Contacts of the helix formed by residues 113 - 129 (chain B) in PDB entry 6EBT
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 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111B GLY 3.2 6.2 + - - -
112B LEU* 1.3 76.6 - - - +
114B PRO* 1.3 71.3 - - - +
115B LYS* 3.1 32.2 + - - +
116B ILE* 3.1 28.0 + - + +
117B ALA* 2.8 26.0 + - - +
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Residues in contact with PRO 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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108B GLN* 3.4 27.0 - - + +
112B LEU 3.3 6.0 - - - +
113B ASP* 1.3 91.6 - - - +
115B LYS* 1.3 55.9 + - - +
117B ALA* 3.7 0.4 - - + +
118B ASN* 2.8 32.6 + - - +
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Residues in contact with LYS 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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113B ASP* 3.1 15.2 + - - +
114B PRO* 1.3 78.0 - - - +
116B ILE* 1.3 60.9 + - + +
118B ASN* 3.8 5.9 + - - +
119B ALA* 3.5 19.1 + - - +
165B LEU* 4.3 21.2 - - + +
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Residues in contact with ILE 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 LEU* 4.3 7.2 - - + -
113B ASP* 3.1 28.5 + - + +
115B LYS* 1.3 77.2 - - + +
117B ALA* 1.3 65.1 + - - +
118B ASN 3.2 0.2 - - - -
119B ALA* 3.1 6.6 + - - +
120B ILE* 2.9 42.0 + - + +
165B LEU* 4.6 8.7 - - + -
174B PRO* 3.6 33.2 - - + +
175B VAL* 4.0 14.6 - - + -
180B HIS* 4.1 22.7 - - + +
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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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104B ALA* 4.0 4.9 - - - +
108B GLN* 3.5 38.6 - - + +
112B LEU* 3.6 21.3 - - + +
113B ASP 2.8 20.1 + - - +
114B PRO 3.7 0.2 - - - +
116B ILE* 1.3 74.0 - - - +
118B ASN* 1.3 56.0 + - - +
120B ILE* 3.4 5.5 + - - +
121B MET* 2.9 38.1 + - - +
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Residues in contact with ASN 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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108B GLN* 5.1 0.2 + - - -
114B PRO 2.8 21.2 + - - +
115B LYS* 4.0 6.7 - - - +
117B ALA* 1.3 74.5 - - - +
119B ALA* 1.3 57.0 + - - +
121B MET* 3.4 15.6 + - - +
122B LYS* 3.0 57.4 + - - +
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Residues in contact with ALA 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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115B LYS 3.5 11.4 + - - +
116B ILE 3.1 8.1 + - - +
118B ASN* 1.3 77.1 + - - +
120B ILE* 1.3 64.8 + - - +
122B LYS* 3.3 13.0 + - - +
123B ALA* 2.9 25.8 + - - +
161B ALA* 3.7 23.3 - - + +
164B MET* 4.1 7.2 - - + +
165B LEU* 3.9 26.0 - - + -
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Residues in contact with ILE 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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100B LYS* 4.5 6.7 - - + +
104B ALA* 3.7 19.1 - - + -
112B LEU* 4.7 6.5 - - + -
116B ILE* 2.9 36.1 + - + +
117B ALA* 3.7 7.9 - - - +
119B ALA* 1.3 75.3 - - - +
121B MET* 1.3 58.7 + - - +
123B ALA* 3.3 1.0 + - - +
124B ALA* 2.7 32.4 + - + +
157B ILE* 3.8 20.3 - - + +
161B ALA* 4.3 3.1 - - + -
175B VAL* 3.8 22.0 - - + -
180B HIS* 3.8 33.0 - - + +
181B VAL* 4.0 14.8 - - + +
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Residues in contact with MET 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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101B ARG* 3.5 48.9 - - - +
104B ALA* 3.8 16.2 - - + -
105B GLU* 4.0 28.0 - - + +
108B GLN* 4.7 7.9 - - - +
117B ALA* 2.9 30.9 + - - +
118B ASN* 3.7 14.4 - - - +
119B ALA 3.2 0.2 - - - -
120B ILE* 1.3 77.9 - - - +
