Contacts of the helix formed by residues 115 - 123 (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 THR 115 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85E HIS* 3.9 3.6 - - - -
106E VAL 4.7 3.4 - - - -
107E ASN* 4.0 12.8 - - + +
108E ALA 3.4 3.6 - - - +
109E VAL* 3.7 28.0 - - + -
113E GLY 4.6 1.1 - - - +
114E ASP* 1.3 75.6 - - - +
116E PRO* 1.3 77.1 - - - +
117E LEU* 3.5 10.6 + - - +
118E HIS* 2.6 42.4 + - + +
119E LEU* 3.4 11.8 + - - +
138E ASP 5.3 1.0 + - - -
141E ALA* 3.8 25.5 - - + +
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Residues in contact with PRO 116 (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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82E THR* 4.9 0.4 - - - +
84E LEU* 3.8 34.5 - - + +
85E HIS* 3.8 24.0 - - + +
88E ALA* 3.7 18.2 - - + +
105E ASP 4.5 2.7 - - - +
106E VAL 3.4 26.0 - - - +
108E ALA 3.3 15.7 - - - +
115E THR* 1.3 82.0 - - - +
117E LEU* 1.3 60.4 + - - +
119E LEU* 3.3 2.7 + - + +
120E ALA 3.1 18.9 + - - -
132E LEU* 3.6 15.3 - - + +
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Residues in contact with LEU 117 (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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106E VAL 5.0 1.6 + - - -
115E THR* 3.1 9.9 + - - +
116E PRO* 1.3 78.4 - - - +
118E HIS* 1.3 65.1 + - + +
120E ALA* 3.4 1.0 + - - -
121E ALA* 2.9 26.1 + - - +
129E VAL* 3.9 34.8 - - + +
132E LEU* 3.7 10.4 - - + +
133E LEU* 4.1 21.1 - - + -
137E ALA* 4.0 28.0 - - + +
138E ASP 4.0 17.7 - - - +
139E VAL* 4.3 8.1 - - + -
149E ALA* 3.7 21.8 - - + -
165E LEU* 4.0 9.4 - - + -
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Residues in contact with HIS 118 (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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113E GLY 4.1 9.2 - - - -
114E ASP* 3.8 24.0 - - + +
115E THR* 2.6 43.1 + - + +
117E LEU* 1.3 79.2 - - + +
119E LEU* 1.3 59.2 + - - +
121E ALA* 3.5 4.9 - - - +
122E ILE* 2.8 38.8 + - + +
138E ASP 5.7 0.2 - - - -
141E ALA* 3.1 31.1 + - + -
143E ASP* 3.6 6.8 + - + -
147E LYS 2.9 28.3 + - - -
148E THR* 3.9 2.2 - - - -
149E ALA* 4.0 16.6 - - + -
152E ILE* 4.0 16.1 - - + +
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Residues in contact with LEU 119 (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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397D ALA* 4.6 7.0 - - + -
401D ARG* 3.7 29.8 - - + +
85E HIS* 3.6 46.9 - - + +
88E ALA 4.3 2.2 - - - -
89E LEU* 4.1 28.5 - - + +
114E ASP* 3.7 28.3 - - + +
115E THR 3.6 8.7 - - - +
116E PRO 3.3 5.8 + - - +
117E LEU 3.2 0.6 - - - -
118E HIS* 1.3 75.2 - - - +
120E ALA* 1.3 66.1 + - - +
122E ILE* 3.4 6.1 + - + +
123E MET* 3.1 29.9 + - - +
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Residues in contact with ALA 120 (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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88E ALA* 3.7 14.0 + - + +
116E PRO 3.1 16.4 + - - +
117E LEU 3.9 1.8 - - - +
119E LEU* 1.3 77.5 - - - +
121E ALA* 1.3 60.9 + - - +
123E MET 3.6 0.2 + - - -
124E GLY 3.1 2.8 + - - -
125E HIS* 2.8 35.5 + - + +
128E ILE* 3.6 31.4 - - + -
129E VAL* 3.8 16.1 - - + +
132E LEU* 4.1 5.2 - - + -
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Residues in contact with ALA 121 (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* 2.9 18.1 + - + +
118E HIS* 3.5 4.9 - - - +
120E ALA* 1.3 75.5 - - - +
122E ILE* 1.3 67.0 + - - +
124E GLY* 3.1 11.4 + - - -
129E VAL* 3.8 8.7 - - + +
149E ALA* 4.2 21.5 - - + +
152E ILE* 5.0 4.7 - - + -
156E ASN* 5.0 2.8 + - - -
158E ASN* 5.0 1.7 + - - -
161E LEU* 3.5 39.7 - - + +
165E LEU* 5.0 0.4 - - + -
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Residues in contact with ILE 122 (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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393D GLU* 3.9 42.2 - - + +
394D GLN* 3.3 31.7 + - + +
397D ALA* 3.9 17.9 - - + -
114E ASP* 4.9 6.5 - - - +
118E HIS* 2.8 29.6 + - + +
119E LEU* 3.9 15.0 - - + +
121E ALA* 1.3 74.0 - - - +
123E MET* 1.3 63.3 + - + +
124E GLY 3.4 0.2 + - - -
143E ASP* 6.0 0.7 - - - +
152E ILE* 3.6 36.3 - - + +
156E ASN* 5.0 6.5 + - - +
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Residues in contact with MET 123 (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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175D PRO* 3.4 20.9 - - - +
181D VAL* 3.9 29.4 - - + +
184D PRO* 4.4 11.4 - - + -
394D GLN* 3.9 29.8 - - + +
397D ALA* 4.2 4.3 - - - -
398D MET* 3.6 28.7 - - + -
89E LEU* 3.5 20.6 - - + +
119E LEU 3.1 18.5 + - - +
122E ILE* 1.3 83.8 - - + +
124E GLY* 1.3 62.1 + - - +
125E HIS* 3.4 27.8 + - + +
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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