Contacts of the helix formed by residues 100 - 114 (chain B) in PDB entry 3E61
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 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B SER* 2.8 22.5 + - - +
98B ASP* 4.2 5.6 - - + +
99B ASN* 1.3 73.7 - - - +
101B ILE* 1.3 59.2 + - - +
102B LYS* 2.9 33.6 + - - +
103B LYS* 3.1 22.0 + - + +
104B ALA* 2.9 27.8 + - - +
124B PHE* 5.7 1.3 - - - -
125B ASN* 5.4 0.9 - - - -
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Residues in contact with ILE 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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99B ASN 4.4 0.8 + - - +
100B ASP* 1.3 71.3 + - - +
102B LYS* 1.3 57.4 + - - +
104B ALA* 3.7 2.4 - - - +
105B GLN* 2.8 35.6 + - + +
124B PHE* 3.7 30.1 - - + -
125B ASN* 3.5 23.1 + - - +
128B ILE* 6.0 3.4 - - + -
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Residues in contact with LYS 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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100B ASP* 2.9 11.2 + - - +
101B ILE* 1.3 76.4 - - - +
103B LYS* 1.3 58.2 + - - +
105B GLN* 3.2 20.0 + - - +
106B GLY* 2.8 26.0 + - - -
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Residues in contact with LYS 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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79A ARG* 5.6 1.1 - - - -
82A GLU* 3.4 39.9 + - - +
83A ASP* 3.8 22.0 - - - -
86A LEU* 5.5 10.7 - - + +
96B ASN 2.8 20.9 + - - +
97B SER* 3.3 30.5 - - - +
98B ASP* 3.7 16.3 - - + +
100B ASP* 3.1 17.0 + - + +
102B LYS* 1.3 75.5 - - - +
104B ALA* 1.3 61.2 + - - +
106B GLY* 3.1 11.0 + - - +
107B TYR* 3.1 30.5 + - + -
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Residues in contact with ALA 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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65B LEU* 3.9 26.9 - - + +
97B SER* 4.1 10.0 - - - -
100B ASP 2.9 16.5 + - - +
101B ILE 3.7 3.8 - - - +
103B LYS* 1.3 71.4 - - - +
105B GLN* 1.3 67.2 + - - +
107B TYR* 3.1 4.2 + - - +
108B LEU* 3.0 23.8 + - - +
125B ASN* 3.1 32.8 - - + +
128B ILE* 6.2 0.9 - - - -
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Residues in contact with GLN 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 ILE* 2.8 22.3 + - + +
102B LYS* 3.4 16.5 + - - +
104B ALA* 1.3 77.0 - - - +
106B GLY* 1.3 62.0 + - - +
108B LEU* 3.5 8.8 + - + +
109B ALA* 3.1 23.3 + - + +
125B ASN* 5.6 0.4 - - - -
128B ILE* 4.4 31.2 - - + +
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Residues in contact with GLY 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 LYS 2.8 17.6 + - - -
103B LYS* 3.1 6.2 + - - -
105B GLN* 1.3 75.8 - - - +
107B TYR* 1.3 51.2 + - - +
109B ALA* 3.4 7.1 + - - +
110B THR* 2.7 37.2 + - - -
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Residues in contact with TYR 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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82A GLU* 2.6 32.0 + - - +
92A VAL* 3.6 29.2 + - + +
94A ILE* 3.6 7.3 - - - +
65B LEU* 3.6 28.0 - - + -
94B ILE 4.2 2.9 - - - -
95B GLY* 3.5 21.1 - - - -
96B ASN 3.3 21.8 - - - -
103B LYS* 3.1 26.9 + - + -
104B ALA 3.1 7.4 + - - +
106B GLY* 1.3 73.3 - - - +
108B LEU* 1.3 58.6 + - - +
110B THR* 3.9 14.8 - - + -
111B PHE* 2.6 57.4 + + + -
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Residues in contact with LEU 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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104B ALA 3.0 12.0 + - - +
105B GLN* 3.6 9.9 - - + +
107B TYR* 1.3 76.5 - - - +
109B ALA* 1.3 52.4 + - - +
111B PHE* 3.6 0.9 - - - +
112B VAL* 2.7 42.8 + - + +
119B MET* 3.7 35.2 - - + +
128B ILE* 3.8 34.8 - - + +
129B ILE* 4.3 8.7 - - + -
132B THR* 3.6 33.9 - - + +
133B LEU* 3.8 27.4 - - + -
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Residues in contact with ALA 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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105B GLN* 3.1 12.8 + - + +
106B GLY* 3.5 9.6 - - - +
108B LEU* 1.3 76.5 - - - +
110B THR* 1.3 56.9 + - - +
112B VAL* 3.9 5.1 - - - +
113B SER* 2.7 44.4 + - - +
132B THR* 6.4 0.4 - - - -
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Residues in contact with THR 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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91A GLN* 3.4 29.8 - - + +
92A VAL 4.5 7.6 - - - +
93A LEU* 3.9 27.6 - - + -
106B GLY 2.7 24.8 + - - -
107B TYR* 3.5 17.2 - - + -
109B ALA* 1.3 72.7 - - - +
111B PHE* 1.3 72.5 + - + +
113B SER* 3.5 3.8 - - - -
114B HIS* 3.0 36.5 + - + +
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Residues in contact with PHE 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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93A LEU* 6.1 0.2 - - + -
63B GLY* 3.6 28.3 - - - -
64B LEU 3.4 30.1 - - - -
65B LEU* 3.9 14.6 - - + -
93B LEU* 3.8 28.5 - - + -
94B ILE 4.7 0.9 - - - -
95B GLY* 4.0 9.9 - - - -
107B TYR* 2.6 40.9 + + + +
108B LEU* 3.7 2.9 - - - +
110B THR* 1.3 81.5 - - + +
112B VAL* 1.3 62.5 + - + +
114B HIS* 3.6 2.3 + - - -
115B ASN 3.5 2.9 + - - -
116B CYS* 3.3 44.9 + - + +
119B MET* 3.8 25.4 - - + -
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Residues in contact with VAL 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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108B LEU* 2.7 52.4 + - + +
109B ALA* 3.9 4.5 - - - +
111B PHE* 1.3 71.3 - - + +
113B SER* 1.3 69.0 + - - +
115B ASN* 3.0 18.7 + - - -
119B MET* 6.1 0.2 - - - -
132B THR* 4.2 9.6 - - + -
133B LEU* 3.9 17.5 - - + -
136B HIS* 3.7 40.8 - - + +
138B ILE* 4.5 11.7 - - + +
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Residues in contact with SER 113 (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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109B ALA* 2.7 29.4 + - - +
110B THR* 3.5 5.6 - - - -
112B VAL* 1.3 75.8 - - - +
114B HIS* 1.3 70.1 + - - +
115B ASN* 3.1 14.9 + - - +
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Residues in contact with HIS 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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61A LEU* 3.8 29.7 - - + +
91A GLN* 5.8 1.1 - - + -
93A LEU* 4.7 6.7 - - + -
114A HIS* 2.8 58.8 + + + +
61B LEU* 3.2 21.8 - - + +
93B LEU* 5.1 8.1 - - + -
110B THR* 3.0 29.5 + - + +
111B PHE 3.8 2.2 - - - +
112B VAL 3.2 0.4 - - - -
113B SER* 1.3 82.5 - - - +
115B ASN* 1.3 69.7 + - - +
116B CYS 3.3 2.5 - - - -
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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