Contacts of the helix formed by residues 261 - 272 (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 ASP 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A ARG* 5.8 0.2 - - - -
190A GLU* 5.3 3.6 - - - +
193A ILE* 3.6 30.4 - - + +
257A LEU* 2.9 29.4 + - + +
258A ILE 4.2 1.7 + - - -
259A LEU 3.8 1.2 - - - -
260A VAL* 1.3 72.1 - - - +
262A LEU* 1.3 62.4 + - - +
263A PRO* 3.5 9.7 - - - +
264A THR* 2.7 38.7 + - - +
265A TYR* 3.3 30.3 + - + +
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Residues in contact with LEU 262 (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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75A ARG* 3.4 28.5 - - - +
130A ASP* 3.6 39.0 - - + +
131A ASP* 4.4 5.4 - - - +
134A ALA* 4.3 4.5 - - + -
155A ASP* 4.6 8.1 - - + +
156A TRP* 5.3 1.6 - - + -
158A THR* 3.5 19.3 - - + +
159A LEU* 3.7 22.7 - - + -
196A LYS* 6.4 0.4 - - - -
259A LEU 4.3 2.2 - - - +
260A VAL* 3.0 27.0 + - - +
261A ASP* 1.3 70.7 - - - +
263A PRO* 1.4 65.7 - - + +
265A TYR* 3.3 1.1 + - - +
266A CYS* 2.9 37.8 + - - +
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Residues in contact with PRO 263 (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* 4.8 4.5 - - + +
138A LYS* 3.3 26.8 + - - -
158A THR* 3.6 24.7 - - - +
159A LEU* 4.4 7.8 - - + -
189A VAL* 5.2 2.0 - - + -
190A GLU* 5.9 2.0 - - - +
193A ILE* 4.3 9.6 - - + -
261A ASP* 3.5 11.7 - - - +
262A LEU* 1.4 95.6 - - + +
264A THR* 1.3 59.2 + - - +
266A CYS* 3.6 9.6 - - - -
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Residues in contact with THR 264 (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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138A LYS* 4.7 6.4 + - - +
261A ASP* 2.7 33.1 + - - +
262A LEU 3.3 0.8 - - - -
263A PRO* 1.3 79.0 - - - +
265A TYR* 1.3 87.5 + - + +
266A CYS 3.6 0.8 + - - -
267A VAL* 5.0 3.5 + - - +
268A ASP* 4.9 2.8 - - - +
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Residues in contact with TYR 265 (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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74A PHE* 3.9 28.4 - + + -
75A ARG* 6.3 0.7 - - - +
131A ASP* 5.2 1.1 - - - -
257A LEU* 4.3 7.4 - - + +
258A ILE* 3.8 48.2 - - + +
261A ASP* 3.3 28.7 + - + +
262A LEU* 3.8 0.9 - - - -
264A THR* 1.3 100.8 - - + +
266A CYS* 1.3 66.1 + - - +
267A VAL 3.2 3.4 - - - -
268A ASP* 3.2 26.4 + - - +
269A ALA* 2.9 22.6 + - - +
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Residues in contact with CYS 266 (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* 3.5 34.0 - - - +
134A ALA* 3.6 12.1 - - + -
135A TYR* 3.8 24.5 - - + -
138A LYS* 4.2 13.7 - - - -
262A LEU 2.9 15.1 + - - +
263A PRO* 3.6 19.7 - - - -
264A THR 3.6 0.2 - - - -
265A TYR* 1.3 76.5 - - - +
267A VAL* 1.3 67.1 + - - +
269A ALA* 3.3 2.5 + - - +
270A ILE* 3.2 29.5 + - - +
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Residues in contact with VAL 267 (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* 3.7 33.0 - - + +
138A LYS* 3.9 23.8 - - + +
264A THR 5.0 3.5 + - - +
265A TYR 3.2 0.4 - - - -
266A CYS* 1.3 74.2 - - - +
268A ASP* 1.3 65.9 + - - +
270A ILE* 3.2 7.1 + - - +
271A ALA* 2.9 27.5 + - + +
278A LEU* 3.9 23.4 - - + +
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Residues in contact with ASP 268 (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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74A PHE* 3.7 20.8 - - + -
264A THR 4.9 2.7 - - - +
265A TYR* 3.2 31.9 + - - +
267A VAL* 1.3 81.6 - - - +
269A ALA* 1.3 57.5 + - - +
271A ALA* 3.2 9.2 + - - +
272A ALA* 2.8 31.4 + - - +
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Residues in contact with ALA 269 (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* 5.4 0.2 - - - +
74A PHE* 3.7 32.1 + - + +
126A GLY 4.9 2.3 - - - +
127A VAL* 4.0 13.5 - - + +
131A ASP* 3.6 31.9 - - - +
265A TYR 2.9 13.4 + - - +
266A CYS 3.5 9.6 - - - +
267A VAL 3.2 0.2 - - - -
268A ASP* 1.3 78.5 - - - +
270A ILE* 1.3 60.6 + - - +
272A ALA* 3.6 12.8 - - - +
273A VAL* 4.3 1.9 + - - +
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Residues in contact with ILE 270 (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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124A ILE* 5.0 4.3 - - + -
127A VAL* 4.0 28.0 - - + -
131A ASP* 4.1 8.3 - - + +
132A MET* 4.4 3.6 - - + -
135A TYR* 3.6 40.6 - - + -
266A CYS 3.2 16.0 + - - +
267A VAL 3.8 4.9 - - - +
269A ALA* 1.3 73.4 - - - +
271A ALA* 1.3 66.3 + - - +
272A ALA 3.2 0.5 + - - -
273A VAL* 3.2 21.3 + - - +
274A GLY 3.9 4.0 - - - +
277A VAL* 4.7 7.6 - - + +
278A LEU* 3.8 31.9 - - + +
281A PHE* 4.1 19.5 - - + -
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Residues in contact with ALA 271 (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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267A VAL* 2.9 18.8 + - + +
268A ASP* 3.5 10.5 - - - +
270A ILE* 1.3 77.2 - - - +
272A ALA* 1.3 55.8 + - - +
274A GLY* 3.0 29.7 + - - -
275A GLN* 4.0 13.3 + - - +
278A LEU* 3.8 18.8 - - + +
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Residues in contact with ALA 272 (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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73A VAL* 4.0 17.1 - - + +
74A PHE* 4.2 27.4 - - + +
77A GLU* 4.4 11.1 - - - +
268A ASP 2.8 16.3 + - - +
269A ALA 3.6 10.5 - - - +
270A ILE 3.1 1.0 - - - -
271A ALA* 1.3 75.5 - - - +
273A VAL* 1.3 59.1 + - - +
274A GLY 3.4 0.4 + - - -
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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