Contacts of the helix formed by residues 249 - 261 (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 SER 249 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A VAL* 3.9 28.1 - - - +
245A ASN* 2.5 24.9 + - - +
246A LEU 3.1 12.6 + - - -
247A ASN 3.4 0.2 - - - -
248A ALA* 1.3 75.1 - - - +
250A GLU* 1.3 65.4 + - - +
251A GLU 3.3 2.7 - - - -
252A LEU* 3.1 19.4 + - - +
253A LEU* 3.0 26.1 + - - +
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Residues in contact with GLU 250 (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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231A ILE* 3.8 31.1 - - + +
234A LEU* 4.3 20.3 - - + +
246A LEU 4.4 1.6 + - - -
247A ASN 4.9 2.0 + - - +
248A ALA 3.6 3.8 + - - -
249A SER* 1.3 75.9 - - - +
251A GLU* 1.3 68.8 + - + +
253A LEU* 3.4 7.0 + - - +
254A PHE* 3.1 38.8 + - + -
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Residues in contact with GLU 251 (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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248A ALA 5.4 0.4 + - - -
249A SER 3.3 0.8 - - - -
250A GLU* 1.3 83.1 - - + +
252A LEU* 1.3 58.0 + - - +
254A PHE* 3.4 7.4 + - - +
255A ARG* 3.0 42.6 + - - +
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Residues in contact with LEU 252 (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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197A ALA 5.5 0.2 - - - +
207A ARG* 3.4 40.2 - - + +
208A GLY* 3.6 34.5 - - - +
209A VAL* 4.0 14.8 - - + +
249A SER* 3.1 17.8 + - - +
251A GLU* 1.3 80.2 - - - +
253A LEU* 1.3 58.1 + - + +
255A ARG* 3.2 34.8 - - - +
256A ASN* 2.9 44.3 + - - +
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Residues in contact with LEU 253 (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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197A ALA* 4.0 6.4 - - - +
198A ILE* 3.8 41.5 - - + +
209A VAL* 4.1 11.7 - - + -
227A VAL* 4.1 21.2 - - + +
230A ILE* 4.9 9.6 - - + -
231A ILE* 4.2 17.7 - - + -
234A LEU* 5.0 2.9 - - + -
246A LEU* 3.8 25.6 - - + +
249A SER* 3.0 28.0 + - - +
250A GLU* 3.8 5.4 - - - +
252A LEU* 1.3 75.0 - - + +
254A PHE* 1.3 64.5 + - - +
256A ASN* 4.0 3.2 - - - +
257A LEU* 3.0 27.2 + - - +
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Residues in contact with PHE 254 (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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228A LEU* 4.0 24.9 - - + -
231A ILE* 3.7 37.8 - - + +
232A ASP* 6.1 0.2 - - - -
250A GLU* 3.1 38.3 + - + +
251A GLU* 3.8 7.0 - - - +
253A LEU* 1.3 76.3 - - - +
255A ARG* 1.3 63.4 + - - +
257A LEU* 3.6 7.5 + - + +
258A ILE* 3.4 29.0 + - + +
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Residues in contact with ARG 255 (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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78A HIS* 3.1 32.0 - - + +
79A LEU* 3.7 26.0 - - - +
207A ARG* 5.3 4.9 - - - +
251A GLU* 3.0 34.6 + - - +
252A LEU* 3.2 33.3 - - - +
254A PHE* 1.3 78.2 - - - +
256A ASN* 1.3 70.3 + - - +
258A ILE* 3.2 21.8 + - - +
259A LEU* 3.2 20.4 + - + +
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Residues in contact with ASN 256 (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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79A LEU* 5.6 0.2 - - - +
196A LYS 5.1 0.4 - - - +
197A ALA* 2.9 34.7 + - - +
200A GLY* 4.2 4.4 - - - -
206A ILE* 3.2 25.8 - - + +
207A ARG 2.8 27.3 + - - +
208A GLY* 4.3 1.0 - - - -
252A LEU* 2.9 32.0 + - - +
253A LEU 4.1 1.1 - - - +
255A ARG* 1.3 81.5 + - - +
257A LEU* 1.3 57.3 + - - +
259A LEU* 3.1 13.6 + - - +
260A VAL* 3.0 34.8 + - + +
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Residues in contact with LEU 257 (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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193A ILE* 3.7 29.4 - - + +
194A SER* 5.2 2.0 - - - +
197A ALA* 3.8 15.6 - - + +
227A VAL* 4.3 18.2 - - + -
228A LEU* 3.6 37.7 - - + -
253A LEU 3.0 17.7 + - - +
254A PHE* 3.6 11.4 - - + +
256A ASN* 1.3 76.3 - - - +
258A ILE* 1.3 57.5 + - + +
260A VAL* 4.0 1.1 - - - -
261A ASP* 2.9 48.0 + - + +
265A TYR* 5.3 7.2 - - + +
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Residues in contact with ILE 258 (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* 3.6 37.4 - - + -
75A ARG* 5.1 1.6 + - - -
78A HIS* 3.9 35.7 - - + +
254A PHE* 3.4 20.6 + - + +
255A ARG* 3.2 10.6 + - - +
257A LEU* 1.3 77.9 - - + +
259A LEU* 1.3 61.5 + - - +
260A VAL 3.6 0.3 + - - -
261A ASP 4.2 2.6 + - - +
265A TYR* 3.8 45.4 - - + +
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Residues in contact with LEU 259 (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* 2.8 76.5 + - + +
78A HIS* 4.1 14.1 - - + +
79A LEU* 3.8 33.2 - - + -
82A TYR* 5.0 2.5 - - + -
206A ILE* 3.9 34.0 - - + +
255A ARG* 3.2 13.8 + - + +
256A ASN* 3.1 16.6 + - - +
258A ILE* 1.3 78.4 - - + +
260A VAL* 1.3 58.7 + - + +
262A LEU* 4.3 1.2 - - - +
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Residues in contact with VAL 260 (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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158A THR* 4.0 16.1 - - - +
193A ILE* 3.5 31.8 - - + +
196A LYS* 4.1 40.2 - - + +
197A ALA* 3.9 7.4 - - - +
200A GLY* 6.2 1.8 - - - -
201A ASP* 6.5 0.9 - - + -
206A ILE* 4.9 12.6 - - + -
256A ASN* 3.0 21.9 + - + +
257A LEU* 3.8 7.0 - - - +
259A LEU* 1.3 84.4 - - + +
261A ASP* 1.3 60.9 + - - +
262A LEU* 3.0 20.5 + - - +
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Residues in contact with ASP 261 (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* 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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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