Contacts of the helix formed by residues 101 - 112 (chain D) in PDB entry 3HR4
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 101 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D TYR 3.5 1.8 + - - -
100D ILE* 1.3 75.5 - - - +
102D ALA* 1.3 59.1 + - - +
103D ALA* 3.5 9.3 + - - +
104D GLU* 2.9 37.6 + - - +
105D LEU* 3.0 27.9 + - - +
125D ILE* 4.7 3.1 - - - +
135D GLN* 3.7 28.7 - - - -
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Residues in contact with ALA 102 (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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101D SER* 1.3 72.4 - - - +
103D ALA* 1.3 57.1 + - - +
105D LEU* 3.3 1.5 + - - +
106D ARG* 2.6 54.2 + - - +
121D VAL* 4.2 8.3 - - + +
122D ASP* 5.2 5.2 - - - +
125D ILE* 3.7 29.5 - - + +
134D GLY 4.9 4.8 + - - +
135D GLN* 5.2 0.6 + - - +
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Residues in contact with ALA 103 (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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101D SER* 3.5 9.8 + - - +
102D ALA* 1.3 79.4 - - - +
104D GLU* 1.3 58.9 + - + +
106D ARG* 3.2 27.1 + - - +
107D HIS* 2.8 29.5 + - - +
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Residues in contact with GLU 104 (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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92D PHE 3.3 23.8 - - - +
93D ASP* 3.5 2.4 - - - +
94D LYS* 4.0 11.9 + - + +
95D ASP* 2.8 27.4 + - - +
99D TYR 3.0 2.8 - - - +
100D ILE* 3.5 5.2 - - + -
101D SER* 2.9 33.0 + - - +
103D ALA* 1.3 74.6 - - + +
105D LEU* 1.3 65.4 + - - +
107D HIS* 3.4 7.5 + - - +
108D VAL* 3.1 28.2 + - - +
203D CA 2.6 30.9 - - - -
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Residues in contact with LEU 105 (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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515C LEU* 4.3 17.0 - - + -
92D PHE* 3.5 32.5 - - + -
100D ILE* 4.2 11.8 - - + +
101D SER 3.0 17.6 + - - +
102D ALA* 3.9 3.4 - - - +
104D GLU* 1.3 74.1 - - - +
106D ARG* 1.3 66.3 + - - +
108D VAL* 3.9 1.3 - - + -
109D MET* 3.0 42.9 + - + +
121D VAL* 3.5 19.5 - - + -
124D MET* 3.1 38.6 - - + -
125D ILE* 5.0 9.2 - - + -
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Residues in contact with ARG 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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102D ALA* 2.6 35.3 + - - +
103D ALA* 3.3 31.1 + - - +
104D GLU 3.1 0.2 - - - -
105D LEU* 1.3 76.2 - - - +
107D HIS* 1.3 65.1 + - - +
109D MET* 2.8 16.8 + - - +
110D THR* 3.0 21.8 + - + +
116D LEU 6.1 1.1 - - - +
118D ASP* 3.8 25.8 + - - -
121D VAL* 4.0 21.8 - - + +
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Residues in contact with HIS 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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94D LYS* 3.8 22.5 + - + +
103D ALA 2.8 16.3 + - - +
104D GLU* 3.6 8.5 - - - +
105D LEU 3.3 0.2 - - - -
106D ARG* 1.3 77.8 - - - +
108D VAL* 1.3 63.1 + - - +
110D THR* 3.2 8.7 + - - -
111D ASN* 2.9 45.5 + - - -
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Residues in contact with VAL 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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518C LEU* 4.4 4.9 - - + -
38D SER 5.9 0.2 - - - -
39D LEU* 4.8 9.4 - - + -
91D VAL* 3.9 28.3 - - + +
92D PHE* 3.6 39.7 - - + -
94D LYS* 4.5 9.9 - - - +
104D GLU 3.1 17.2 + - - +
105D LEU* 4.1 2.5 - - + +
107D HIS* 1.3 77.7 - - - +
109D MET* 1.3 64.6 + - - +
111D ASN* 3.3 10.7 + - - +
112D LEU* 3.2 39.6 + - + +
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Residues in contact with MET 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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513C ILE* 4.2 14.4 - - + -
518C LEU* 3.4 29.6 - - - -
105D LEU* 3.0 26.8 + - + +
106D ARG* 2.8 8.3 + - - +
108D VAL* 1.3 76.9 - - - +
110D THR* 1.3 61.3 + - + +
112D LEU* 3.3 19.6 + - + +
113D GLY 3.7 0.2 + - - -
114D GLU* 3.1 59.2 - - + +
116D LEU* 3.8 17.7 - - + +
121D VAL* 5.6 1.3 - - + -
124D MET* 3.6 30.5 - - + +
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Residues in contact with THR 110 (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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106D ARG* 3.0 21.8 + - + +
107D HIS* 3.2 13.1 + - - -
109D MET* 1.3 72.6 - - + +
111D ASN* 1.3 65.5 + - - +
112D LEU 3.0 2.2 - - - -
113D GLY* 2.7 26.3 + - - -
114D GLU 3.5 20.3 + - - +
116D LEU 6.1 0.9 - - - +
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Residues in contact with ASN 111 (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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38D SER* 3.2 43.5 + - - +
94D LYS* 4.2 12.9 - - - +
107D HIS* 2.9 42.0 + - - +
108D VAL* 3.6 9.2 - - - +
109D MET 3.3 0.2 - - - -
110D THR* 1.3 84.7 + - - +
112D LEU* 1.3 57.1 + - + +
113D GLY 3.0 2.8 + - - -
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Residues in contact with LEU 112 (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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513C ILE* 6.1 1.1 - - + -
518C LEU* 3.6 28.9 - - + -
18D LEU* 4.3 22.1 - - + +
21D LYS* 5.0 10.8 + - - +
35D VAL* 4.3 18.2 - - + -
38D SER* 3.9 21.5 - - - +
39D LEU* 4.2 17.9 - - + -
108D VAL* 3.2 27.2 + - + +
109D MET* 3.7 19.5 - - + +
110D THR 3.0 0.8 - - - -
111D ASN* 1.3 76.6 - - + +
113D GLY* 1.3 65.8 + - - +
114D GLU* 3.8 8.3 - - - +
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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