Contacts of the helix formed by residues 125 - 135 (chain E) in PDB entry 5EIB
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 HIS 125 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D ASP* 6.0 0.2 + - - -
181D VAL* 3.7 14.0 - - + +
88E ALA 3.1 25.6 - - - -
89E LEU 2.9 20.7 + - - -
90E ILE 3.5 14.0 - - - -
91E GLY* 3.5 14.7 + - - -
120E ALA* 2.8 12.8 + - + +
123E MET* 3.4 26.4 + - + +
124E GLY* 1.3 72.4 + - - +
126E LEU* 1.3 60.8 + - - +
127E GLU 3.4 2.5 - - - -
128E ILE* 3.2 19.5 + - + +
129E VAL* 3.0 28.2 + - - +
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Residues in contact with LEU 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D LYS* 5.8 7.4 - - + -
124E GLY* 3.0 28.7 + - - +
125E HIS* 1.3 69.8 - - - +
127E GLU* 1.3 63.7 + - + +
129E VAL* 3.4 6.1 + - + +
130E GLU* 3.0 32.5 + - - +
158E ASN* 4.7 5.2 - - - +
160E ASP* 4.1 26.2 - - + +
161E LEU* 3.9 38.8 - - + +
164E ILE* 3.9 17.5 - - + +
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Residues in contact with GLU 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E LEU* 3.3 34.4 - - + +
125E HIS 3.4 0.2 - - - -
126E LEU* 1.3 74.4 - - + +
128E ILE* 1.3 67.8 + - + +
130E GLU* 3.3 18.2 + - - +
131E VAL* 3.1 26.1 + - + +
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Residues in contact with ILE 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87E ALA 4.0 2.2 - - - +
88E ALA* 4.2 5.8 - - + +
91E GLY* 3.4 42.2 - - - +
92E HIS 3.7 3.8 - - - +
93E LEU* 3.9 27.4 - - + +
96E VAL* 3.8 27.4 - - + -
120E ALA* 3.6 18.6 - - + -
125E HIS* 3.2 16.9 + - + +
127E GLU* 1.3 75.6 - - + +
129E VAL* 1.3 66.0 + - - +
131E VAL* 3.1 4.6 + - - +
132E LEU* 2.9 35.7 + - + +
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E LEU* 3.9 10.8 - - + -
120E ALA* 3.8 19.5 - - + +
121E ALA* 3.8 15.3 - - + +
125E HIS 3.0 20.6 + - - +
126E LEU* 3.5 10.1 - - + +
128E ILE* 1.3 76.5 - - - +
130E GLU* 1.3 63.9 + - - +
132E LEU* 3.3 2.6 + - - +
133E LEU* 3.0 32.7 + - + +
161E LEU* 3.9 17.9 - - + -
164E ILE* 3.7 22.2 - - + -
165E LEU* 3.9 17.3 - - + -
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Residues in contact with GLU 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E LEU* 3.0 20.7 + - - +
127E GLU* 3.3 15.2 + - - +
129E VAL* 1.3 77.1 - - - +
131E VAL* 1.3 65.3 + - + +
133E LEU* 3.4 10.1 + - - +
134E LYS* 3.0 42.9 + - + +
164E ILE* 3.8 30.9 - - + +
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Residues in contact with VAL 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E LEU* 3.9 15.0 - - + -
96E VAL* 4.2 5.8 - - + -
97E GLU* 3.7 33.2 - - + +
100E LEU* 3.8 23.8 - - + -
127E GLU* 3.1 14.7 + - + +
128E ILE* 3.5 9.4 - - - +
130E GLU* 1.3 75.6 - - + +
132E LEU* 1.3 65.8 + - - +
134E LYS* 3.1 12.0 + - - +
135E HIS* 3.0 36.1 + - + +
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Residues in contact with LEU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E LEU* 4.2 19.5 - - + -
88E ALA* 4.4 1.6 - - + -
96E VAL* 4.4 7.9 - - + -
100E LEU* 4.3 11.4 - - + -
106E VAL* 3.7 21.5 - - + +
116E PRO* 3.6 39.0 - - + +
117E LEU* 3.7 11.7 - - + +
120E ALA* 4.1 4.3 - - + -
128E ILE* 2.9 40.5 + - + +
129E VAL 3.7 3.4 - - - +
131E VAL* 1.3 73.0 - - - +
133E LEU* 1.3 62.8 + - - +
135E HIS* 3.0 13.9 + - - +
136E GLY 3.2 0.7 + - - -
137E ALA* 3.0 28.9 + - + +
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Residues in contact with LEU 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E LEU* 4.1 28.0 - - + -
129E VAL* 3.0 35.9 + - + +
130E GLU* 3.5 7.2 - - - +
132E LEU* 1.3 75.7 - - - +
134E LYS* 1.3 58.7 - - + +
136E GLY* 3.0 19.4 + - - -
137E ALA* 3.9 14.1 + - - +
139E VAL* 5.1 8.1 - - + -
164E ILE* 3.6 28.9 - - + +
165E LEU* 4.1 16.2 - - + +
167E LYS 6.0 0.9 - - - +
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Residues in contact with LYS 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E GLU* 3.0 36.4 + - - +
131E VAL* 3.1 13.5 + - - +
133E LEU* 1.3 75.3 - - + +
135E HIS* 1.3 67.3 + - + +
136E GLY 3.2 1.4 + - - -
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Residues in contact with HIS 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E GLU* 5.4 5.3 + - - +
100E LEU* 3.8 53.3 + - + +
101E LYS* 5.5 1.1 - - - -
106E VAL* 3.6 14.8 - - + +
131E VAL* 3.0 31.2 + - + +
132E LEU 3.0 10.9 + - - +
134E LYS* 1.3 84.5 - - + +
136E GLY* 1.3 59.9 + - - +
137E ALA 3.6 0.2 - - - -
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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