Contacts of the helix formed by residues 128 - 141 (chain A) in PDB entry 5HNK
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 GLU 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ASP* 3.9 11.7 - - - +
70A GLY 5.2 4.5 - - - +
71A LYS* 6.0 0.2 - - - -
72A SER* 3.6 22.3 - - - +
75A ARG* 3.7 9.6 + - - -
82A TYR* 2.6 36.8 + - - -
83A LYS* 3.6 18.9 + - - +
126A GLY 4.2 0.8 + - - -
127A VAL* 1.3 83.2 - - - +
129A ALA* 1.3 63.5 + - - +
130A ASP* 3.2 26.9 - - + +
131A ASP* 3.2 26.0 + - - +
132A MET* 3.4 9.1 + - - +
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Residues in contact with ALA 129 (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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26A ASP* 4.2 11.0 - - - +
66A LEU* 3.4 29.4 - - + +
67A GLY 4.5 6.0 + - - +
68A ASP* 3.2 20.9 + - - +
127A VAL 3.8 1.2 + - - -
128A GLU* 1.3 70.4 - - - +
130A ASP* 1.3 66.2 + - - +
132A MET* 3.4 15.6 + - + +
133A ALA* 3.0 23.2 + - - +
156A TRP* 3.9 14.3 - - + -
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Residues in contact with ASP 130 (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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26A ASP* 5.0 0.3 - - - +
68A ASP* 4.8 2.8 - - - +
75A ARG* 5.1 3.4 + - - +
128A GLU* 3.7 26.2 - - + +
129A ALA* 1.3 77.4 + - - +
131A ASP* 1.3 59.1 + - - +
133A ALA* 3.6 2.3 + - - +
134A ALA* 3.1 27.7 + - - +
153A LYS* 4.6 10.8 - - - +
155A ASP* 4.3 14.2 - - - +
156A TRP* 3.1 38.0 + - - +
159A LEU* 4.1 1.2 - - - +
262A LEU* 3.6 30.5 - - + +
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Residues in contact with ASP 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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72A SER* 4.3 1.4 + - - -
75A ARG* 2.8 44.4 + - - -
127A VAL* 4.0 9.4 - - + +
128A GLU* 3.2 21.9 + - - +
130A ASP* 1.3 74.0 - - - +
132A MET* 1.3 66.1 + - - +
134A ALA* 4.3 0.9 - - - -
135A TYR* 3.1 24.6 + - - +
262A LEU* 4.4 5.2 - - - +
265A TYR 5.2 0.9 - - - -
266A CYS* 3.5 22.5 - - - +
269A ALA* 3.6 29.5 - - + +
270A ILE* 4.1 2.7 - - + +
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Residues in contact with MET 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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66A LEU* 3.8 23.1 - - + -
67A GLY 3.7 22.9 - - - +
122A PHE* 3.9 14.8 - - - +
124A ILE* 3.7 35.2 - - + +
127A VAL* 4.1 19.5 - - + +
128A GLU 3.4 7.5 + - - +
129A ALA* 3.4 23.2 + - - +
131A ASP* 1.3 76.9 - - - +
133A ALA* 1.3 56.5 + - - +
135A TYR* 3.3 3.5 + - - +
136A ILE* 2.9 34.4 + - - +
270A ILE* 4.4 3.8 - - + -
281A PHE* 3.9 27.2 - - + -
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Residues in contact with ALA 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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24A ILE* 3.9 15.6 - - + +
66A LEU* 3.5 11.1 - - + +
129A ALA 3.0 17.9 + - - +
130A ASP 3.8 3.6 - - - +
132A MET* 1.3 72.2 - - - +
134A ALA* 1.3 66.2 + - - +
136A ILE* 3.3 4.2 + - - +
137A VAL* 3.1 27.8 + - - +
149A LEU* 4.7 1.1 - - + -
156A TRP* 3.8 28.7 - - + -
159A LEU* 4.0 11.0 - - + -
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Residues in contact with ALA 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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130A ASP 3.1 18.1 + - - +
131A ASP 3.6 0.2 - - - +
133A ALA* 1.3 76.6 - - - +
135A TYR* 1.3 61.6 + - - +
137A VAL* 3.4 6.5 + - - +
138A LYS* 3.2 21.0 + - - +
159A LEU* 3.6 29.1 - - + +
262A LEU* 4.2 10.3 - - + +
263A PRO* 4.7 3.3 - - + +
