Contacts of the helix formed by residues 95 - 107 (chain B) in PDB entry 1EN5
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 GLN 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B THR* 3.3 31.9 + - - +
94B LEU* 1.3 81.5 - - - +
96B GLY* 1.3 70.8 + - - +
97B ASP 3.8 0.3 + - - -
98B LEU* 3.8 7.8 + - - +
99B LYS* 3.5 22.6 + - + -
195B ASP* 4.7 10.3 + - - -
198B ALA* 5.3 5.2 - - - +
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Residues in contact with GLY 96 (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* 1.3 79.4 - - - +
97B ASP* 1.3 65.2 + - - -
99B LYS* 3.3 4.9 + - - +
100B ALA* 3.2 19.8 + - - +
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Residues in contact with ASP 97 (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 GLY* 1.3 69.3 - - - -
98B LEU* 1.3 60.3 + - - +
100B ALA* 3.2 9.0 + - - +
101B ALA* 2.9 29.8 + - - +
201B PHE* 4.2 17.1 - - + -
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Residues in contact with LEU 98 (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 LEU* 3.9 19.7 - - + -
95B GLN 3.8 7.6 + - - +
96B GLY 3.3 1.0 - - - -
97B ASP* 1.3 77.5 - - - +
99B LYS* 1.3 63.8 + - - +
101B ALA* 3.2 1.3 + - - +
102B ILE* 2.9 36.0 + - + +
131B LEU* 5.0 2.0 - - + -
138B LEU* 4.2 16.2 - - + -
163B ILE* 4.7 9.0 - - + -
194B TRP* 4.1 9.0 - - + +
197B ALA* 3.8 18.2 - - + +
198B ALA* 3.7 36.1 - - + +
201B PHE* 3.9 37.3 - - + -
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Residues in contact with LYS 99 (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 LEU* 3.5 41.9 - - + +
95B GLN* 3.5 21.3 + - + +
96B GLY 3.3 10.6 + - - +
98B LEU* 1.3 79.9 - - - +
100B ALA* 1.3 62.0 + - - +
102B ILE* 3.5 2.6 + - - +
103B GLU* 3.0 55.8 + - - +
109B VAL* 4.4 15.0 - - + +
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Residues in contact with ALA 100 (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 GLY 3.2 10.0 + - - +
97B ASP* 3.4 13.2 - - - +
98B LEU 3.1 0.2 - - - -
99B LYS* 1.3 78.7 - - - +
101B ALA* 1.3 58.9 + - - +
103B GLU* 3.3 12.5 + - - +
104B ARG* 2.9 28.8 + - - +
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Residues in contact with ALA 101 (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 ASP 2.9 16.8 + - - +
98B LEU* 3.7 4.5 - - - +
100B ALA* 1.3 76.8 - - - +
102B ILE* 1.3 57.3 + - - +
104B ARG* 3.3 23.3 + - - +
105B ASP* 2.9 35.6 + - - +
138B LEU* 4.0 11.2 - - + -
201B PHE* 3.6 27.4 - - + -
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Residues in contact with ILE 102 (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 LEU* 3.9 28.0 - - + -
98B LEU* 2.9 28.5 + - + +
99B LYS* 3.7 5.2 - - - +
100B ALA 3.2 0.2 - - - -
101B ALA* 1.3 73.8 - - - +
103B GLU* 1.3 59.7 + - - +
106B PHE* 2.8 40.9 + - + +
108B SER 4.2 0.7 - - - +
109B VAL* 4.2 21.1 - - + -
112B PHE* 3.7 45.1 - - + -
131B LEU* 4.6 6.5 - - + -
138B LEU* 3.8 16.8 - - + -
194B TRP* 4.4 5.4 - - + -
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Residues in contact with GLU 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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99B LYS* 3.0 45.5 + - - +
100B ALA* 3.8 10.6 - - - +
102B ILE* 1.3 75.9 - - - +
104B ARG* 1.3 58.9 + - - +
107B GLY* 2.9 33.5 + - - +
108B SER* 4.0 21.1 - - - +
109B VAL* 4.4 13.2 + - + +
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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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100B ALA 2.9 18.0 + - - +
101B ALA* 3.4 20.3 + - - +
103B GLU* 1.3 81.2 - - - +
105B ASP* 1.3 91.2 + - - +
106B PHE 3.8 0.2 + - - -
107B GLY* 4.4 1.9 + - - -
133B LEU* 5.9 0.2 - - - +
136B ASP* 2.9 27.7 + - - +
137B LYS* 4.2 2.4 - - - +
138B LEU* 4.7 1.0 - - - +
201B PHE* 5.4 3.6 - - - -
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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 ALA 2.9 16.2 + - - +
104B ARG* 1.3 116.8 + - - +
106B PHE* 1.3 74.0 + - + +
137B LYS* 3.7 23.0 - - + +
138B LEU* 3.1 39.3 + - - +
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Residues in contact with PHE 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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102B ILE* 2.8 32.0 + - + +
105B ASP* 1.3 78.9 - - + +
107B GLY* 1.3 58.2 + - - +
108B SER 3.2 13.7 - - - +
111B ASN* 3.1 24.3 + - + +
112B PHE* 3.8 41.7 - + + +
115B GLU* 4.6 15.5 - - + -
131B LEU* 4.3 4.0 - - + -
138B LEU* 3.8 41.3 - - + -
139B ALA* 3.9 13.2 - - - -
140B VAL* 4.0 21.3 - - + -
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Residues in contact with GLY 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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103B GLU* 2.9 26.2 + - - +
104B ARG 4.4 2.3 + - - -
105B ASP 3.7 1.2 - - - -
106B PHE* 1.3 77.2 - - - +
108B SER* 1.3 60.4 + - - +
111B ASN* 3.7 6.5 - - - -
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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