Contacts of the helix formed by residues 117 - 132 (chain B) in PDB entry 2E98
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 ASN 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B SER* 6.3 0.4 - - - -
86B MET* 3.7 30.9 - - + +
87B GLU* 5.8 1.6 + - - -
90B VAL* 5.4 0.7 - - - +
115B ARG 3.8 0.4 + - - -
116B PHE* 1.3 77.4 - - - +
118B SER* 1.3 65.4 + - - +
119B ARG* 3.2 12.1 + - - +
120B LEU* 2.8 35.8 + - - +
121B GLN* 2.9 19.1 + - - +
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE 3.6 1.4 + - - -
117B ASN* 1.3 71.9 - - - +
119B ARG* 1.3 63.9 + - - +
121B GLN* 3.7 12.2 - - - +
122B GLU* 2.9 25.0 + - - +
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Residues in contact with ARG 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 2.9 34.2 + - - -
90B VAL* 3.9 19.1 - - + +
94B ASP* 5.0 0.4 + - - -
117B ASN* 3.2 10.2 + - - +
118B SER* 1.3 82.6 + - - +
120B LEU* 1.3 64.7 + - - +
122B GLU* 3.2 6.1 + - - +
123B ARG* 3.0 65.3 + - + +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B MET* 3.7 34.1 - - + +
89B PHE* 3.8 32.8 - - + -
90B VAL* 3.9 26.9 - - + +
93B LEU* 4.1 15.5 - - + -
116B PHE* 3.6 30.7 - - + -
117B ASN* 2.8 22.5 + - - +
119B ARG* 1.3 78.7 - - - +
121B GLN* 1.3 62.3 - - - +
123B ARG* 3.1 2.1 + - + +
124B ILE* 3.0 26.1 + - + +
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Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B THR* 3.3 27.2 + - - +
114B SER* 3.1 26.8 + - - +
116B PHE* 2.6 27.4 + - + +
117B ASN 2.9 14.6 + - - +
118B SER* 3.2 11.5 + - - +
120B LEU* 1.3 75.6 - - - +
122B GLU* 1.3 58.4 + - - +
124B ILE* 3.5 9.7 + - - +
125B ARG* 3.0 27.7 + - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B SER 2.9 16.8 + - - +
119B ARG* 3.6 6.5 - - - +
121B GLN* 1.3 75.2 - - - +
123B ARG* 1.3 65.8 + - - +
125B ARG* 2.7 44.1 + - - -
126B LYS* 2.9 56.6 + - - +
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 3.8 16.7 - - + +
93B LEU* 4.0 19.3 - - + -
94B ASP* 2.7 40.9 + - - +
119B ARG* 3.0 61.6 + - + +
120B LEU* 3.1 7.8 + - + +
122B GLU* 1.3 77.8 - - - +
124B ILE* 1.3 58.0 + - - +
126B LYS* 3.7 26.8 - - - +
127B SER* 2.8 36.5 + - - +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B PHE* 4.2 9.6 - - + -
93B LEU* 4.0 19.7 - - + -
109B ILE* 3.6 29.4 - - + -
113B THR* 4.1 19.1 - - + +
116B PHE* 3.9 30.5 - - + -
120B LEU* 3.0 25.2 + - + +
121B GLN* 3.7 9.0 - - - +
123B ARG* 1.3 76.9 - - - +
125B ARG* 1.3 66.3 + - - +
127B SER* 3.2 5.1 + - - -
128B GLU* 2.9 38.4 + - - +
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Residues in contact with ARG 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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121B GLN 3.0 14.6 + - - +
122B GLU* 2.7 39.7 + - - +
124B ILE* 1.3 81.4 - - - +
126B LYS* 1.3 69.7 + - - +
128B GLU* 3.3 13.5 + - - +
129B ALA* 2.8 40.8 + - - +
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Residues in contact with LYS 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 GLU* 2.9 58.8 + - - +
123B ARG* 3.7 37.8 - - - +
125B ARG* 1.3 85.5 - - - +
127B SER* 1.3 55.1 + - - +
129B ALA* 3.3 7.1 + - - +
130B LEU* 2.8 36.0 + - - +
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Residues in contact with SER 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.8 19.5 - - - +
97B VAL* 3.2 37.5 - - - +
107B LEU* 4.1 10.8 - - - +
109B ILE* 6.6 0.2 - - - -
123B ARG* 2.8 25.3 + - - +
124B ILE* 3.6 4.5 - - - -
126B LYS* 1.3 75.6 - - - +
128B GLU* 1.3 61.7 + - - +
130B LEU* 3.7 0.9 + - - +
131B THR* 3.0 30.1 + - - +
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Residues in contact with GLU 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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107B LEU* 3.5 26.5 - - + +
108B ARG* 3.4 40.2 + - - +
109B ILE* 2.9 36.4 + - + +
124B ILE* 2.9 33.7 + - + +
125B ARG* 3.7 10.6 - - - +
127B SER* 1.3 77.3 - - - +
129B ALA* 1.3 58.5 + - - +
131B THR* 3.3 2.3 + - - -
132B ALA* 2.8 32.2 + - - +
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Residues in contact with ALA 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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125B ARG* 2.8 31.1 + - + +
126B LYS* 3.3 8.7 + - - +
128B GLU* 1.3 77.1 - - - +
130B LEU* 1.3 63.9 + - - +
131B THR 3.1 0.7 + - - -
132B ALA* 3.3 18.4 + - - +
133B GLY 4.8 0.5 + - - -
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Residues in contact with LEU 130 (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 VAL* 3.6 29.2 - - + +
98B LYS* 5.0 6.1 - - + -
101B HIS* 3.1 52.3 - - + +
126B LYS 2.8 21.4 + - - +
127B SER 4.0 4.0 - - - +
128B GLU 3.3 0.2 - - - -
129B ALA* 1.3 73.9 - - - +
131B THR* 1.3 57.2 + - + +
133B GLY 4.9 1.4 + - - -
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 4.3 13.9 - - + +
100B LEU* 5.0 2.2 - - + -
101B HIS* 4.0 19.7 - - + +
105B VAL 3.3 24.0 - - - +
106B ARG* 3.4 10.9 - - - +
107B LEU* 3.0 27.6 + - + +
127B SER 3.0 18.9 + - - +
128B GLU 3.5 4.2 + - - -
129B ALA 3.2 0.4 - - - -
130B LEU* 1.3 79.5 - - - +
132B ALA* 1.3 65.7 + - - +
133B GLY 3.1 3.6 - - - -
134B ASN* 2.9 26.8 + - - +
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Residues in contact with ALA 132 (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 ARG* 3.5 37.5 + - - +
128B GLU 2.8 18.0 + - - +
129B ALA* 3.3 14.4 + - - +
131B THR* 1.3 77.9 - - - +
133B GLY* 1.3 58.8 + - - +
134B ASN 3.6 0.9 + - - +
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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