122B LYS* 1.3 57.2 + - + +
124B ALA* 3.3 4.1 + - - +
125B ASP* 2.9 36.9 + - - +
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Residues in contact with LYS 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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118B ASN* 3.0 43.2 + - - +
119B ALA* 3.8 12.6 - - - +
121B MET* 1.3 77.0 - - + +
123B ALA* 1.3 62.6 + - - +
125B ASP* 3.3 11.6 + - - +
126B GLU* 3.1 25.3 + - - +
164B MET* 3.9 26.0 - - + -
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Residues in contact with ALA 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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119B ALA 2.9 16.3 + - - +
120B ILE 3.8 2.7 - - - +
122B LYS* 1.3 73.6 - - - +
124B ALA* 1.3 65.9 + - - +
126B GLU* 3.2 6.0 + - - +
127B VAL* 3.1 24.8 + - - +
132B LEU* 4.2 1.4 - - - +
157B ILE* 3.6 31.0 - - + +
160B ARG* 3.6 25.1 - - + -
161B ALA* 4.0 3.4 - - - +
164B MET* 4.1 7.8 - - + +
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Residues in contact with ALA 124 (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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97B GLY* 3.4 26.6 - - - +
100B LYS* 4.2 2.0 - - + -
101B ARG* 3.6 18.6 - - + +
120B ILE* 2.7 22.5 + - + +
121B MET 3.6 4.3 - - - +
123B ALA* 1.3 73.5 - - - +
125B ASP* 1.3 58.3 + - - +
127B VAL* 3.2 4.3 + - - +
128B ALA* 2.9 25.5 + - - +
157B ILE* 4.1 24.1 - - + +
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Residues in contact with ASP 125 (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 ARG* 3.4 33.2 + - - +
121B MET* 2.9 24.4 + - - +
122B LYS* 3.5 11.1 - - - +
123B ALA 3.2 0.2 - - - -
124B ALA* 1.3 77.0 - - - +
126B GLU* 1.3 57.5 + - + +
128B ALA* 3.3 4.9 + - - +
129B GLU* 2.9 41.8 + - - +
601B GOL 3.9 24.6 + - - +
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Residues in contact with GLU 126 (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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122B LYS 3.1 11.9 + - - +
123B ALA 3.2 7.6 + - - +
125B ASP* 1.3 76.6 - - + +
127B VAL* 1.3 61.0 + - - +
129B GLU* 3.4 5.8 + - - +
131B LYS* 3.0 59.3 + - + +
132B LEU* 3.9 15.5 - - + +
160B ARG* 2.7 51.7 + - - +
164B MET* 3.4 12.2 - - - +
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Residues in contact with VAL 127 (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 ILE* 3.4 39.2 - - + +
94B LYS* 3.7 10.0 + - - +
97B GLY* 4.0 10.5 - - - +
123B ALA 3.1 15.0 + - - +
124B ALA 3.2 6.7 + - - +
126B GLU* 1.3 73.9 - - - +
128B ALA* 1.3 65.0 + - - +
130B GLY* 3.1 13.2 + - - -
132B LEU* 3.7 24.9 - - + +
133B ASN* 4.6 2.9 - - - +
136B PHE* 4.1 9.4 - - + -
153B VAL* 5.2 3.6 - - + -
156B VAL* 4.3 9.6 - - + -
157B ILE* 4.0 20.0 - - + -
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Residues in contact with ALA 128 (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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94B LYS* 3.3 45.9 - - - +
97B GLY* 4.0 0.6 - - - -
98B ILE* 3.8 23.2 - - + +
101B ARG* 6.4 0.2 - - + -
124B ALA 2.9 16.0 + - - +
125B ASP* 3.3 6.0 + - - +
127B VAL* 1.3 76.7 - - - +
129B GLU* 1.3 58.8 + - - +
601B GOL 4.1 22.1 + - - +
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Residues in contact with GLU 129 (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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94B LYS* 4.4 5.3 + - - -
125B ASP* 2.9 32.0 + - - +
126B GLU* 3.9 5.2 - - - +
127B VAL 3.1 0.4 - - - -
128B ALA* 1.3 76.2 - - - +
130B GLY* 1.3 62.3 + - - +
131B LYS* 3.0 42.7 + - + +
601B GOL 3.0 27.2 + - - +
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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