Contacts of the helix formed by residues 106 - 119 (chain D) in PDB entry 3KHU
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 LEU 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D THR* 4.4 2.7 - - + -
104D ALA 3.7 5.4 + - - +
105D ASP* 1.3 72.9 + - - +
107D LYS* 1.3 65.1 + - - +
108D TYR 3.3 2.7 - - - -
109D ILE* 3.1 31.8 + - + +
110D GLU* 2.9 23.2 + - + +
133D PRO* 4.0 36.1 - - + -
135D ARG 5.6 0.7 - - - +
136D ALA* 4.2 15.7 - - + +
139D SER* 4.2 22.7 - - - +
323F PHE* 3.7 29.7 + - + +
324F ASN 5.5 0.2 + - - -
325F THR* 4.2 10.3 - - + -
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Residues in contact with LYS 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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92D PRO* 4.8 7.9 - - - -
96D TYR* 5.3 1.8 + - - -
105D ASP* 3.1 33.5 + - - +
106D LEU* 1.3 75.6 - - - +
108D TYR* 1.3 101.9 + - + +
110D GLU* 3.3 4.8 + - - +
111D ALA* 2.9 29.7 + - - +
325F THR* 3.8 17.3 - - + +
327F THR* 4.5 27.8 + - + +
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Residues in contact with TYR 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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89D VAL* 3.7 19.7 - - + -
90D ASN* 3.2 45.7 + - - +
92D PRO* 4.0 12.1 - - + -
105D ASP 4.7 0.8 + - - -
106D LEU 3.3 0.8 - - - -
107D LYS* 1.3 111.5 + - + +
109D ILE* 1.3 65.8 + - - +
111D ALA* 3.2 7.3 + - + +
112D CYS* 2.9 27.5 + - - -
502D UPG 3.5 32.8 - + + +
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Residues in contact with ILE 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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87D ILE* 3.6 27.4 - - + +
89D VAL* 3.7 15.3 - - + +
91D THR* 3.4 30.7 - - + +
106D LEU* 3.1 23.6 + - + +
108D TYR* 1.3 75.5 - - - +
110D GLU* 1.3 59.5 + - - +
112D CYS* 3.3 5.4 + - - +
113D ALA* 2.9 26.5 + - - +
128D GLU* 5.9 2.2 - - + -
130D SER* 6.0 0.9 - - - -
132D VAL* 4.2 15.3 - - + -
136D ALA* 5.2 4.5 - - + +
139D SER* 6.1 1.6 - - - -
140D ILE* 3.8 34.1 - - + -
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Residues in contact with GLU 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 LEU* 2.9 16.8 + - + +
107D LYS* 3.6 5.9 - - - +
109D ILE* 1.3 80.8 - - - +
111D ALA* 1.3 62.4 + - - +
113D ALA* 3.1 2.6 + - - +
114D ARG* 2.8 64.2 + - - +
140D ILE* 6.3 0.2 - - - -
143D ILE* 3.7 17.7 - - + -
323F PHE* 3.4 20.5 - - + -
325F THR* 3.6 9.9 - - + +
329F LYS* 2.9 39.8 + - - -
409F HIS* 4.2 0.7 - - - -
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Residues in contact with ALA 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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107D LYS 2.9 17.2 + - - +
108D TYR* 3.6 9.2 - - + +
110D GLU* 1.3 76.6 - - - +
112D CYS* 1.3 63.4 + - - +
114D ARG* 3.3 9.3 + - - +
115D ARG* 2.9 25.3 + - - +
502D UPG 4.7 8.5 - - - +
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Residues in contact with CYS 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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10D ILE* 3.6 36.3 - - + -
87D ILE* 4.1 24.7 - - + -
89D VAL* 3.8 18.2 - - - -
108D TYR 2.9 17.3 + - - +
109D ILE 3.5 7.9 - - - +
111D ALA* 1.3 76.8 - - - +
113D ALA* 1.3 57.5 + - - +
115D ARG* 3.2 5.8 + - - +
116D ILE* 2.8 35.5 + - - +
502D UPG 4.7 6.3 - - - -
