Contacts of the helix formed by residues 102 - 109 (chain E) in PDB entry 1H4O
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 GLY 102 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75E VAL* 3.9 18.6 - - - +
99E ASP* 3.0 20.2 + - - -
100E PRO 3.3 1.4 + - - -
101E THR* 1.3 78.0 - - - +
103E ALA* 1.3 65.2 + - - +
104E PHE 3.3 3.1 + - - -
105E GLY* 3.3 2.6 + - - -
106E LYS* 2.9 28.7 + - - +
111E LEU* 4.0 8.6 - - - +
123E ARG 5.5 0.7 - - - -
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Residues in contact with ALA 103 (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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12E VAL* 3.9 17.9 - - + -
13E GLU 5.5 1.6 - - - +
99E ASP* 3.0 12.3 + - - +
101E THR* 3.3 12.8 - - - +
102E GLY* 1.3 78.1 - - - +
104E PHE* 1.3 62.6 + - - +
106E LYS* 3.3 13.0 + - - +
107E GLU* 3.0 29.5 + - + +
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Residues in contact with PHE 104 (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 ILE* 5.3 1.1 - - + -
9E ILE* 4.2 6.7 - - + -
10E PRO* 4.1 24.5 - - + -
12E VAL* 4.0 16.4 - - + +
14E VAL* 5.5 0.2 - - + -
25E LEU* 3.3 31.2 - - + -
36E LEU* 3.7 17.5 - - + -
73E LEU* 3.6 21.1 - - + -
99E ASP* 2.7 23.1 + - - +
103E ALA* 1.3 73.9 - - - +
105E GLY* 1.3 60.3 + - - +
107E GLU* 3.2 3.3 + - - +
108E THR* 2.9 40.0 + - + +
110E LEU* 3.9 14.4 - - + -
125E LEU* 4.3 10.3 - - + -
128E PHE* 3.8 22.0 - + - -
130E MET* 4.5 11.4 - - + -
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Residues in contact with GLY 105 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99E ASP* 4.1 1.0 + - - -
102E GLY 3.3 4.0 + - - -
104E PHE* 1.3 80.6 - - - +
106E LYS* 1.3 56.8 + - - +
108E THR* 3.6 6.5 - - - -
109E ASP* 2.9 28.1 + - - -
110E LEU 3.0 6.1 + - - -
111E LEU* 3.6 32.2 + - - +
125E LEU* 3.8 14.5 - - - +
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Residues in contact with LYS 106 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101E THR* 3.0 32.3 + - - +
102E GLY* 2.9 23.2 + - - +
103E ALA* 3.6 9.2 - - - +
105E GLY* 1.3 76.9 - - - +
107E GLU* 1.3 67.8 + - - +
108E THR 3.4 0.5 + - - -
109E ASP* 3.8 5.0 + - - -
111E LEU* 3.8 17.5 - - + +
123E ARG* 6.0 1.1 - - - +
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Residues in contact with GLU 107 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E ALA 4.0 11.1 + - - +
10E PRO* 4.4 16.6 - - + +
12E VAL* 4.2 15.3 - - + -
103E ALA* 3.0 18.5 + - + +
104E PHE* 3.5 8.1 - - - +
106E LYS* 1.3 82.5 - - - +
108E THR* 1.3 63.7 + - + +
109E ASP 3.7 0.4 - - - -
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Residues in contact with THR 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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1E ALA 4.0 7.0 - - - -
2E PRO* 3.3 1.6 - - - +
3E ILE* 3.1 56.2 + - + +
10E PRO* 4.3 8.5 - - + -
104E PHE* 2.9 40.3 + - + +
105E GLY* 3.5 0.7 + - - -
107E GLU* 1.3 80.1 - - - +
109E ASP* 1.3 69.4 + - - +
110E LEU* 3.2 29.3 + - - +
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Residues in contact with ASP 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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1E ALA 4.5 5.1 - - - +
2E PRO* 3.9 32.6 - - + +
105E GLY 2.9 8.5 + - - -
106E LYS 3.8 5.2 + - - +
107E GLU 3.7 1.4 - - - -
108E THR* 1.3 81.2 - - - +
110E LEU* 1.3 61.7 + - - +
111E LEU 3.4 5.6 - - - +
123E ARG* 5.4 4.9 + - - -
126E LYS* 3.3 23.7 + - - -
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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