266A CYS* 3.6 26.2 - - + -
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Residues in contact with TYR 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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131A ASP 3.1 18.8 + - - +
132A MET 3.3 2.4 + - - +
134A ALA* 1.3 73.9 - - - +
136A ILE* 1.3 60.9 + - + +
138A LYS* 3.4 12.3 + - + +
139A LEU* 2.8 65.9 + - + +
266A CYS* 3.8 10.3 - - - -
267A VAL* 3.7 33.8 - - + +
270A ILE* 3.6 23.1 - - + -
278A LEU* 3.8 17.7 - - + +
281A PHE* 3.8 20.2 - + - -
282A THR* 2.7 31.6 + - - +
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Residues in contact with ILE 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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22A LEU* 4.1 5.4 - - + -
24A ILE* 3.7 19.5 - - + -
64A ILE* 4.1 26.0 - - + -
66A LEU* 4.2 9.2 - - + -
132A MET 2.9 25.3 + - - +
133A ALA* 3.3 7.2 + - - +
135A TYR* 1.3 76.8 - - - +
137A VAL* 1.3 57.4 + - - +
139A LEU* 4.4 4.7 - - - -
140A ILE* 2.9 52.9 + - + +
281A PHE* 4.0 11.7 - - + -
285A ILE* 3.6 36.8 - - + -
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Residues in contact with VAL 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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22A LEU* 5.6 1.8 - - - -
24A ILE* 4.0 17.3 - - + -
133A ALA 3.1 18.6 + - - +
134A ALA* 3.6 9.2 - - - +
136A ILE* 1.3 76.4 - - - +
138A LYS* 1.3 58.7 + - - +
141A GLY* 3.0 32.9 + - - +
147A VAL* 4.2 15.0 - - + -
149A LEU* 4.6 4.5 - - + -
159A LEU* 4.8 11.2 - - + +
161A THR* 5.3 4.7 - - + -
164A VAL* 3.8 32.1 - - + -
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Residues in contact with LYS 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 ALA 3.2 10.1 + - - +
135A TYR* 3.4 23.8 + - + +
137A VAL* 1.3 80.9 - - - +
139A LEU* 1.3 63.7 + - + +
141A GLY 4.8 0.5 + - - -
142A HIS* 5.0 3.3 + - - -
263A PRO* 3.3 26.9 + - - -
264A THR* 4.7 5.7 + - - +
266A CYS* 4.2 7.4 - - - -
267A VAL* 3.9 19.7 - - + +
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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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135A TYR* 2.8 53.3 + - + +
136A ILE* 3.8 3.8 - - - +
137A VAL 3.3 0.2 - - - -
138A LYS* 1.3 77.5 - - + +
140A ILE* 1.3 62.4 + - + +
141A GLY 3.8 0.2 - - - -
142A HIS* 3.4 20.6 - - - -
282A THR* 3.8 34.1 - - + +
285A ILE* 3.7 25.4 - - + -
286A LEU* 4.1 21.8 - - + +
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Residues in contact with ILE 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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22A LEU* 4.1 13.0 - - + -
62A THR* 5.4 0.2 - - + -
64A ILE* 4.5 6.5 - - + -
136A ILE* 2.9 33.3 + - + +
139A LEU* 1.3 79.6 - - + +
141A GLY* 1.3 64.3 + - - +
142A HIS* 3.3 8.1 - - + -
143A LEU* 3.1 20.7 + - + +
144A TYR* 3.3 29.2 - - + +
285A ILE* 3.9 31.9 - - + +
286A LEU* 4.3 14.8 - - + -
289A ALA* 3.7 35.0 - - + +
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Residues in contact with GLY 141 (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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22A LEU* 5.2 1.1 - - - -
136A ILE 3.8 1.6 + - - -
137A VAL* 3.0 25.8 + - - -
138A LYS 4.7 0.2 - - - -
139A LEU 3.8 0.8 - - - -
140A ILE* 1.3 78.3 - - - +
142A HIS* 1.3 60.4 + - - +
143A LEU 3.3 1.0 + - - -
144A TYR* 3.4 11.3 + - - +
147A VAL* 4.4 17.3 - - - +
163A LYS* 3.1 25.7 + - - -
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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