Contacts of the helix formed by residues 107 - 112 (chain E) in PDB entry 3BBX
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 107 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21E ARG* 4.6 8.3 + - - +
22E ASP 3.5 24.4 + - - -
23E PHE* 3.3 29.6 - - - -
104E ALA* 4.4 5.0 - - - +
105E LEU 2.6 24.7 + - - -
106E LYS* 1.3 70.3 - - - +
108E ILE* 1.3 64.9 + - - +
109E LEU 3.5 0.6 + - - -
110E SER* 3.6 7.5 + - - -
111E GLU* 3.3 27.5 + - - +
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Residues in contact with ILE 108 (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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23E PHE* 6.2 2.0 - - + -
105E LEU 3.4 20.4 - - - +
106E LYS* 2.8 17.1 - - + -
107E SER* 1.3 78.8 - - - +
109E LEU* 1.3 60.9 + - - +
110E SER 3.2 0.3 + - - -
111E GLU* 5.2 0.7 - - - -
112E LEU* 2.6 40.4 + - + +
116E ASP* 3.0 47.6 - - + +
177E PRO* 6.5 0.4 - - + -
180E LEU* 4.7 18.8 - - + +
181E ILE* 5.7 4.3 - - + +
186E VAL* 5.9 0.4 - - + -
188E MET* 4.1 8.3 - - + -
12L SER 3.1 23.6 - - - +
13L LYS* 4.9 4.3 - - + -
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Residues in contact with LEU 109 (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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3E LEU* 3.4 39.9 - - + -
15E SER 6.1 0.9 - - - +
17E THR* 5.1 14.6 - - + +
106E LYS* 4.0 11.0 + - + +
108E ILE* 1.3 78.5 - - - +
110E SER* 1.3 79.5 + - - +
113E VAL* 2.9 30.1 - - - +
116E ASP 3.7 11.0 - - - -
117E ARG* 3.3 23.4 + - + +
188E MET* 5.3 6.2 - - - +
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Residues in contact with SER 110 (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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21E ARG 6.0 1.6 - - - -
107E SER* 3.6 7.9 + - - -
108E ILE 3.3 0.8 - - - -
109E LEU* 1.3 88.5 - - - +
111E GLU* 1.3 67.7 + - - +
113E VAL* 2.9 27.5 - - - +
117E ARG* 4.8 2.5 - - - +
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Residues in contact with GLU 111 (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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22E ASP 4.3 13.6 - - - +
23E PHE* 3.6 33.5 - - - +
107E SER* 3.3 19.2 + - - +
108E ILE* 5.0 0.6 - - - -
110E SER* 1.3 82.5 + - - +
112E LEU* 1.3 61.1 + - + +
113E VAL* 2.6 24.6 + - - +
114E ARG* 4.6 10.7 + - - -
17L LYS* 4.8 8.8 - - - -
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Residues in contact with LEU 112 (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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108E ILE* 2.6 28.4 + - + +
109E LEU 3.8 0.4 - - - -
111E GLU* 1.3 77.0 - - + +
113E VAL* 1.3 50.5 + - - -
114E ARG* 3.4 3.1 - - - +
115E GLN* 2.7 32.5 + - - +
116E ASP 2.8 14.5 + - - +
10L GLU 5.0 0.2 - - - -
11L GLY* 2.2 60.3 - - - +
12L SER* 1.7 72.9 - - - +
13L LYS* 3.9 3.4 - - - +
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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