GLU* 1.3 58.6 + - - +
111B LEU* 3.2 10.9 + - + +
112B ARG* 2.9 35.3 + - - +
145B SER* 3.8 34.8 - - - +
148B GLY* 4.0 20.4 - - - +
149B LEU* 3.8 18.8 - - + -
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Residues in contact with GLU 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 3.0 14.3 + - - +
106B LYS* 2.8 46.7 + - - +
107B ALA 3.2 0.2 - - - -
108B VAL* 1.3 77.6 - - - +
110B SER* 1.3 63.7 + - - +
112B ARG* 3.3 12.6 + - - +
113B ALA* 3.0 22.8 + - + +
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Residues in contact with SER 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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69B ALA 2.9 25.4 + - - -
70B GLU* 4.0 6.1 + - - -
73B GLY* 3.5 22.0 - - - -
92B LEU* 4.0 12.6 - - - -
106B LYS* 3.0 12.7 + - - +
107B ALA 3.5 7.4 - - - -
109B GLU* 1.3 76.9 + - - +
111B LEU* 1.3 66.6 + - - +
113B ALA* 3.1 8.2 + - - +
114B ILE* 3.0 28.1 + - - +
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Residues in contact with LEU 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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89B LEU* 3.9 26.5 - - + +
92B LEU* 3.6 41.1 - - + +
93B GLU 5.2 0.2 - - - +
96B ALA* 4.7 9.9 - - + -
107B ALA 2.8 21.2 + - - +
108B VAL* 3.2 14.1 + - + +
110B SER* 1.3 76.3 - - - +
112B ARG* 1.3 63.6 + - - +
114B ILE* 3.5 6.8 + - + +
115B SER* 3.0 23.6 + - - -
127B PHE* 3.6 10.5 - - + -
130B LEU* 3.9 15.5 - - + -
134B LEU* 5.1 2.5 - - + -
149B LEU* 3.9 28.9 - - + -
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Residues in contact with ARG 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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108B VAL* 2.9 25.3 + - - +
109B GLU* 3.6 12.1 - - - +
111B LEU* 1.3 75.4 - - - +
113B ALA* 1.3 63.1 + - - +
115B SER* 2.5 25.7 + - - -
116B HIS* 3.3 11.8 + - - +
148B GLY* 3.0 28.1 + - - +
149B LEU* 4.2 5.8 - - + -
151B SER* 3.1 20.0 + - - -
152B VAL* 3.5 29.3 - - + +
187B LYS* 4.7 4.8 - - - +
190B GLU* 2.9 32.5 + - - +
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Residues in contact with ALA 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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73B GLY* 4.8 10.5 - - - +
109B GLU* 3.0 15.4 + - + +
110B SER* 3.1 11.4 + - - +
112B ARG* 1.3 78.4 - - - +
114B ILE* 1.3 60.3 + - - +
116B HIS* 3.5 23.9 - - - +
117B GLU* 4.5 4.3 + - - +
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Residues in contact with ILE 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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72B LEU 4.6 2.9 - - - +
73B GLY* 3.5 31.6 - - - +
76B THR* 4.0 13.5 - - - +
85B VAL* 4.1 12.1 - - + +
88B LEU* 4.0 20.9 - - + -
89B LEU* 4.1 19.7 - - + -
92B LEU* 4.0 22.7 - - + -
110B SER 3.0 16.6 + - - +
111B LEU* 3.5 8.5 - - - +
113B ALA* 1.3 73.1 - - - +
115B SER* 1.3 66.1 + - - +
116B HIS 3.1 2.2 - - - -
117B GLU* 3.0 18.3 + - + +
118B HIS* 2.7 26.3 + - + -
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Residues in contact with SER 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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111B LEU 3.0 13.9 + - - -
112B ARG 2.5 22.9 + - - -
114B ILE* 1.3 76.6 - - - +
116B HIS* 1.3 60.3 + - - +
118B HIS* 2.7 38.3 + - - +
123B LEU* 3.8 6.7 - - - +
127B PHE* 3.8 23.6 - - - -
152B VAL* 3.8 23.7 + - - +
156B ARG* 2.8 16.8 + - - -
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Residues in contact with HIS 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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112B ARG* 3.3 24.5 + - - +
113B ALA* 3.5 16.6 - - - +
115B SER* 1.3 88.8 + - - +
117B GLU* 1.3 64.9 + - - +
118B HIS 3.7 1.6 - - - +
152B VAL* 4.5 23.8 + - + +
156B ARG* 3.4 25.2 + - - +
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Residues in contact with GLU 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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76B THR* 3.8 25.7 - - - +
82B PRO* 3.5 44.9 - - - +
85B VAL* 4.1 19.1 - - + -
113B ALA 4.6 4.0 - - - +
114B ILE* 3.0 19.3 + - + +
116B HIS* 1.3 81.6 - - - +
118B HIS* 1.3 60.7 + - - +
119B SER 3.8 1.0 + - - -
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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