Contacts of the helix formed by residues 130 - 146 (chain A) in PDB entry 1HK2
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A ALA 3.0 18.5 + - - +
128A HIS 3.0 0.8 + - - -
129A ASP* 1.3 87.3 + - + +
131A GLU* 1.3 61.4 + - - +
132A GLU* 3.5 6.9 + - - +
133A THR* 3.4 35.5 + - - -
134A PHE* 3.4 14.2 + - - +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE* 3.1 53.6 + - + +
128A HIS* 4.1 4.5 + - - +
130A ASN* 1.3 72.8 + - - +
132A GLU* 1.3 76.9 - - + +
133A THR 3.5 0.2 - - - -
134A PHE* 3.5 4.2 - - - +
135A LEU* 3.4 28.5 + - + +
162A LYS* 5.9 0.6 - - - +
166A THR* 4.3 3.6 + - - -
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 5.1 6.6 - - - +
130A ASN* 3.5 6.3 + - - +
131A GLU* 1.3 93.3 - - + +
133A THR* 1.3 61.9 + - - +
134A PHE 3.1 1.8 - - - -
135A LEU* 3.5 14.3 + - - +
136A LYS* 3.0 27.9 + - - +
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Residues in contact with THR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.4 25.6 - - + -
130A ASN* 3.4 30.6 + - - -
132A GLU* 1.3 78.2 - - - +
134A PHE* 1.3 62.4 + - - +
135A LEU 3.5 0.2 - - - -
136A LYS* 3.8 5.8 - - - -
137A LYS* 3.0 21.4 + - + +
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Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A MET* 3.9 24.0 - - + -
126A ALA* 4.0 11.9 - - + +
127A PHE* 3.5 28.7 - + + -
130A ASN 3.4 19.1 + - - +
131A GLU* 3.5 9.4 - - - +
132A GLU 3.1 0.4 - - - -
133A THR* 1.3 78.5 - - - +
135A LEU* 1.3 63.7 + - + +
137A LYS* 3.0 25.9 - - + +
138A TYR* 3.2 6.2 + - - +
161A TYR* 3.9 19.5 + + - -
165A PHE* 3.3 58.3 - + - -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE* 5.4 1.1 - - + -
131A GLU* 3.4 25.8 + - + +
132A GLU* 4.1 17.7 - - - +
134A PHE* 1.3 82.3 - - + +
136A LYS* 1.3 67.1 - - - +
137A LYS 2.9 1.8 - - - -
138A TYR* 2.8 16.8 + - + +
139A LEU* 2.9 23.5 + - + +
158A ALA* 4.0 11.9 - - + +
161A TYR* 3.8 24.2 - - + -
162A LYS* 3.5 35.9 - - + -
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Residues in contact with LYS 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.4 20.2 - - + +
36A PHE* 3.3 23.2 - - + -
40A VAL* 5.2 5.2 - - + -
132A GLU 3.0 19.7 + - - +
133A THR* 3.8 3.1 - - - +
135A LEU* 1.3 77.1 - - - +
137A LYS* 1.3 56.1 + - - +
139A LEU* 4.7 4.3 - - - -
140A TYR* 2.9 30.5 + - - +
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Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.6 17.5 - - + -
133A THR* 3.0 15.2 + - + +
134A PHE* 3.0 18.2 - - + +
136A LYS* 1.3 75.4 - - - +
138A TYR* 1.3 56.9 + - - +
140A TYR* 3.2 4.8 + - + +
141A GLU* 2.9 38.7 + - + +
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Residues in contact with TYR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PHE 3.2 2.2 + - - +
135A LEU* 2.8 12.7 + - + +
137A LYS* 1.3 77.1 - - - +
139A LEU* 1.3 83.3 + - + +
140A TYR 3.0 0.7 + - - -
141A GLU* 3.1 4.6 + - - +
142A ILE* 3.1 48.5 + - + +
154A LEU* 4.7 2.7 - - + -
157A PHE* 4.1 20.1 + - + +
158A ALA* 3.8 18.8 - - + -
161A TYR* 3.2 63.5 - + + +
185A LEU* 4.4 8.1 + - - +
