Contacts of the helix formed by residues 104 - 110 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLY* 3.9 24.3 - - - +
155A HIS* 3.3 25.4 - - - +
157A THR* 3.9 14.9 + - - +
102D LYS* 2.6 39.6 - - - +
103D ASP* 1.3 81.0 + - - +
105D SER* 1.3 64.1 + - - +
106D ILE 3.1 3.2 + - - -
107D ARG* 3.2 24.2 + - - +
108D ILE* 3.0 28.1 + - + +
442D SER* 4.4 6.8 - - - -
460D ASP 5.2 0.9 - - - -
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Residues in contact with SER 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ASP* 2.7 16.7 + - - -
104D ASN* 1.3 71.7 - - - +
106D ILE* 1.3 59.0 + - - +
108D ILE* 3.7 1.5 - - - +
109D GLY* 2.8 26.9 + - - -
114D VAL* 3.7 16.8 - - - +
115D PHE 5.8 0.2 - - - -
117D ILE* 5.1 0.7 - - - +
140D LEU* 3.9 0.6 - - - +
166D ALA* 3.9 10.1 - - - -
167D PRO* 3.6 31.9 - - - +
441D GLY 3.4 22.0 + - - -
442D SER* 3.5 9.6 + - - -
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Residues in contact with ILE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D ASN 3.2 1.2 - - - -
105D SER* 1.3 73.8 + - - +
107D ARG* 1.3 67.8 + - - +
108D ILE 3.1 2.3 + - - -
109D GLY* 3.2 8.7 + - - -
110D SER 3.3 9.4 + - - -
140D LEU* 4.0 15.2 - - + +
428D ARG* 3.7 23.8 - - + -
438D TRP* 4.5 15.0 - - + -
440D SER* 4.1 6.7 - - - +
441D GLY* 3.6 34.8 - - - +
442D SER* 3.2 10.9 + - - +
460D ASP* 3.4 20.4 - - - +
462D ALA* 3.4 21.5 - - + -
466D PHE* 3.6 18.0 - - + -
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Residues in contact with ARG 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLN 2.7 27.4 + - - -
137A GLY 2.8 27.7 + - - +
138A ALA* 3.9 2.5 - - - +
139A LEU* 5.2 0.3 + - - +
142A ASP* 3.7 5.0 - - - +
144A HIS* 3.3 58.0 + - + +
148A THR* 5.5 1.6 - - - +
150A LYS* 5.6 5.7 - - - +
155A HIS* 3.4 24.6 + - - +
104D ASN* 3.2 21.8 + - - +
106D ILE* 1.3 77.7 - - - +
108D ILE* 1.3 61.5 + - - +
110D SER* 3.6 4.7 - - - -
460D ASP* 3.2 22.4 + - - +
461D GLY* 3.0 39.0 + - - +
462D ALA* 3.6 7.6 - - + +
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Residues in contact with ILE 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A PHE* 3.7 29.8 - - + -
137A GLY* 4.1 14.4 - - - +
138A ALA* 4.6 2.7 - - - +
139A LEU* 3.6 30.2 - - + +
142A ASP* 5.5 0.3 - - - +
169A PRO* 4.4 14.6 - - + -
103D ASP 3.4 25.8 - - - +
104D ASN* 3.0 15.6 + - + +
105D SER* 3.7 4.3 - - - +
107D ARG* 1.3 74.5 - - - +
109D GLY* 1.3 53.2 + - - +
110D SER 3.2 3.1 + - - -
111D LYS* 3.3 2.6 + - - +
112D GLY* 2.8 29.6 + - - -
114D VAL* 4.0 13.7 - - + -
166D ALA* 4.0 11.4 - - + +
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Residues in contact with GLY 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LYS* 3.1 10.0 + - - -
105D SER 2.8 17.5 + - - -
106D ILE 3.2 2.8 + - - -
108D ILE* 1.3 69.3 - - - +
110D SER* 1.3 61.7 + - - +
111D LYS 2.8 7.4 + - - -
112D GLY 3.0 16.1 - - - +
114D VAL* 3.4 24.2 - - - +
140D LEU* 3.9 19.3 - - - +
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Residues in contact with SER 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASP* 2.7 27.0 + - - +
143A LYS* 4.2 8.8 - - - +
144A HIS* 3.3 30.7 + - - -
111B LYS* 4.3 0.9 + - - -
106D ILE 3.3 5.1 + - - -
107D ARG 3.6 3.1 - - - -
108D ILE 3.2 0.6 - - - -
109D GLY* 1.3 76.5 - - - +
111D LYS* 1.3 56.5 + - - +
141D ASN* 2.8 25.9 + - - +
466D PHE* 3.3 28.7 - - - -
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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