Contacts of the helix formed by residues 104 - 110 (chain E) in PDB entry 2HU4
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 ASN 104 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LYS* 2.6 41.4 - - - +
103E ASP* 1.3 80.5 + - - +
105E SER* 1.3 64.0 + - - +
106E ILE 3.2 3.1 - - - -
107E ARG* 3.0 25.4 + - + +
108E ILE* 3.0 28.5 + - + +
442E SER* 4.0 6.8 + - - -
460E ASP 4.9 1.6 - - - -
137G GLY* 3.6 24.6 - - - +
155G HIS* 3.1 24.9 - - - +
157G THR* 3.9 14.0 + - - +
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Residues in contact with SER 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E ASP* 2.8 13.4 + - - -
104E ASN* 1.3 76.3 - - - +
106E ILE* 1.3 57.1 + - - +
108E ILE 3.7 0.3 - - - -
109E GLY* 2.8 26.2 + - - -
114E VAL* 3.6 13.3 - - - +
115E PHE 5.8 0.2 - - - -
117E ILE* 5.4 0.6 - - - +
140E LEU* 3.8 1.1 - - - +
166E ALA* 4.0 10.1 - - - -
167E PRO* 3.5 33.2 - - - -
441E GLY 3.3 17.2 + - - -
442E SER* 2.8 25.2 + - - -
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Residues in contact with ILE 106 (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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104E ASN 3.1 0.6 + - - -
105E SER* 1.3 78.3 + - - +
107E ARG* 1.3 68.1 + - - +
108E ILE 3.1 2.0 - - - -
109E GLY* 3.3 7.8 + - - -
110E SER 3.4 9.0 + - - -
140E LEU* 4.0 15.3 - - + -
426E LEU 4.4 0.2 - - - +
428E ARG* 3.6 33.4 - - + -
438E TRP* 4.2 11.9 - - + -
440E SER* 3.7 28.3 - - - +
441E GLY* 4.1 10.1 - - - +
442E SER* 3.5 5.8 + - - +
460E ASP* 3.4 16.2 - - - +
462E ALA* 3.6 18.4 - - + -
464E LEU* 5.1 0.2 - - + -
466E PHE* 3.6 23.3 - - + -
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Residues in contact with ARG 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E ASN* 3.0 21.1 + - - +
106E ILE* 1.3 79.3 - - - +
108E ILE* 1.3 59.6 + - - +
110E SER* 3.6 4.2 - - - -
460E ASP* 3.1 27.0 + - - +
461E GLY* 3.0 35.1 + - - +
462E ALA* 3.5 7.6 - - - +
136G GLN* 2.7 26.7 + - - +
137G GLY 2.8 27.2 + - - +
138G ALA* 4.0 2.6 - - - +
139G LEU* 5.3 0.9 + - - +
142G ASP* 4.0 3.8 - - - +
144G HIS* 3.4 54.6 + - + +
148G THR* 5.4 1.8 - - - +
150G LYS* 6.1 0.4 - - - +
155G HIS* 3.4 29.1 + - - +
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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
----------------------------------------------------------
103E ASP 3.7 23.3 - - - +
104E ASN* 3.0 13.8 + - + +
105E SER 3.9 3.4 - - - +
107E ARG* 1.3 75.6 - - - +
109E GLY* 1.3 51.8 + - - +
110E SER 3.1 6.0 + - - -
111E LYS 3.2 2.3 + - - -
112E GLY* 2.7 32.4 + - - -
114E VAL* 4.1 13.0 - - + -
166E ALA* 4.2 10.1 - - + +
115G PHE* 3.5 33.7 - - + -
137G GLY* 4.2 14.4 - - - +
138G ALA* 4.5 3.1 - - - +
139G LEU* 3.5 29.1 - - + +
169G PRO* 4.2 15.0 - - + -
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Residues in contact with GLY 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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105E SER 2.8 22.1 + - - -
106E ILE 3.3 1.7 + - - -
108E ILE* 1.3 68.3 - - - +
110E SER* 1.3 64.6 + - - +
111E LYS 3.0 4.0 + - - -
112E GLY 3.2 12.2 - - - +
114E VAL* 3.4 7.8 - - - +
140E LEU* 3.6 27.3 - - - +
466E PHE* 4.6 0.4 - - - -
111H LYS* 3.2 20.3 + - - -
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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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106E ILE 3.4 4.9 + - - -
107E ARG 3.6 4.0 - - - -
108E ILE 3.1 0.6 - - - -
109E GLY* 1.3 76.6 - - - +
111E LYS* 1.3 57.5 + - - +
141E ASN* 2.7 34.1 + - - +
466E PHE* 3.9 12.8 - - - -
142G ASP* 2.5 30.1 + - - +
143G LYS* 4.3 9.9 - - - +
144G HIS* 3.4 30.8 + - - -
111H LYS* 4.3 0.7 + - - -
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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