Contacts of the helix formed by residues 116 - 129 (chain B) in PDB entry 1E2R
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 SER 116 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B GLY 4.6 2.2 + - - -
114B GLU 4.3 0.2 - - - -
115B LEU* 1.3 76.2 - - - +
117B ALA* 1.3 64.5 + - - +
118B GLU* 3.5 8.9 + - - +
119B GLN* 2.9 40.3 + - - +
120B VAL* 2.9 22.6 + - - +
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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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116B SER* 1.3 73.0 - - - +
118B GLU* 1.3 68.5 + - + +
120B VAL* 3.3 10.9 + - - +
121B ASP* 3.1 27.6 + - - +
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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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116B SER* 3.2 8.1 + - - +
117B ALA* 1.3 82.1 - - + +
119B GLN* 1.3 57.8 + - + +
121B ASP* 3.3 15.9 + - - +
122B LEU* 3.0 33.8 + - + +
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Residues in contact with GLN 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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56B GLU* 4.3 18.2 + - - +
60B ILE* 3.7 30.5 - - + +
64B ARG* 5.7 4.0 - - - +
114B GLU 4.1 3.3 - - - +
115B LEU* 3.4 19.2 - - + +
116B SER* 2.9 44.8 + - - +
118B GLU* 1.3 73.8 - - + +
120B VAL* 1.3 65.4 + - - +
122B LEU* 3.1 11.1 + - + +
123B MET* 2.9 29.2 + - - +
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Residues in contact with VAL 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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95B GLN* 3.7 22.7 - - + +
98B ILE* 3.9 25.5 - - + +
99B THR* 3.3 22.9 - - - +
110B GLY* 4.0 27.1 - - - -
115B LEU* 4.0 11.9 - - + -
116B SER 2.9 19.1 + - - +
117B ALA* 3.3 10.7 + - - +
119B GLN* 1.3 74.6 - - - +
121B ASP* 1.3 60.1 + - - +
123B MET* 3.2 5.7 + - - +
124B ALA* 3.0 26.2 + - - +
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Residues in contact with ASP 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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91B PHE* 3.7 16.1 - - + -
95B GLN* 2.9 37.1 + - - +
117B ALA* 3.1 12.8 + - - +
118B GLU* 3.6 17.7 - - - +
120B VAL* 1.3 74.2 - - - +
122B LEU* 1.3 67.3 + - - +
124B ALA* 3.2 2.5 + - - +
125B ASN* 3.0 35.5 + - - +
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Residues in contact with LEU 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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49B LEU* 4.0 15.5 - - + +
53B GLN* 3.8 39.0 - - + +
56B GLU* 3.6 43.7 - - + +
57B ALA* 3.9 13.8 - - + +
60B ILE* 5.4 1.3 - - + -
118B GLU* 3.0 21.2 + - + +
119B GLN* 3.1 16.6 + - + +
121B ASP* 1.3 76.6 - - - +
123B MET* 1.3 54.1 + - - +
125B ASN* 3.4 4.9 + - - +
126B TYR* 2.8 36.5 + - - +
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Residues in contact with MET 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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57B ALA* 3.4 37.5 - - - +
60B ILE* 3.7 28.3 - - + -
61B TYR* 3.7 28.9 - - + +
65B CYS* 4.1 9.0 - - - -
98B ILE* 3.8 16.2 - - + -
115B LEU* 4.1 12.8 - - + -
119B GLN 2.9 16.6 + - - +
120B VAL* 3.2 7.6 + - - +
122B LEU* 1.3 75.2 - - - +
124B ALA* 1.3 60.4 + - - +
126B TYR* 3.2 14.2 + - + +
127B LEU* 2.9 34.8 + - - +
601B HEC 4.0 8.5 - - + -
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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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91B PHE* 3.4 29.6 - - + -
94B LEU* 3.5 14.6 - - + +
95B GLN* 3.9 26.2 - - - +
98B ILE* 3.8 8.0 - - + +
120B VAL 3.0 13.8 + - - +
121B ASP* 3.2 3.1 + - - +
123B MET* 1.3 77.3 - - - +
125B ASN* 1.3 61.9 + - - +
127B LEU* 3.3 6.7 + - - -
128B LEU* 3.4 17.7 + - - +
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Residues in contact with ASN 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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46B VAL* 5.0 0.5 - - - +
47B THR* 4.4 25.1 + - - +
49B LEU* 4.0 26.8 - - + +
91B PHE* 3.5 25.1 - - - -
121B ASP* 3.0 30.2 + - - +
122B LEU* 3.8 3.3 - - - +
124B ALA* 1.3 74.0 - - - +
126B TYR* 1.3 65.4 + - - +
128B LEU* 3.0 24.7 + - - +
129B LEU* 3.2 17.6 + - - +
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Residues in contact with TYR 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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49B LEU* 4.1 6.7 - - + +
54B TYR* 3.5 39.4 + + - -
57B ALA* 3.6 23.1 - - + -
58B ASN* 2.8 36.3 + - + -
61B TYR* 3.5 42.0 - + + +
62B PHE* 4.2 2.8 - - - -
73B ARG* 3.6 25.9 + - - -
122B LEU 2.8 18.8 + - - +
123B MET* 3.4 17.7 - - + +
125B ASN* 1.3 75.7 - - - +
127B LEU* 1.3 69.4 + - + +
129B LEU* 3.1 25.0 + - - +
132B ALA* 4.4 4.7 + - - +
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Residues in contact with LEU 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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61B TYR* 4.2 7.6 - - + -
73B ARG* 2.9 46.5 + - - +
81B LEU* 3.9 26.2 - - + -
83B PRO* 4.4 0.7 - - - +
86B THR* 2.8 29.0 + - + +
94B LEU* 4.2 8.7 - - + -
98B ILE* 4.2 5.6 - - + -
123B MET 2.9 20.2 + - - +
124B ALA 3.7 5.4 - - - +
125B ASN 3.2 0.4 - - - -
126B TYR* 1.3 86.4 - - + +
128B LEU* 1.3 59.5 + - - +
129B LEU 3.3 0.2 - - - -
601B HEC 3.8 43.3 - - + -
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Residues in contact with LEU 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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46B VAL* 3.8 28.5 - - + +
47B THR 5.8 0.7 - - - +
83B PRO* 4.2 2.0 - - - +
86B THR* 3.5 28.0 - - - +
87B ARG* 2.8 49.4 + - + -
90B GLY* 4.6 1.1 - - - -
91B PHE* 4.1 36.1 - - + +
94B LEU* 3.6 11.0 - - + -
124B ALA 3.5 15.7 - - - +
125B ASN* 3.0 16.2 + - - +
127B LEU* 1.3 77.4 - - - +
129B LEU* 1.3 60.5 + - - +
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Residues in contact with LEU 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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40B PRO* 4.0 15.0 - - + +
41B GLY 3.9 15.0 - - - +
42B ALA* 3.9 20.4 - - + -
43B PRO* 4.6 1.3 - - + -
46B VAL* 3.9 20.2 - - + -
47B THR 3.9 4.5 - - - +
48B ALA* 4.6 1.1 - - - -
49B LEU* 3.9 30.1 - - + +
54B TYR* 3.9 26.0 - - + -
73B ARG* 2.9 21.1 + - - -
83B PRO* 3.4 3.9 - - - +
87B ARG* 4.3 1.1 - - - +
125B ASN 3.5 14.1 - - - +
126B TYR* 3.1 9.5 + - - +
128B LEU* 1.3 81.5 - - - +
130B ASP* 1.3 68.1 + - - +
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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