Contacts of the helix formed by residues 261 - 272 (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 ASP 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B ARG* 5.7 0.7 - - - -
190B GLU* 5.1 6.8 - - - +
193B ILE* 3.5 31.1 - - + +
257B LEU* 2.9 27.1 + - + +
258B ILE 4.2 1.8 + - - -
259B LEU 3.8 0.8 - - - -
260B VAL* 1.3 71.8 - - - +
262B LEU* 1.3 62.2 + - - +
263B PRO* 3.5 10.0 - - - +
264B THR* 2.7 37.9 + - - +
265B TYR* 3.3 31.3 + - + +
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Residues in contact with LEU 262 (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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75B ARG* 4.0 11.4 - - - +
130B ASP* 3.5 46.9 - - + +
131B ASP* 3.4 27.4 - - - +
134B ALA* 4.0 5.2 - - + -
155B ASP* 4.0 13.0 - - + +
156B TRP* 4.6 9.2 - - + -
158B THR* 3.5 18.8 - - - +
159B LEU* 4.5 13.0 - - + -
260B VAL 2.8 12.1 + - - +
261B ASP* 1.3 70.5 - - - +
263B PRO* 1.4 73.5 - - + +
265B TYR* 5.7 0.7 - - - +
266B CYS* 3.2 29.0 + - - +
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Residues in contact with PRO 263 (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* 4.8 0.7 - - + -
138B LYS* 3.5 37.6 + - - +
158B THR* 3.4 33.4 - - - +
159B LEU* 4.1 10.5 - - + -
189B VAL* 4.9 2.7 - - + -
193B ILE* 4.3 7.4 - - + -
261B ASP* 3.5 11.9 - - - +
262B LEU* 1.4 95.7 - - + +
264B THR* 1.3 61.7 + - - +
266B CYS* 3.7 9.9 - - - -
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Residues in contact with THR 264 (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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190B GLU* 5.7 1.0 + - - -
261B ASP* 2.7 33.5 + - - +
262B LEU 3.3 0.2 - - - -
263B PRO* 1.3 79.3 - - - +
265B TYR* 1.3 89.4 + - + +
266B CYS* 3.6 0.9 + - - -
267B VAL* 5.1 2.1 + - - +
268B ASP* 4.6 4.2 - - - +
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Residues in contact with TYR 265 (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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74B PHE* 3.8 26.9 - + + -
75B ARG* 6.0 3.4 - - - +
131B ASP* 4.8 1.8 - - - +
257B LEU* 4.2 4.9 - - + +
258B ILE* 3.7 50.8 - - + +
261B ASP* 3.3 29.5 + - + +
262B LEU* 4.0 1.3 - - - +
264B THR* 1.3 100.4 - - + +
266B CYS* 1.3 58.8 + - - +
267B VAL 3.3 2.7 - - - -
268B ASP* 3.2 25.1 + - - +
269B ALA* 2.9 29.9 + - - +
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Residues in contact with CYS 266 (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* 3.5 31.3 - - - +
134B ALA* 3.6 13.2 - - + -
135B TYR* 3.9 24.2 - - - -
138B LYS* 4.4 9.9 - - - -
262B LEU 3.2 14.2 + - - +
263B PRO 3.7 16.6 - - - -
264B THR 3.6 1.2 - - - -
265B TYR* 1.3 76.8 - - - +
267B VAL* 1.3 79.0 + - - +
269B ALA* 3.3 4.2 + - - +
270B ILE* 3.2 27.8 + - - +
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Residues in contact with VAL 267 (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* 3.6 34.3 - - + +
138B LYS* 6.2 0.9 - - + -
264B THR 5.1 2.3 + - - +
265B TYR 3.3 0.2 - - - -
266B CYS* 1.3 80.5 - - - +
268B ASP* 1.3 64.0 + - - +
270B ILE* 3.1 9.3 + - - +
271B ALA* 2.9 28.3 + - + +
278B LEU* 3.7 29.4 - - + -
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Residues in contact with ASP 268 (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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74B PHE* 3.7 22.7 - - + -
264B THR 4.6 4.0 + - - +
265B TYR* 3.2 33.5 + - - +
267B VAL* 1.3 79.0 - - - +
269B ALA* 1.3 57.3 + - - +
271B ALA* 3.9 7.3 - - - +
272B ALA* 3.0 28.9 + - - +
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Residues in contact with ALA 269 (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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72B SER* 4.9 1.8 + - - +
74B PHE* 3.6 31.2 + - + +
75B ARG* 4.8 0.9 - - - +
126B GLY 4.8 2.3 - - - +
127B VAL* 3.9 14.0 - - - +
131B ASP* 3.3 38.6 - - - +
265B TYR 2.9 10.8 + - - +
266B CYS 3.5 4.0 - - - +
267B VAL 3.2 0.4 - - - -
268B ASP* 1.3 78.5 - - - +
270B ILE* 1.3 61.4 + - - +
272B ALA* 3.7 11.3 - - - +
273B VAL* 4.5 2.1 + - - +
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Residues in contact with ILE 270 (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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124B ILE* 4.5 18.2 - - + -
127B VAL* 3.9 22.9 - - + -
131B ASP* 3.9 12.1 - - + +
132B MET* 4.3 4.3 - - + -
135B TYR* 3.7 39.5 - - + -
266B CYS 3.2 15.4 + - - +
267B VAL* 3.1 6.1 + - - +
269B ALA* 1.3 75.2 - - - +
271B ALA* 1.3 65.8 + - - +
272B ALA 3.3 0.5 + - - -
273B VAL* 3.4 21.8 + - - +
274B GLY 4.1 3.8 - - - +
277B VAL* 4.5 2.7 - - + +
278B LEU* 3.8 31.0 - - + +
281B PHE* 4.3 11.0 - - + -
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Residues in contact with ALA 271 (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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267B VAL* 2.9 18.0 + - + +
268B ASP* 4.0 7.9 - - - +
270B ILE* 1.3 77.5 - - - +
272B ALA* 1.3 63.9 + - - +
274B GLY* 2.9 25.4 + - - -
275B GLN* 4.1 12.3 + - - +
278B LEU* 4.0 20.1 - - + +
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Residues in contact with ALA 272 (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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73B VAL* 4.4 11.7 - - + +
74B PHE* 4.0 25.6 - - + +
77B GLU* 4.1 20.5 - - - +
268B ASP 3.0 17.8 + - - +
269B ALA 3.7 9.9 - - - +
270B ILE 3.2 0.2 - - - -
271B ALA* 1.3 75.5 - - - +
273B VAL* 1.3 58.7 - - + +
274B GLY 3.4 0.9 + - - -
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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