Contacts of the helix formed by residues 234 - 251 (chain A) in PDB entry 5KAL
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 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ALA 5.4 0.9 - - - -
9A GLY* 3.1 17.1 - - - -
10A ARG 5.0 0.2 - - - -
13A VAL* 3.9 17.2 - - - +
230A PRO* 4.3 5.8 - - - +
232A ASP* 3.1 8.6 + - - -
233A GLU* 1.3 79.7 - - - +
235A LEU* 1.3 65.6 + - - +
236A GLU 3.4 1.8 - - - -
237A LEU* 3.3 10.0 + - - +
238A GLY 3.1 19.1 + - - -
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Residues in contact with LEU 235 (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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5A PRO* 4.4 11.4 - - + +
6A ALA* 3.9 35.2 - - + +
232A ASP* 3.6 21.5 + - + +
233A GLU 3.7 1.6 - - - -
234A GLY* 1.3 77.1 - - - +
236A GLU* 1.3 65.6 + - - +
238A GLY* 3.2 0.9 + - - -
239A THR* 3.0 30.5 + - - +
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Residues in contact with GLU 236 (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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204A HIS* 5.4 6.4 + - - -
232A ASP* 3.3 15.9 + - - +
235A LEU* 1.3 77.9 - - - +
237A LEU* 1.3 64.6 + - - +
239A THR* 3.4 10.6 + - - +
240A GLN* 2.9 60.6 + - - +
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Residues in contact with LEU 237 (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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9A GLY* 4.9 0.7 - - - +
12A LEU* 3.7 32.5 - - + -
13A VAL* 4.7 13.9 - - + +
16A PHE* 5.6 4.3 - - + -
163A TRP* 4.5 19.7 - - + -
164A LEU* 4.2 25.8 - - + +
167A SER* 4.7 7.9 - - - +
230A PRO* 5.5 8.1 - - + -
234A GLY* 3.3 14.6 + - - +
235A LEU 3.2 0.8 - - - -
236A GLU* 1.3 79.4 - - - +
238A GLY* 1.3 63.1 + - - +
240A GLN* 3.1 10.2 + - - +
241A VAL* 2.9 38.3 + - + +
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Residues in contact with GLY 238 (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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5A PRO* 3.6 23.6 - - - -
8A VAL* 4.1 13.2 - - - -
9A GLY* 4.0 9.3 - - - -
12A LEU* 4.9 0.2 - - - -
234A GLY 3.1 11.7 + - - -
237A LEU* 1.3 76.0 - - - +
239A THR* 1.3 63.1 + - - +
241A VAL* 3.2 3.8 + - - +
242A LEU* 3.0 28.6 + - - +
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Residues in contact with THR 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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5A PRO* 3.6 23.6 - - + +
235A LEU* 3.0 23.3 + - - +
236A GLU* 3.6 14.0 + - - +
238A GLY* 1.3 73.7 - - - +
240A GLN* 1.3 61.1 + - + +
242A LEU* 3.5 3.1 + - - +
243A ASP* 2.9 32.7 + - + +
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Residues in contact with GLN 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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160A PRO* 5.4 2.1 - - - +
161A CYS* 4.3 25.8 - - - +
164A LEU* 4.0 32.9 + - + +
198A TYR* 3.6 14.3 + - + +
199A LEU* 5.6 3.5 - - + +
204A HIS* 5.3 12.2 + - + +
236A GLU* 2.9 53.5 + - - +
237A LEU* 3.1 9.8 + - - +
239A THR* 1.3 75.9 - - + +
241A VAL* 1.3 58.2 + - - +
243A ASP* 3.5 0.8 + - - -
244A PHE* 2.9 31.1 + - - +
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Residues in contact with VAL 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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8A VAL* 4.7 8.3 - - + -
12A LEU* 4.0 13.2 - - + -
164A LEU* 3.7 17.9 - - + -
167A SER* 5.3 1.6 - - - -
168A ILE* 5.4 2.9 - - + -
237A LEU* 2.9 36.4 + - + +
238A GLY* 3.2 8.0 + - - +
240A GLN* 1.3 75.1 - - - +
242A LEU* 1.3 70.3 + - + +
244A PHE* 3.1 6.0 + - - +
245A LEU* 3.0 35.8 + - + +
328A ALA* 5.9 0.9 - - - -
329A LEU* 3.9 33.2 - - + -
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Residues in contact with LEU 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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3A PRO 4.8 5.2 - - - +
4A SER 4.5 1.3 - - - -
5A PRO* 3.8 36.8 - - + -
8A VAL* 4.3 22.4 - - + -
238A GLY 3.0 21.9 + - - +
239A THR* 4.0 3.4 - - - +
241A VAL* 1.3 87.4 - - + +
243A ASP* 1.3 64.1 + - - +
245A LEU* 3.2 6.1 + - + +
246A HIS* 2.9 24.5 + - - +
