Contacts of the helix formed by residues 107 - 123 (chain B) in PDB entry 4B94
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 GLU 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLN 3.6 4.2 + - - -
106B ASN* 1.3 69.9 + - - +
108B SER* 1.3 60.4 + - - +
110B ALA* 3.3 3.0 + - - +
111B ARG* 3.0 34.9 + - + +
142B PHE* 3.6 38.1 - - + -
144B PHE* 4.2 17.0 - - + -
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Residues in contact with SER 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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62B PRO* 3.9 26.9 - - - -
63B GLU* 3.6 20.4 + - - +
66B LEU* 3.9 20.9 - - - +
106B ASN* 3.0 10.5 + - - -
107B GLU* 1.3 73.6 - - - +
109B PHE* 1.3 59.8 + - - +
111B ARG* 3.2 5.6 + - - +
112B ILE* 3.1 30.5 + - - +
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Residues in contact with PHE 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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62B PRO* 3.6 10.5 - - + +
95B ILE* 5.6 4.3 - - + -
98B LEU* 3.7 41.3 - - + -
100B PRO* 3.8 31.0 - - + -
103B TYR* 3.3 39.5 - + + -
106B ASN* 3.0 16.6 + - - +
108B SER* 1.3 73.6 - - - +
110B ALA* 1.4 63.1 + - - +
112B ILE* 3.2 8.8 + - + +
113B GLN* 3.0 50.7 + - + +
138B ASN* 4.0 11.7 - - + -
139B CYS* 3.7 23.8 - - - -
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Residues in contact with ALA 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 ASN 3.1 8.4 + - - +
107B GLU 3.5 9.0 - - - +
108B SER 3.3 0.4 - - - -
109B PHE* 1.4 76.5 - - - +
111B ARG* 1.3 56.2 + - - +
113B GLN* 3.4 1.9 + - - +
114B VAL* 3.0 34.3 + - - +
139B CYS* 3.6 25.4 - - + -
142B PHE* 3.7 26.2 - - + -
144B PHE* 3.6 16.8 - - + -
145B VAL* 3.9 2.5 - - + -
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Residues in contact with ARG 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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66B LEU* 3.9 32.6 - - + +
70B LEU* 3.7 29.1 - - - +
107B GLU* 3.0 24.8 + - - +
108B SER* 3.2 10.0 + - - +
110B ALA* 1.3 72.5 - - - +
112B ILE* 1.3 60.2 + - - +
114B VAL* 4.0 1.1 - - - +
115B ARG* 2.9 33.4 + - - +
144B PHE* 3.7 23.1 - - + -
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Residues in contact with ILE 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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62B PRO* 3.5 28.9 - - + +
65B TRP* 3.8 12.3 - - + -
66B LEU* 3.9 16.8 - - + +
69B LEU* 4.1 6.5 - - + -
91B TYR* 3.6 20.6 - - + -
94B ALA* 4.2 12.1 - - + -
95B ILE* 4.0 22.7 - - + +
98B LEU* 3.8 26.2 - - + -
108B SER 3.1 18.0 + - - +
109B PHE* 3.2 9.8 + - + +
111B ARG* 1.3 75.7 - - - +
113B GLN* 1.4 57.1 + - + +
115B ARG 3.5 0.2 + - - -
116B PHE* 3.0 29.6 + - - +
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 4.0 23.6 - - + +
100B PRO* 5.1 2.0 - - - +
109B PHE* 3.0 50.6 + - + +
110B ALA 3.4 4.5 + - - +
112B ILE* 1.4 74.9 - - + +
114B VAL* 1.3 60.4 + - - +
116B PHE* 3.7 7.6 + - - +
117B ALA* 3.3 21.3 + - - +
131B TYR 4.5 1.7 - - - +
134B MET 3.5 0.5 - - - +
135B ALA* 3.4 32.1 - - + +
138B ASN* 2.9 30.1 + - - +
139B CYS* 3.9 8.3 - - - -
92D SER* 5.5 0.2 + - - -
96D GLU* 3.4 21.5 + - - +
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Residues in contact with VAL 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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110B ALA 3.0 20.0 + - - +
111B ARG 4.0 2.9 - - - +
113B GLN* 1.3 74.1 - - - +
115B ARG* 1.4 60.2 + - - +
117B ALA* 3.2 6.8 + - - +
118B GLU* 2.9 40.6 + - - +
132B PHE* 6.0 1.1 - - + -
135B ALA* 4.3 7.2 - - + -
144B PHE* 3.8 16.8 - - + -
145B VAL* 3.7 42.6 - - + +
148B SER* 3.4 26.0 - - - +
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Residues in contact with ARG 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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66B LEU* 6.1 0.9 - - + -
70B LEU* 5.8 3.8 - - + -
