Contacts of the helix formed by residues 274 - 291 (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 GLY 274 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B ILE 4.1 4.0 - - - +
271B ALA 2.9 12.4 + - - +
272B ALA 3.4 1.8 + - - -
273B VAL* 1.3 80.1 - - - +
275B GLN* 1.3 65.6 + - - -
276B ASP* 3.2 4.0 - - - -
277B VAL* 3.2 17.3 + - - +
278B LEU* 3.2 10.4 + - - +
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Residues in contact with GLN 275 (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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271B ALA* 4.1 12.9 + - - +
274B GLY* 1.3 70.8 - - - -
276B ASP* 1.3 61.6 + - - +
278B LEU* 3.3 26.7 + - - +
279B ASP* 3.0 57.0 + - - +
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Residues in contact with ASP 276 (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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274B GLY* 3.2 1.3 - - - -
275B GLN* 1.3 80.1 - - - +
277B VAL* 1.3 59.8 + - + +
279B ASP* 3.6 15.3 - - - +
280B LYS* 3.1 29.3 + - - +
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 3.4 40.6 - - + -
125B ARG* 6.1 3.1 - - - +
270B ILE* 4.5 4.3 - - + -
273B VAL* 3.7 28.7 - - + +
274B GLY* 3.2 11.2 + - - +
276B ASP* 1.3 76.1 - - + +
278B LEU* 1.3 65.2 + - - +
280B LYS* 3.4 6.5 + - - +
281B PHE* 3.0 23.4 + - - +
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Residues in contact with LEU 278 (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* 3.8 29.6 - - + +
267B VAL* 3.7 26.7 - - + -
270B ILE* 3.8 31.8 - - + +
271B ALA* 4.0 20.0 - - + -
274B GLY 3.2 7.9 + - - +
275B GLN* 3.5 26.7 - - - +
277B VAL* 1.3 80.1 - - - +
279B ASP* 1.3 54.9 + - - +
281B PHE* 3.8 1.2 - - + +
282B THR* 2.7 41.2 + - - +
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Residues in contact with ASP 279 (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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275B GLN* 3.0 41.4 + - - +
276B ASP* 3.6 21.3 - - - +
278B LEU* 1.3 77.3 - - - +
280B LYS* 1.3 63.1 + - - +
282B THR* 3.4 6.0 + - - -
283B LYS* 3.1 39.1 + - - +
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Residues in contact with LYS 280 (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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276B ASP 3.1 15.1 + - - +
277B VAL* 3.9 5.8 - - - +
278B LEU 3.4 0.2 - - - -
279B ASP* 1.3 78.5 - - - +
281B PHE* 1.3 58.0 + - - +
283B LYS* 3.3 16.0 + - - +
284B ASP* 2.9 55.3 + - - +
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Residues in contact with PHE 281 (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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122B PHE* 3.9 30.1 - + + -
124B ILE* 3.6 22.2 - - + -
132B MET* 3.8 32.3 - - + -
135B TYR* 3.8 32.3 - + - -
136B ILE* 3.8 19.3 - - + -
270B ILE* 4.3 9.0 - - + -
277B VAL 3.0 18.9 + - - +
278B LEU* 3.8 4.9 - - - +
280B LYS* 1.3 72.0 - - - +
282B THR* 1.3 65.8 + - - +
284B ASP* 3.4 5.9 + - - +
285B ILE* 3.0 60.1 + - + +
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Residues in contact with THR 282 (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* 2.7 31.8 + - - +
139B LEU* 4.1 17.8 - - + +
278B LEU* 2.7 26.0 + - - +
279B ASP* 3.6 7.3 - - - -
280B LYS 3.3 0.2 - - - -
281B PHE* 1.3 78.7 - - - +
283B LYS* 1.3 62.2 + - + +
285B ILE* 3.4 1.7 + - - +
286B LEU* 3.1 44.0 + - + +
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Residues in contact with LYS 283 (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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279B ASP* 3.1 36.3 + - - +
