Contacts of the helix formed by residues 128 - 141 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASP* 5.7 7.0 - - + +
70B GLY 4.2 8.0 - - - +
71B LYS* 4.1 3.1 - - - -
72B SER* 3.5 27.3 + - - +
75B ARG* 3.5 14.1 + - - +
82B TYR* 2.7 38.4 + - - -
83B LYS* 3.1 23.5 + - - +
126B GLY 4.4 0.4 + - - -
127B VAL* 1.3 81.7 - - - +
129B ALA* 1.3 65.6 + - - +
130B ASP* 3.2 17.1 - - + +
131B ASP* 3.1 24.8 + - - +
132B MET* 3.5 9.0 + - - +
153B LYS* 5.1 0.9 + - - -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ASP* 3.8 21.8 - - - +
66B LEU* 3.5 23.8 - - + +
67B GLY 4.4 6.7 + - - +
68B ASP* 4.1 16.1 + - - +
127B VAL 4.0 1.0 + - - -
128B GLU* 1.3 73.2 - - - +
130B ASP* 1.3 65.2 + - - +
132B MET* 3.4 14.7 + - - +
133B ALA* 2.9 26.2 + - - +
156B TRP* 4.1 6.7 - - + -
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Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASP* 4.9 0.2 - - - +
75B ARG* 4.9 6.3 + - - +
128B GLU* 4.6 14.3 - - + +
129B ALA* 1.3 76.8 + - - +
131B ASP* 1.3 61.5 + - - +
133B ALA* 3.4 2.3 + - - +
134B ALA* 3.1 23.2 + - - +
153B LYS* 2.6 32.6 + - - +
155B ASP* 3.9 5.9 - - - +
156B TRP* 3.1 31.8 + - - +
159B LEU* 4.9 0.3 - - - +
262B LEU* 3.5 31.2 - - + +
101Y MG 3.9 13.2 - - - -
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Residues in contact with ASP 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER* 4.3 1.4 + - - -
75B ARG* 2.8 43.4 + - - -
127B VAL* 4.3 8.4 - - + +
128B GLU* 3.1 20.5 + - - +
130B ASP* 1.3 73.0 - - - +
132B MET* 1.3 64.8 + - - +
134B ALA 3.5 0.2 + - - -
135B TYR* 3.1 25.3 + - - +
262B LEU* 3.4 11.4 - - - +
265B TYR 4.6 0.7 - - - +
266B CYS* 3.5 27.4 + - - +
269B ALA* 3.3 25.0 - - + +
270B ILE* 3.9 3.3 - - + +
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Residues in contact with MET 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LEU* 4.0 13.9 - - + -
67B GLY 3.7 23.6 - - - +
122B PHE* 3.8 20.2 - - - +
124B ILE* 3.9 35.9 - - + +
127B VAL* 4.0 18.8 - - + +
128B GLU 3.5 2.6 + - - +
129B ALA* 3.4 22.6 + - - +
131B ASP* 1.3 77.7 - - - +
133B ALA* 1.3 56.3 + - - +
135B TYR* 3.4 2.1 + - - +
136B ILE* 2.9 35.6 + - - +
270B ILE* 4.3 4.0 - - + -
281B PHE* 3.8 32.9 - - + -
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Residues in contact with ALA 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.1 10.7 - - + +
66B LEU* 3.7 10.5 - - + +
129B ALA 2.9 17.4 + - - +
130B ASP 3.6 4.5 - - - +
132B MET* 1.3 72.5 - - - +
134B ALA* 1.3 67.7 + - - +
136B ILE* 3.3 4.1 + - - +
137B VAL* 3.0 30.9 + - - +
149B LEU* 5.0 1.1 - - + -
156B TRP* 3.6 34.3 - - + -
159B LEU* 4.3 5.6 - - + -
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ASP 3.1 16.4 + - - +
133B ALA* 1.3 76.9 - - - +
135B TYR* 1.3 63.0 + - - +
137B VAL* 3.6 3.7 + - - +
138B LYS* 3.4 27.2 + - - +
159B LEU* 3.6 33.8 - - + +
