Contacts of the helix formed by residues 291 - 307 (chain A) in PDB entry 4KAL
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A GLY 4.0 0.2 + - - -
290A ARG* 1.3 76.6 - - - +
292A LEU* 1.3 60.2 + - - +
293A GLU* 3.7 8.7 + - - +
294A ASP* 3.1 35.2 + - - +
295A CYS* 2.9 26.6 + - - -
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Residues in contact with LEU 292 (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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239A ILE* 4.2 18.2 - - + -
251A ILE* 3.8 24.3 - - + +
253A LYS* 3.9 39.9 - - + +
256A GLU* 4.5 1.6 - - - +
258A TYR* 4.0 28.0 - - + -
282A PHE* 4.0 22.8 - - + -
286A TYR* 4.2 15.9 - - + -
290A ARG 3.8 1.5 + - - +
291A SER* 1.3 73.3 - - - +
293A GLU* 1.3 62.2 + - - +
295A CYS* 3.3 6.5 + - - +
296A GLY 3.0 18.0 + - - -
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Residues in contact with GLU 293 (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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251A ILE* 5.2 0.2 - - - -
258A TYR* 4.4 29.7 - - + -
259A TYR 4.4 10.0 - - - +
260A VAL* 3.6 18.2 - - + +
291A SER* 3.2 8.4 + - - +
292A LEU* 1.3 79.2 - - - +
294A ASP* 1.3 59.0 + - - +
296A GLY* 3.1 4.3 + - - -
297A LYS* 2.9 51.8 + - - +
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Residues in contact with ASP 294 (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 ARG* 3.0 43.3 + - + +
291A SER* 3.1 26.1 + - - +
293A GLU* 1.3 75.3 - - - +
295A CYS* 1.3 60.7 + - - +
297A LYS* 3.7 25.6 + - - +
298A LEU* 3.0 35.1 + - - +
327A LEU* 5.0 5.1 - - + +
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Residues in contact with CYS 295 (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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282A PHE* 3.4 39.5 - - + +
285A GLY* 3.4 6.7 - - - -
286A TYR* 3.2 43.3 - - - -
290A ARG* 3.8 9.6 - - - -
291A SER 2.9 20.7 + - - -
292A LEU* 3.5 9.9 - - - +
293A GLU 3.3 0.2 - - - -
294A ASP* 1.3 74.8 - - - +
296A GLY* 1.3 58.7 + - - +
298A LEU* 3.3 7.1 + - - +
299A GLY* 2.9 24.8 + - - -
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Residues in contact with GLY 296 (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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251A ILE* 4.2 17.9 - - - -
260A VAL* 3.8 16.2 - - - -
278A PHE* 3.8 6.0 - - - -
282A PHE* 3.8 3.9 - - - -
292A LEU 3.0 13.4 + - - -
293A GLU 3.1 4.0 + - - -
295A CYS* 1.3 76.1 - - - +
297A LYS* 1.3 55.5 + - - +
299A GLY* 3.3 1.4 + - - -
300A CYS* 2.9 34.0 + - - -
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Residues in contact with LYS 297 (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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260A VAL* 3.7 21.1 - - + +
263A ILE* 5.4 0.9 - - - +
293A GLU* 2.9 41.8 + - - +
294A ASP* 3.7 25.5 + - - +
295A CYS 3.3 0.2 - - - -
296A GLY* 1.3 71.3 - - - +
298A LEU* 1.3 60.9 + - - +
300A CYS* 3.4 3.0 + - - +
301A LEU* 3.0 28.8 + - - +
327A LEU* 3.7 28.9 - - + +
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Residues in contact with LEU 298 (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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69A LEU* 4.8 7.6 - - + +
281A GLY* 3.4 23.2 - - - +
284A TYR* 4.1 18.4 - - + -
285A GLY* 3.6 30.3 - - - +
290A ARG* 4.4 19.1 - - + +
294A ASP 3.0 23.0 + - - +
295A CYS 3.6 1.1 - - - +
297A LYS* 1.3 75.8 - - - +
299A GLY* 1.3 61.7 + - - +
301A LEU* 3.4 5.5 + - + +
302A ALA* 3.0 19.2 + - - +
322A ALA* 4.2 17.5 - - + -
327A LEU* 3.8 33.2 - - + +
328A ILE 5.6 0.7 - - - -
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Residues in contact with GLY 299 (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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278A PHE* 3.3 41.0 - - - -
281A GLY* 3.7 2.8 - - - -
282A PHE 3.8 4.0 - - - -
295A CYS 2.9 12.7 + - - -
296A GLY 3.6 3.1 - - - -
298A LEU* 1.3 76.7 - - - +
300A CYS* 1.3 57.2 + - - +
302A ALA* 3.3 1.0 + - - -
303A ALA* 2.9 31.2 + - - +