280B LYS* 3.7 12.2 - - - +
282B THR* 1.3 73.9 - - + +
284B ASP* 1.3 67.5 + - - +
286B LEU* 3.4 9.0 + - + +
287B GLU* 3.0 25.3 + - - +
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Residues in contact with ASP 284 (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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122B PHE* 3.8 29.6 - - + -
280B LYS* 2.9 54.9 + - - +
281B PHE* 3.7 6.5 - - - +
283B LYS* 1.3 76.4 - - - +
285B ILE* 1.3 62.2 + - - +
287B GLU* 3.4 6.7 + - - +
288B ILE* 3.2 28.5 + - - +
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Residues in contact with ILE 285 (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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64B ILE* 4.4 8.3 - - + -
122B PHE* 3.8 26.7 - - + -
136B ILE* 3.8 22.9 - - + -
139B LEU* 3.8 24.2 - - + -
140B ILE* 3.8 29.6 - - + +
281B PHE* 3.0 54.6 + - + +
284B ASP* 1.3 73.2 - - - +
286B LEU* 1.3 65.7 + - - +
288B ILE* 3.2 14.9 + - + +
289B ALA* 3.2 12.5 + - - +
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Residues in contact with LEU 286 (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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139B LEU* 4.2 20.6 - - + +
140B ILE* 4.2 20.6 - - + -
143B LEU* 6.3 0.9 - - + -
282B THR* 3.1 33.8 + - + +
283B LYS* 3.4 7.6 + - + +
285B ILE* 1.3 75.2 - - - +
287B GLU* 1.3 61.2 + - - +
289B ALA* 3.4 5.2 + - + +
290B GLU* 3.4 25.6 + - - +
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Residues in contact with GLU 287 (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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283B LYS 3.0 18.1 + - - +
284B ASP* 3.6 6.6 - - - +
285B ILE 3.2 0.2 - - - -
286B LEU* 1.3 73.7 - - - +
288B ILE* 1.3 69.6 + - - +
290B GLU* 3.3 17.5 + - + +
291B GLN* 2.9 39.9 + - - +
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Residues in contact with ILE 288 (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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62B THR* 3.6 31.7 + - + +
64B ILE* 4.3 11.0 - - + -
120B PRO* 3.8 38.6 - - + -
122B PHE* 4.6 12.8 - - + -
140B ILE* 5.5 0.9 - - + -
144B TYR* 4.7 1.7 + - - -
284B ASP 3.2 20.6 + - - +
285B ILE* 3.2 12.3 + - + +
287B GLU* 1.3 77.9 - - - +
289B ALA* 1.3 62.5 + - - +
291B GLN* 3.1 42.0 + - - +
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Residues in contact with ALA 289 (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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61B ARG* 5.3 6.1 + - - -
140B ILE* 3.7 31.6 - - + +
143B LEU* 3.8 22.3 - - + +
144B TYR* 3.7 23.5 + - - +
285B ILE 3.2 2.6 + - - -
286B LEU* 3.7 9.2 - - + +
287B GLU 3.3 0.4 - - - -
288B ILE* 1.3 79.4 - - - +
290B GLU* 1.3 64.1 + - - +
291B GLN 3.6 2.8 + - - -
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Residues in contact with GLU 290 (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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143B LEU* 5.4 5.9 - - - +
286B LEU 3.4 14.9 + - - +
287B GLU* 3.3 12.1 + - + +
288B ILE 3.2 0.8 - - - -
289B ALA* 1.3 78.8 - - - +
291B GLN* 1.3 63.7 + - + +
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Residues in contact with GLN 291 (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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62B THR* 6.0 1.3 - - - -
120B PRO* 5.4 4.4 - - - +
287B GLU* 2.9 42.8 + - - +
288B ILE* 3.1 37.0 + - - +
289B ALA 4.6 2.9 - - - -
290B GLU* 1.3 81.3 - - - +
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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