Contacts of the helix formed by residues 238 - 248 (chain A) in PDB entry 5HKZ
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 VAL 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ILE* 4.1 12.1 - - + -
176A GLY 5.0 0.9 - - - +
179A PHE* 3.7 31.6 - - + +
181A ILE* 3.5 33.6 - - + +
190A TRP* 3.7 34.4 - - + +
197A LYS 4.1 2.2 - - - +
198A THR* 2.9 27.8 + - + +
237A SER* 1.3 72.7 - - - +
239A PHE* 1.3 59.5 + - - +
241A PHE* 3.6 3.5 - - - +
242A ASP* 2.9 27.0 + - - +
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Residues in contact with PHE 239 (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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160A HIS 4.5 2.0 - - - -
163A ALA* 3.6 31.9 - - + -
164A GLU* 3.7 37.5 - - + -
167A GLY* 4.2 10.3 - - - -
168A ILE* 4.3 6.5 - - + -
179A PHE* 3.7 33.0 - + + -
230A LEU* 5.4 2.9 - - + -
237A SER* 3.1 8.2 + - - +
238A VAL* 1.3 79.2 - - - +
240A GLU* 1.3 72.2 + - + +
242A ASP* 3.1 5.2 + - - +
243A ILE* 3.0 46.1 + - + +
300A LEU* 3.8 23.8 - - + -
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Residues in contact with GLU 240 (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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164A GLU* 3.6 15.3 - - - +
199A ILE* 6.0 0.2 - - - +
228A ILE* 3.6 27.2 - - + +
229A ASP* 4.3 0.4 - - - -
230A LEU* 3.2 16.7 + - + +
231A THR* 2.9 27.7 + - + +
235A TYR 3.3 2.8 - - - +
236A ILE* 3.5 2.0 - - + -
237A SER* 2.9 36.6 + - - +
239A PHE* 1.3 83.4 - - + +
241A PHE* 1.3 56.2 + - - +
243A ILE* 3.3 6.6 + - - +
244A PHE* 3.0 30.1 + - - +
401A NA 2.5 31.1 - - - -
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Residues in contact with PHE 241 (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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181A ILE* 4.0 16.4 - - + -
186A ALA* 3.3 33.4 - - + -
189A PHE* 3.5 34.3 - + - -
190A TRP* 3.6 29.6 - + + -
205A PHE* 3.6 27.1 - + - -
209A LEU* 5.5 0.4 - - + -
228A ILE* 4.2 9.0 - - + -
236A ILE* 4.4 3.9 - - + +
237A SER 2.9 16.3 + - - +
238A VAL 3.6 4.0 - - - +
240A GLU* 1.3 74.1 - - - +
242A ASP* 1.3 65.4 + - - +
244A PHE* 3.4 1.1 + + - +
245A THR* 2.9 42.2 + - + +
251A TRP* 3.8 17.9 - + - -
254A LEU* 5.8 0.7 - - + -
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Residues in contact with ASP 242 (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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179A PHE* 3.9 21.8 - - + -
180A ARG 4.6 1.5 - - - +
181A ILE* 3.7 6.1 - - - +
182A THR* 2.8 46.8 + - - -
183A LYS 4.5 0.2 + - - -
238A VAL 2.9 15.7 + - - +
239A PHE* 3.4 11.2 - - + +
241A PHE* 1.3 79.0 - - - +
243A ILE* 1.3 65.4 + - - +
245A THR* 3.2 6.2 + - - -
246A ARG* 3.0 45.6 + - - +
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Residues in contact with ILE 243 (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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230A LEU* 4.0 22.4 - - + -
239A PHE* 3.0 44.9 + - + +
240A GLU 3.7 6.1 - - - +
242A ASP* 1.3 78.5 - - - +
244A PHE* 1.3 63.2 + - - +
246A ARG* 3.2 22.1 + - - +
247A LEU* 2.9 41.6 + - + +
295A LEU* 4.9 0.2 - - + -
300A LEU* 3.7 38.4 - - + +
301A GLY 3.8 11.7 - - - +
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Residues in contact with PHE 244 (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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205A PHE* 6.1 0.2 - + - -
209A LEU* 5.5 2.9 - - + -
224A LEU* 3.6 27.8 - - + -
227A THR* 3.8 19.7 - - + -
228A ILE* 3.7 37.7 - - + -
240A GLU 3.0 17.2 + - - +
241A PHE* 3.9 2.5 - + - +
243A ILE* 1.3 78.6 - - - +
245A THR* 1.3 63.5 + - + +
247A LEU* 3.3 8.1 + - + -
248A PHE* 3.0 57.6 + + - +
254A LEU* 3.8 36.1 - - + -
255A LEU* 4.2 3.4 - - + -
258A TRP* 3.8 15.9 - + + -
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Residues in contact with THR 245 (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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181A ILE* 4.7 2.3 - - - +
183A LYS* 4.0 9.8 + - - +
186A ALA* 3.6 20.2 - - + +
241A PHE* 2.9 50.1 + - + +
242A ASP* 3.2 11.4 + - - -
244A PHE* 1.3 79.9 - - + +
246A ARG* 1.3 64.0 + - - +
248A PHE 4.1 0.2 - - - -
249A GLN* 3.2 24.4 + - - +
251A TRP* 3.7 22.6 + - + -
254A LEU* 4.2 14.0 - - + +
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Residues in contact with ARG 246 (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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182A THR* 3.5 41.6 + - + +
183A LYS* 4.5 7.4 - - + -
242A ASP* 3.0 38.2 + - - +
243A ILE* 3.5 14.2 - - - +
245A THR* 1.3 75.3 - - - +
247A LEU* 1.3 65.4 + - - +
248A PHE 3.4 0.3 + - - -
249A GLN* 2.9 33.8 + - - +
300A LEU 3.4 25.5 + - - -
301A GLY* 3.9 21.3 + - - +
302A GLN* 4.2 15.6 - - - +
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Residues in contact with LEU 247 (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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227A THR* 6.3 0.4 - - + -
243A ILE* 2.9 36.1 + - + +
244A PHE* 4.5 2.7 - - - -
246A ARG* 1.3 77.9 - - - +
248A PHE* 1.3 78.4 + - + +
249A GLN* 3.5 3.5 + - - +
261A LEU* 5.0 4.2 - - - +
295A LEU* 3.5 34.3 - - + -
301A GLY* 3.5 29.2 - - - +
302A GLN 3.8 13.2 - - - +
303A TRP* 3.0 49.9 + - + +
324A LEU* 5.1 1.7 - - - +
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Residues in contact with PHE 248 (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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227A THR* 3.9 12.3 - - + -
244A PHE* 3.0 54.2 + + + +
245A THR 4.0 2.5 - - - -
247A LEU* 1.3 92.7 - - + +
249A GLN* 1.3 61.1 + - - +
250A PRO 3.9 0.2 - - - +
254A LEU* 3.7 28.2 - - + +
257A ASN* 2.8 26.0 + - - +
258A TRP* 3.5 39.9 - + + +
261A LEU* 4.2 15.7 - - + -
262A ALA* 4.1 13.2 - - + -
268A TYR* 5.0 2.5 - + - -
295A LEU* 5.5 1.1 - - + -
303A TRP* 3.6 30.5 - + - -
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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