73B GLU* 2.9 31.5 + - - +
91B TYR* 3.3 33.2 - - + +
111B ARG 2.9 21.7 + - - +
114B VAL* 1.4 70.1 - - - +
116B PHE* 1.3 59.8 + - - +
118B GLU* 3.1 38.0 + - - +
119B LEU* 2.8 57.6 + - + +
122B ILE* 4.8 9.7 - - - +
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Residues in contact with PHE 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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88B ILE* 4.0 9.4 - - + -
91B TYR* 3.7 28.4 - - + -
92B SER* 3.3 27.1 - - - -
95B ILE* 3.4 25.4 - - + -
112B ILE 3.0 17.7 + - - +
113B GLN 3.8 3.1 - - - +
115B ARG* 1.3 76.4 - - - +
117B ALA* 1.4 64.2 + - - +
119B LEU* 3.3 4.5 + - - +
120B LYS* 3.1 54.9 + - - +
131B TYR* 3.6 28.5 - + + -
96D GLU* 3.6 36.1 - - + -
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Residues in contact with ALA 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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113B GLN 3.3 9.6 + - - +
114B VAL* 3.2 9.7 + - - +
116B PHE* 1.4 78.5 - - - +
118B GLU* 1.4 56.8 + - - +
120B LYS* 3.3 4.7 + - - +
121B ALA 3.0 23.0 + - - -
128B ALA* 4.1 0.5 - - - +
131B TYR* 3.7 40.8 - - + +
132B PHE* 3.5 34.4 - - + +
135B ALA* 5.2 0.4 - - + -
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Residues in contact with GLU 118 (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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114B VAL* 2.9 29.4 + - - +
115B ARG* 3.1 37.9 + - - +
117B ALA* 1.4 76.1 - - - +
119B LEU* 1.4 61.3 + - - +
121B ALA* 3.3 6.5 + - - +
122B ILE* 3.2 27.5 + - + +
132B PHE* 4.0 11.4 - - + -
148B SER* 2.8 29.2 + - - +
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Residues in contact with LEU 119 (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 GLU* 4.8 0.7 - - + +
79B LEU* 6.0 1.1 - - + -
84B LEU* 3.8 21.5 - - + +
87B LEU* 4.0 22.4 - - + -
88B ILE* 3.7 23.4 - - + +
91B TYR* 3.6 38.1 - - + -
115B ARG* 2.8 53.1 + - + +
116B PHE* 3.8 3.8 - - - +
118B GLU* 1.4 68.6 - - - +
120B LYS* 1.3 63.7 + - - +
122B ILE* 3.2 13.8 + - + +
123B GLN* 3.1 22.7 + - - +
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Residues in contact with LYS 120 (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 ILE* 3.6 25.9 - - + +
92B SER* 5.2 1.9 + - - -
116B PHE* 3.1 39.7 + - + +
117B ALA 3.3 8.9 + - - +
119B LEU* 1.3 75.4 - - - +
121B ALA* 1.4 53.0 + - - +
123B GLN* 3.3 25.7 + - - +
124B GLU* 2.8 37.6 + - - +
127B ASP 5.9 0.2 - - - -
128B ALA* 3.7 4.7 - - + -
131B TYR* 3.6 44.0 + - + -
96D GLU 5.5 0.2 - - - -
99D PRO* 5.1 8.5 - - - +
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Residues in contact with ALA 121 (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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117B ALA 3.0 14.5 + - - +
118B GLU* 3.5 10.8 - - - +
119B LEU 3.3 0.2 - - - -
120B LYS* 1.4 73.2 - - - +
122B ILE* 1.3 61.6 + - + +
125B PRO* 3.2 28.5 - - + +
128B ALA* 3.5 8.7 - - + +
132B PHE* 4.0 8.5 - - + -
152B PHE* 3.9 28.3 - - + -
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Residues in contact with ILE 122 (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 LEU* 5.6 6.5 - - + -
84B LEU* 3.9 20.2 - - + -
115B ARG* 4.8 11.0 - - - +
118B GLU* 3.2 15.8 + - + +
119B LEU* 3.2 26.8 + - + +
121B ALA* 1.3 77.6 - - - +
123B GLN* 1.4 65.0 + - - +
124B GLU 3.6 0.2 + - - -
125B PRO* 4.2 4.7 - - - +
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Residues in contact with GLN 123 (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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81B ASP 5.3 0.9 - - - +
84B LEU* 4.1 14.1 - - + +
85B ASN* 2.9 33.5 + - - +
88B ILE* 3.6 25.1 - - + +
119B LEU 3.1 15.7 + - - +
120B LYS* 3.7 30.6 + - - +
122B ILE* 1.4 78.8 - - - +
124B GLU* 1.4 65.3 + - + +
125B PRO* 4.5 0.5 - - - +
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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