Contacts of the helix formed by residues 310 - 328 (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 THR 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A HIS* 3.7 26.2 - - + +
292A GLN* 4.6 1.3 - - - -
308A ASN 3.3 9.7 + - - +
309A VAL* 1.3 76.5 - - - +
311A PRO* 1.3 70.5 - - - +
312A LEU* 3.2 10.6 + - - +
313A LYS* 3.2 32.1 + - + +
314A ARG* 2.9 27.8 + - - +
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Residues in contact with PRO 311 (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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290A HIS* 4.7 9.4 - - + +
292A GLN* 4.3 21.1 - - + +
310A THR* 1.3 88.7 - - - +
312A LEU* 1.3 56.1 + - - +
314A ARG* 3.1 35.8 + - + +
315A ASP* 3.0 25.6 + - - +
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Residues in contact with LEU 312 (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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310A THR* 3.1 10.6 + - - +
311A PRO* 1.3 78.9 - - - +
313A LYS* 1.3 65.9 + - + +
315A ASP* 3.0 11.9 + - + +
316A PHE* 2.9 64.8 + - + -
319A ARG* 5.8 0.4 - - - +
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Residues in contact with LYS 313 (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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177A LEU* 5.4 1.6 - - - +
183A GLY* 3.3 29.4 + - - +
184A GLY 4.8 4.0 - - - -
185A SER* 3.7 35.5 + - - +
308A ASN 3.8 14.6 - - - +
309A VAL* 4.1 5.9 - - + +
310A THR* 3.2 26.0 + - - +
312A LEU* 1.3 81.4 - - + +
314A ARG* 1.3 56.5 + - - +
316A PHE* 3.6 22.2 - - + +
317A LEU* 2.9 28.4 + - - +
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Residues in contact with ARG 314 (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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254A SER* 4.8 12.1 - - - -
255A ASP* 5.7 2.8 + - - -
292A GLN* 3.3 38.4 + - + +
293A TRP* 4.5 20.9 - - + -
309A VAL* 3.8 10.9 - - + +
310A THR 2.9 14.2 + - - +
311A PRO* 3.1 43.4 + - + +
313A LYS* 1.3 73.6 - - - +
315A ASP* 1.3 70.5 + - - +
317A LEU* 3.1 8.6 + - - +
318A ARG* 3.0 50.2 + - - +
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Residues in contact with ASP 315 (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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311A PRO 3.0 13.5 + - - +
312A LEU* 3.4 13.0 - - + +
314A ARG* 1.3 79.8 - - - +
316A PHE* 1.3 65.4 + - + +
318A ARG* 2.8 35.5 + - - +
319A ARG* 2.4 63.7 + - - +
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Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 4.8 5.6 - - + -
183A GLY 6.1 0.9 - - - -
312A LEU* 2.9 53.2 + - + -
313A LYS* 3.6 24.7 - - + +
315A ASP* 1.3 74.8 - - - +
317A LEU* 1.3 63.9 + - - +
319A ARG* 3.0 31.8 + - - +
320A HIS* 2.9 36.8 + + + -
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Residues in contact with LEU 317 (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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171A TRP* 5.1 0.7 - - + -
177A LEU* 4.1 33.4 - - + +
186A ILE* 4.6 14.1 - - + -
191A PHE* 5.2 10.5 - - + -
194A MET* 5.8 2.2 - - - -
293A TRP* 3.7 50.9 - - + +
309A VAL* 5.7 2.2 - - + -
313A LYS 2.9 15.5 + - - +
314A ARG* 3.1 11.9 + - - +
316A PHE* 1.3 76.1 - - - +
318A ARG* 1.3 64.7 + - - +
320A HIS* 3.3 0.9 + - - +
321A LEU* 2.9 48.3 + - + +
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Residues in contact with ARG 318 (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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249A LEU* 4.1 15.7 - - + -
314A ARG* 3.0 45.8 + - - +
315A ASP* 2.8 39.8 + - - +
317A LEU* 1.3 76.5 - - - +
319A ARG* 1.3 65.6 + - - +
321A LEU* 3.2 11.9 + - + +
322A GLU* 3.0 40.8 + - - +
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Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU* 5.8 0.2 - - - +
315A ASP* 2.4 56.0 + - - +
316A PHE* 3.2 41.5 - - - +
318A ARG* 1.3 76.9 - - + +
320A HIS* 1.3 61.8 + - + +
322A GLU* 3.1 16.7 + - - +
323A LYS* 2.9 36.2 + - + +