262B LEU* 4.0 11.2 - - + +
263B PRO* 4.8 1.8 - - + -
266B CYS* 3.6 24.9 - - + -
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Residues in contact with TYR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ASP 3.1 18.1 + - - +
132B MET 3.7 3.6 - - - +
134B ALA* 1.3 75.1 - - - +
136B ILE* 1.3 58.3 + - - +
138B LYS* 3.4 8.6 + - + +
139B LEU* 3.0 60.0 + - + +
266B CYS* 3.9 9.1 - - - -
267B VAL* 3.6 29.3 - - + +
270B ILE* 3.7 20.6 - - + -
278B LEU* 3.8 19.7 - - + +
281B PHE* 3.8 20.9 - + - -
282B THR* 2.7 37.6 + - - +
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 4.1 2.9 - - + -
24B ILE* 3.8 19.5 - - + -
64B ILE* 4.0 23.8 - - + -
66B LEU* 4.0 22.2 - - + -
132B MET 2.9 26.8 + - - +
133B ALA* 3.7 4.7 - - - +
135B TYR* 1.3 74.1 - - - +
137B VAL* 1.3 63.1 + - - +
139B LEU* 3.1 6.2 + - - -
140B ILE* 3.0 43.5 + - + +
281B PHE* 3.8 17.5 - - + -
285B ILE* 3.8 28.5 - - + -
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 5.3 0.4 - - - -
24B ILE* 3.6 20.0 - - + -
133B ALA 3.0 22.5 + - - +
134B ALA* 3.7 6.5 - - - +
135B TYR 3.3 0.2 - - - -
136B ILE* 1.3 76.5 - - - +
138B LYS* 1.3 62.4 + - + +
141B GLY* 2.8 33.1 + - - +
142B HIS* 4.5 3.6 + - - -
147B VAL* 4.2 10.5 - - + -
149B LEU* 4.2 14.1 - - + -
159B LEU* 4.6 15.5 - - + +
161B THR* 6.2 1.1 - - + -
164B VAL* 3.9 28.7 - - + -
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B ALA* 3.4 15.8 + - - +
135B TYR* 3.8 10.3 - - + +
136B ILE 3.3 0.4 - - - -
137B VAL* 1.3 84.4 - - + +
139B LEU* 1.3 62.9 + - + +
142B HIS* 4.4 18.0 + - - -
159B LEU* 6.0 1.6 - - - -
263B PRO* 3.5 44.0 + - - +
266B CYS* 4.4 10.8 - - - -
267B VAL* 6.2 0.9 - - + -
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TYR* 3.0 60.1 + - + +
136B ILE* 3.1 5.6 + - - +
138B LYS* 1.3 80.6 - - + +
140B ILE* 1.3 65.9 + - + +
142B HIS* 6.2 0.2 - - - -
143B LEU* 5.4 1.4 - - - +
282B THR* 4.1 21.8 - - + +
285B ILE* 3.8 28.5 - - + -
286B LEU* 4.2 20.1 - - + +
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Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 3.9 19.1 - - + -
62B THR* 5.5 0.4 - - + -
64B ILE* 4.2 10.8 - - + -
136B ILE* 3.0 26.5 + - + +
139B LEU* 1.3 82.1 - - - +
141B GLY* 1.3 66.1 + - - +
142B HIS* 3.2 2.9 - - - -
143B LEU* 3.0 23.7 + - + +
144B TYR* 3.2 25.3 - - + +
285B ILE* 3.8 30.7 - - + +
286B LEU* 4.2 16.6 - - + -
289B ALA* 3.7 31.9 - - + +
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Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU* 4.5 3.1 - - - -
136B ILE 3.8 0.4 + - - -
137B VAL* 2.8 23.4 + - - -
138B LYS 4.6 0.2 - - - -
139B LEU 3.9 0.2 - - - -
140B ILE* 1.3 78.0 - - - +
142B HIS* 1.3 56.9 + - - +
144B TYR* 3.1 30.4 + - - +
147B VAL* 3.8 27.0 - - - +
163B LYS* 4.1 5.3 + - - -
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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