186A ARG* 3.1 32.3 + - - -
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA* 3.8 33.0 - - + +
24A LEU* 4.2 13.9 - - + -
25A ILE* 4.4 13.5 - - + +
28A ALA* 4.7 0.2 - - - +
135A LEU* 2.9 19.9 + - + +
136A LYS* 4.0 4.9 - - - +
138A TYR* 1.3 88.7 - - + +
140A TYR* 1.3 57.8 + - - +
142A ILE* 4.9 0.9 - - - -
143A ALA* 2.9 31.7 + - - +
154A LEU* 4.1 26.9 - - + +
155A LEU* 5.1 2.5 - - + -
158A ALA* 3.4 33.9 - - + -
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Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 4.4 7.6 - - + +
28A ALA* 3.9 14.9 - - + +
31A LEU 5.5 0.7 - - - -
32A GLN 5.4 0.4 - - - -
34A CYS 2.6 22.8 + - - -
35A PRO* 3.7 1.6 - - - +
36A PHE* 3.5 46.3 + + + -
39A HIS* 3.7 32.1 - + + -
136A LYS 2.9 20.7 + - - +
137A LYS* 3.3 6.3 - - - +
138A TYR 3.0 0.2 - - - -
139A LEU* 1.3 75.1 - - - +
141A GLU* 1.3 93.3 + - - +
143A ALA* 3.8 1.4 - - - +
144A ARG* 3.1 59.6 + - + +
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A LEU* 3.4 33.2 - - + +
137A LYS* 2.9 25.9 + - + +
138A TYR* 3.9 3.6 - - + +
140A TYR* 1.3 99.7 - - - +
142A ILE* 1.3 65.1 + - + +
144A ARG* 2.8 36.2 + - - +
145A ARG* 2.4 51.2 + - - +
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU* 5.6 7.6 - - + -
138A TYR* 3.1 45.6 + - + +
139A LEU 4.4 0.7 - - - +
141A GLU* 1.3 77.6 - - + +
143A ALA* 1.3 57.4 + - - +
145A ARG* 4.8 1.8 - - - +
146A HIS* 2.9 48.3 + - + +
149A PHE* 3.6 31.9 - - + -
154A LEU* 3.7 23.6 - - + -
186A ARG* 4.9 7.6 - - - +
189A GLY* 6.3 2.0 - - - -
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.8 26.5 - - + -
28A ALA* 3.5 20.4 - - + -
29A GLN* 3.4 14.8 - - + +
139A LEU 2.9 20.9 + - - +
140A TYR 3.8 0.2 - - - +
142A ILE* 1.3 82.0 - - - +
144A ARG* 1.3 57.9 + - - +
146A HIS 3.0 26.3 - - - +
147A PRO* 3.3 4.0 - - - +
149A PHE* 5.3 0.2 - - - -
154A LEU* 4.4 3.8 - - + +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA* 3.6 20.6 + - + +
32A GLN* 2.9 67.0 + - - +
33A GLN 3.6 12.1 + - - -
110A PRO* 3.7 4.5 - - - +
112A LEU* 3.1 27.4 - - + +
113A PRO* 5.6 4.2 - - - +
140A TYR* 3.1 53.9 + - + +
141A GLU* 2.8 49.2 + - - +
143A ALA* 1.3 77.0 - - - +
145A ARG* 1.3 69.0 + - - +
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Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ASP 4.7 4.5 - - - +
110A PRO* 4.4 13.6 - - + +
112A LEU* 4.1 21.4 - - + +
113A PRO* 3.2 30.3 + - - +
114A ARG 4.4 0.6 + - - -
115A LEU* 3.4 39.6 - - - +
141A GLU* 2.4 50.7 + - - +
142A ILE* 5.5 1.3 - - - +
144A ARG* 1.3 91.5 - - + +
146A HIS* 1.3 84.9 + - + +
147A PRO* 3.6 6.7 - - - +
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Residues in contact with HIS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLN* 3.1 5.4 + - - -
142A ILE* 2.9 35.5 + - + +
143A ALA 3.0 9.3 - - - +
145A ARG* 1.3 101.7 + - + +
147A PRO* 1.3 60.0 - - - +
148A TYR 2.8 11.3 + - - -
149A PHE* 3.0 27.3 + + + +
189A GLY 5.4 0.7 - - - -
190A LYS* 4.8 23.6 - - + -
193A SER* 3.0 34.5 + - - +
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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