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Residues in contact with HIS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TRP* 3.7 17.2 + - + -
175A THR* 3.6 43.9 + - + +
177A LEU* 4.1 22.9 - - + -
316A PHE* 2.9 32.7 + - + +
317A LEU 3.9 3.4 - - - +
319A ARG* 1.3 76.0 - - + +
321A LEU* 1.3 66.2 + - - +
323A LYS* 3.3 17.5 + - + +
324A ALA* 2.9 26.3 + - - +
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Residues in contact with LEU 321 (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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171A TRP* 3.9 18.6 - - + -
244A PHE* 5.0 9.6 - - + -
245A LEU* 3.7 32.5 - - + +
248A PHE* 3.9 35.0 - - + +
249A LEU* 3.6 25.5 - - + +
293A TRP* 5.1 5.2 - - + -
317A LEU* 2.9 42.2 + - + +
318A ARG* 3.5 8.7 - - - +
320A HIS* 1.3 76.0 - - - +
322A GLU* 1.3 62.3 + - - +
324A ALA* 3.5 11.0 + - - +
325A ARG* 4.0 3.8 + - - +
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Residues in contact with GLU 322 (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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249A LEU* 3.9 23.0 - - + +
318A ARG* 3.0 35.6 + - - +
319A ARG* 3.4 17.9 - - - +
321A LEU* 1.3 78.6 - - - +
323A LYS* 1.3 62.0 + - + +
325A ARG* 3.2 33.5 + - - +
326A ASP* 4.0 6.1 - - - +
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Residues in contact with LYS 323 (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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319A ARG* 2.9 21.6 + - + +
320A HIS* 3.3 18.8 + - + +
322A GLU* 1.3 76.9 - - + +
324A ALA* 1.3 64.4 + - - +
325A ARG 3.3 0.7 + - - -
326A ASP* 3.3 16.1 + - - +
327A THR* 3.6 24.2 + - - +
330A LEU* 5.0 14.5 - - - +
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Residues in contact with ALA 324 (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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171A TRP* 4.0 26.7 - - + +
245A LEU* 3.8 19.8 - - + +
320A HIS 2.9 18.0 + - - +
321A LEU 3.8 3.4 - - - +
322A GLU 3.2 1.0 - - - -
323A LYS* 1.3 77.1 - - - +
325A ARG* 1.3 62.7 + - - +
327A THR* 3.3 6.9 + - - -
328A ALA* 3.0 23.0 + - - -
329A LEU* 3.3 16.6 + - + +
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Residues in contact with ARG 325 (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* 4.3 12.0 - - - +
8A VAL* 4.9 2.9 - - - +
242A LEU* 4.3 23.2 - - + +
245A LEU* 3.6 22.9 - - + +
246A HIS* 5.0 9.5 + - - +
249A LEU* 4.2 21.8 - - - +
250A HIS* 3.9 28.7 + - - -
321A LEU 4.0 1.3 + - - +
322A GLU* 3.2 30.1 + - - +
324A ALA* 1.3 80.1 - - - +
326A ASP* 1.3 70.0 + - - +
328A ALA* 4.3 4.2 + - - +
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Residues in contact with ASP 326 (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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2A PRO* 4.5 9.0 - - - +
3A PRO* 3.6 32.6 - - + +
322A GLU 4.0 13.3 - - - +
323A LYS* 3.3 8.3 + - - +
324A ALA 3.2 1.0 - - - -
325A ARG* 1.3 89.3 + - - +
327A THR* 1.3 63.2 + - + +
328A ALA 3.5 0.7 - - - -
332A ILE* 4.4 6.1 - - - +
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Residues in contact with THR 327 (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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323A LYS* 3.6 25.6 + - + +
324A ALA* 3.6 5.7 + - - -
326A ASP* 1.3 81.1 - - + +
328A ALA* 1.3 68.2 + - - +
330A LEU* 3.2 35.6 + - + +
331A THR 3.0 16.6 + - - -
332A ILE* 3.1 20.3 + - + +
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Residues in contact with ALA 328 (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* 6.1 0.9 - - + -
8A VAL* 3.7 45.3 - - + +
11A SER* 4.6 1.1 - - - -
12A LEU* 4.2 3.0 - - + +
241A VAL* 6.0 1.3 - - - -
242A LEU* 6.1 0.7 - - - -
324A ALA 3.0 7.5 + - - -
325A ARG* 4.3 2.9 + - - +
326A ASP 3.5 2.8 - - - -
327A THR* 1.3 79.5 - - - +
329A LEU* 1.3 68.2 + - - +
331A THR* 2.6 38.8 + - - +
332A ILE* 4.0 11.9 - - + -
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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