Contacts of the helix formed by residues 103 - 111 (chain H) in PDB entry 5G04
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 103 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101H LYS 3.3 10.4 + - - -
102H SER* 1.3 86.2 - - - +
104H ASP* 1.3 57.0 + - - +
105H ASP 3.2 1.3 - - - +
106H ILE* 3.0 24.9 + - - +
107H VAL* 2.8 32.9 + - - +
118H LEU* 4.3 16.8 - - + +
121H LEU* 5.6 1.5 - - + +
125H TYR* 5.3 9.2 - + - -
133H LYS* 5.2 16.8 - - + +
136H GLU* 5.3 8.8 + - + +
137H CYS* 4.9 19.9 - - + -
140H LYS* 3.8 33.6 - - + +
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Residues in contact with ASP 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H SER* 2.3 48.1 + - - +
103H HIS* 1.3 70.5 - - - +
105H ASP* 1.3 66.1 + - - -
107H VAL* 3.2 12.6 + - + +
108H THR* 2.8 36.8 + - + +
140H LYS* 4.4 10.6 + - - +
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Residues in contact with ASP 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H LYS* 3.5 22.2 - - + +
102H SER* 3.3 25.7 + - - +
104H ASP* 1.3 82.6 + - - +
106H ILE* 1.3 51.9 - - - +
108H THR* 2.7 24.6 + - - -
109H GLU* 2.8 42.0 + - - +
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Residues in contact with ILE 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H LEU* 3.7 21.1 - - + +
93H SER* 4.5 2.9 - - - -
101H LYS* 4.1 21.1 - - + +
103H HIS* 3.0 30.2 + - - +
105H ASP* 1.3 73.7 - - - +
107H VAL* 1.3 58.0 + - - +
109H GLU* 4.3 2.0 - - - -
110H PHE* 3.0 63.5 + - + +
114H ALA* 4.5 0.7 - - - +
117H THR* 3.7 17.0 - - - +
118H LEU* 4.5 14.8 - - + +
121H LEU* 3.9 28.3 - - + -
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Residues in contact with VAL 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H HIS 2.8 24.9 + - - +
104H ASP* 3.2 12.5 + - + +
106H ILE* 1.3 72.9 - - - +
108H THR* 1.3 58.7 + - + +
111H GLY* 2.9 31.4 + - - +
114H ALA* 3.7 11.2 - - + -
118H LEU* 3.8 23.1 - - + -
140H LYS* 5.2 7.6 - - + +
144H LEU* 4.2 21.3 - - + -
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Residues in contact with THR 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H ASP* 2.8 23.2 + - + +
105H ASP* 2.7 28.6 + - - -
107H VAL* 1.3 73.8 - - + +
109H GLU* 1.3 63.6 + - - +
111H GLY* 3.9 5.4 + - - -
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Residues in contact with GLU 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H PRO* 3.7 17.4 - - - +
72H LYS* 4.6 16.4 + - - +
101H LYS* 3.5 37.1 + - - +
105H ASP* 2.8 38.9 + - - +
106H ILE 3.7 3.8 - - - +
108H THR* 1.3 76.6 + - - +
110H PHE* 1.3 82.1 + - + +
111H GLY 3.8 0.2 + - - -
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Residues in contact with PHE 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H PRO* 3.5 41.4 - - + +
72H LYS* 4.1 17.5 - - + -
73H TYR* 4.2 3.8 - - + -
91H ILE 5.3 0.4 - - - -
92H LEU* 3.7 39.3 - - + -
106H ILE* 3.0 50.9 + - + +
109H GLU* 1.3 98.2 - - + +
111H GLY* 1.3 63.4 + - - +
112H ASP 3.1 2.3 + - - -
113H SER* 2.9 26.4 + - - +
114H ALA* 3.7 17.0 - - - -
117H THR* 3.8 15.9 - - + -
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Residues in contact with GLY 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H VAL* 2.9 19.6 + - - +
108H THR 3.9 5.3 + - - -
109H GLU 3.4 2.4 - - - -
110H PHE* 1.3 75.0 - - - +
112H ASP* 1.3 63.8 + - - +
114H ALA* 3.0 21.7 - - - +
144H LEU* 4.6 6.9 - - - +
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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