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Residues in contact with ALA 113 (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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87D ILE* 4.8 2.6 - - + +
109D ILE 2.9 15.0 + - - +
110D GLU* 3.1 7.8 + - - +
112D CYS* 1.3 75.5 - - - +
114D ARG* 1.3 62.3 + - - +
116D ILE* 3.4 4.2 + - - +
117D VAL* 3.2 24.9 + - - +
140D ILE* 4.3 16.8 - - + -
143D ILE* 3.8 27.8 - - + -
144D PHE* 3.3 22.7 - - + -
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Residues in contact with ARG 114 (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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110D GLU* 2.8 53.5 + - + +
111D ALA* 3.8 6.3 - - - +
113D ALA* 1.3 74.0 - - - +
115D ARG* 1.3 64.9 + - - +
117D VAL* 3.1 11.3 - - + +
118D GLN* 3.0 31.6 + - - +
143D ILE* 3.9 16.4 - - + +
147D ASN* 4.1 7.2 + - - +
323F PHE* 4.6 2.6 - - - -
409F HIS* 3.8 26.2 + - - -
433F LEU* 4.7 11.8 - - - +
434F LYS 2.6 35.8 + - - +
435F PRO* 4.0 12.5 + - - +
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Residues in contact with ARG 115 (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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10D ILE* 5.7 1.1 - - + -
37D VAL* 4.2 12.9 - - - +
75D ILE* 3.5 37.2 - - + +
76D ASP* 3.0 34.2 + - - -
79D ILE* 3.7 19.3 - - + -
111D ALA 2.9 17.9 + - - +
112D CYS* 3.7 6.5 - - - +
114D ARG* 1.3 76.0 - - - +
116D ILE* 1.3 61.8 + - - +
118D GLN* 3.3 9.8 + - - +
119D ASN* 2.9 34.1 + - - +
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Residues in contact with ILE 116 (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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10D ILE* 3.9 20.2 - - + -
79D ILE* 4.1 14.1 - - + -
85D VAL* 3.7 28.3 - - + -
87D ILE* 4.1 12.8 - - + -
112D CYS 2.8 24.5 + - - +
113D ALA* 3.7 6.3 - - - +
114D ARG 3.3 0.2 - - - -
115D ARG* 1.3 72.8 - - - +
117D VAL* 1.3 62.3 + - - +
119D ASN 3.3 2.1 + - - -
120D SER* 2.6 40.2 + - - +
124D LYS* 5.4 0.2 - - + -
126D VAL* 3.9 38.4 - - + -
144D PHE* 4.2 8.5 - - + -
154D LEU* 4.4 5.8 - - + -
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Residues in contact with VAL 117 (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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113D ALA 3.2 13.8 + - - +
114D ARG* 3.1 23.8 - - + +
116D ILE* 1.3 81.3 - - - +
118D GLN* 1.3 51.4 + - - +
119D ASN 3.4 0.2 + - - -
120D SER* 3.5 6.0 + - - +
143D ILE* 4.4 8.7 - - + -
144D PHE* 4.1 15.3 - - + +
147D ASN* 3.0 46.9 - - + +
149D LYS* 2.7 34.4 + - - -
152D LEU* 3.9 13.8 - - + +
154D LEU* 4.5 7.9 - - + -
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Residues in contact with GLN 118 (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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114D ARG* 3.0 26.4 + - - +
115D ARG* 3.5 10.5 - - - +
117D VAL* 1.3 79.1 - - - +
119D ASN* 1.3 63.9 + - - +
149D LYS* 3.2 15.9 + - - +
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Residues in contact with ASN 119 (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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76D ASP* 3.1 52.1 + - - +
79D ILE* 4.0 14.6 - - + -
80D LYS* 3.6 30.8 - - + +
115D ARG* 2.9 35.2 + - - +
116D ILE 3.3 0.2 + - - -
118D GLN* 1.3 84.8 - - - +
120D SER* 1.3 60.7 + - - +
121D ASN* 4.4 2.8 + - - -
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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