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Residues in contact with CYS 300 (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 GLY* 4.3 9.0 - - - -
249A ALA* 4.2 11.4 - - - -
260A VAL* 3.7 11.9 - - + -
261A ASN 3.6 29.8 - - - +
262A ALA* 4.5 6.7 - - - -
263A ILE* 3.9 12.3 + - + +
278A PHE* 3.6 17.0 - - - -
296A GLY 2.9 21.9 + - - +
297A LYS* 3.9 4.0 - - - +
299A GLY* 1.3 72.8 - - - +
301A LEU* 1.3 56.7 + - - +
303A ALA* 3.9 3.9 - - - +
304A GLY* 2.9 27.0 + - - -
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Residues in contact with LEU 301 (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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69A LEU* 5.9 1.6 - - + -
263A ILE* 4.0 26.4 - - + +
297A LYS 3.0 18.0 + - - +
298A LEU* 3.6 7.4 - - + +
299A GLY 3.3 0.2 - - - -
300A CYS* 1.3 75.9 - - - +
302A ALA* 1.3 62.7 + - - +
304A GLY* 3.3 2.1 + - - -
305A ILE* 3.0 46.2 + - + +
318A LEU 4.8 2.0 - - - +
321A ALA* 3.8 8.3 - - + +
322A ALA* 3.5 42.0 - - + +
325A ALA* 4.2 13.2 - - + -
327A LEU* 4.0 17.0 - - + -
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Residues in contact with ALA 302 (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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69A LEU* 4.9 4.3 - - + -
277A LEU* 3.3 38.2 - - + +
281A GLY* 4.3 6.7 - - - +
298A LEU 3.0 16.0 + - - +
299A GLY 3.9 0.2 - - - +
301A LEU* 1.3 75.7 - - - +
303A ALA* 1.3 62.4 + - - +
305A ILE* 3.3 3.6 + - - +
306A VAL* 3.1 18.7 + - - +
318A LEU* 4.3 30.7 - - + +
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Residues in contact with ALA 303 (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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274A ALA* 3.4 31.4 - - + +
277A LEU* 4.1 2.1 - - - +
278A PHE* 4.0 8.7 - - + +
299A GLY 2.9 17.3 + - - +
300A CYS* 3.9 5.4 - - - +
302A ALA* 1.3 77.6 - - - +
304A GLY* 1.3 61.5 + - - +
306A VAL* 3.3 10.2 + - - +
307A ILE* 3.3 28.1 + - - +
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Residues in contact with GLY 304 (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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263A ILE* 3.6 18.6 - - - -
265A ILE* 3.7 3.8 - - - +
300A CYS 2.9 18.9 + - - -
301A LEU 3.8 0.2 - - - -
303A ALA* 1.3 75.5 - - - +
305A ILE* 1.3 61.9 + - - +
307A ILE* 3.5 14.8 - - - +
308A GLN* 2.9 28.9 + - - +
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Residues in contact with ILE 305 (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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263A ILE* 4.7 4.5 - - + -
301A LEU* 3.0 35.0 + - + +
302A ALA 3.7 5.8 - - - +
303A ALA 3.2 0.2 - - - -
304A GLY* 1.3 77.2 - - - +
306A VAL* 1.3 63.7 + - - +
308A GLN* 3.1 24.9 + - - +
309A GLN* 4.1 8.1 + - - +
314A PRO* 4.5 7.4 - - + -
316A THR* 3.9 22.0 - - - +
317A SER 5.4 0.2 - - - +
318A LEU* 3.8 24.5 - - + -
321A ALA* 3.5 32.1 - - + -
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Residues in contact with VAL 306 (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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272A THR 4.1 4.5 - - - +
273A GLY 3.7 28.9 - - - +
274A ALA* 3.8 5.8 - - - +
277A LEU* 4.0 5.6 - - + -
302A ALA 3.1 14.9 + - - +
303A ALA 3.4 11.2 - - - +
305A ILE* 1.3 78.2 - - - +
307A ILE* 1.3 57.4 + - + +
308A GLN 3.1 0.2 - - - -
309A GLN* 3.2 20.4 - - - +
311A GLY 3.8 7.2 - - - +
312A PRO 3.5 32.5 - - - +
314A PRO* 3.8 23.3 - - + -
405A K 2.8 24.4 - - - -
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Residues in contact with ILE 307 (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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265A ILE* 3.8 28.3 - - + -
268A VAL* 3.9 14.8 - - + -
269A VAL 2.9 24.6 + - - -
270A ASP 3.2 18.2 + - - +
271A THR* 3.8 21.3 - - + +
274A ALA* 3.5 28.3 - - + -
303A ALA 3.4 13.7 - - - +
304A GLY* 3.5 19.5 - - - +
306A VAL* 1.3 78.6 - - + +
308A GLN* 1.3 59.9 + - + +
309A GLN 3.3 1.8 - - - -
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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