325A ARG* 4.3 29.6 - - + +
328A ALA* 6.1 0.9 - - - -
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Residues in contact with ASP 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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198A TYR* 2.8 20.9 + - - +
202A ARG* 2.9 38.6 + - - +
204A HIS* 5.7 1.6 - - - -
239A THR* 2.9 23.0 + - + +
240A GLN* 4.6 0.7 - - - -
242A LEU* 1.3 76.3 - - - +
244A PHE* 1.3 57.8 + - - +
246A HIS* 3.4 10.1 + - - +
247A PHE* 2.9 28.2 + - - +
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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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164A LEU* 4.9 9.4 - - + -
168A ILE* 4.1 29.2 - - + -
171A TRP* 5.8 2.2 - + - -
191A PHE* 6.0 2.5 - + - -
194A MET* 4.9 7.4 - - + -
195A VAL* 4.2 31.6 - - + -
198A TYR* 3.6 35.6 + + + -
240A GLN 2.9 18.8 + - - +
241A VAL* 3.3 7.4 - - + +
243A ASP* 1.3 76.7 - - - +
245A LEU* 1.3 82.3 + - + +
247A PHE* 3.0 4.2 + - - +
248A PHE* 3.0 54.6 + + - -
321A LEU* 5.0 7.9 - - + -
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Residues in contact with LEU 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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168A ILE* 5.7 1.1 - - + -
171A TRP* 5.1 2.5 - - + -
241A VAL* 3.0 32.6 + - + +
242A LEU* 3.7 8.7 - - + +
244A PHE* 1.3 87.2 - - + +
246A HIS* 1.3 63.6 + - - +
248A PHE* 3.3 3.6 + - - +
249A LEU* 3.0 32.5 + - + +
321A LEU* 3.7 41.8 - - + +
324A ALA* 3.8 15.7 - - + -
325A ARG* 3.6 42.0 - - + +
329A LEU* 4.9 7.2 - - + -
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Residues in contact with HIS 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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202A ARG* 4.9 0.2 - - - -
242A LEU 2.9 17.1 + - - +
243A ASP* 3.7 13.5 - - - +
245A LEU* 1.3 75.9 - - - +
247A PHE* 1.3 64.0 + - - +
249A LEU* 3.1 5.7 + - - +
250A HIS* 2.9 56.6 + + + +
251A GLU* 3.3 29.4 + - + +
325A ARG* 5.0 9.4 + - - +
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Residues in contact with PHE 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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197A TYR* 4.1 21.8 - + - -
198A TYR* 3.9 25.4 - + + -
201A GLN* 4.0 31.0 - - + -
202A ARG* 3.7 19.7 - - - +
243A ASP 2.9 18.1 + - - +
244A PHE 3.4 4.3 - - - +
246A HIS* 1.3 76.7 - - - +
248A PHE* 1.3 79.0 + + - +
251A GLU* 3.1 48.8 + - + +
252A PHE* 3.0 42.7 + + + -
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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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194A MET* 3.7 31.4 - - + -
197A TYR* 4.5 6.7 - + - -
198A TYR* 3.9 12.8 - - + -
244A PHE* 3.0 56.6 + + - +
245A LEU 3.7 2.9 - - - +
247A PHE* 1.3 93.3 - + - +
249A LEU* 1.3 59.0 + - - +
252A PHE* 4.1 23.7 - + + +
259A ILE* 3.9 26.5 - - + -
293A TRP* 4.2 25.6 - + + -
321A LEU* 3.9 27.8 - - + +
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Residues in contact with LEU 249 (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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245A LEU* 3.0 22.0 + - + +
246A HIS 3.1 2.4 + - - +
248A PHE* 1.3 79.6 - - - +
250A HIS* 1.3 79.7 + - + +
251A GLU 3.9 0.2 - - - -
252A PHE 5.1 4.8 - - - +
318A ARG* 4.0 17.2 - - + +
321A LEU* 3.6 50.5 - - + +
322A GLU* 3.9 27.6 - - + +
325A ARG* 4.2 25.4 - - - +
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Residues in contact with HIS 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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246A HIS* 2.9 44.8 + + + +
249A LEU* 1.3 97.2 + - + +
251A GLU* 1.3 63.3 + - + +
252A PHE 4.0 2.2 - - - -
325A ARG* 3.9 26.9 + - - -
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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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202A ARG* 2.7 42.7 + - - -
246A HIS* 3.3 27.6 + - + +
247A PHE* 3.1 28.6 + - + +
250A HIS* 1.3 82.5 - - + +
252A PHE* 1.3 65.0 + - - +
253A ASP* 3.5 5.5 + - - +
257A GLN* 4.1 5.7 + - - +
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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