Contacts of the helix formed by residues 299 - 311 (chain P) in PDB entry 5L4K
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 ILE 299 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263P TRP* 4.0 30.5 - - + -
264P GLN* 4.3 24.2 - - + +
267P LEU* 4.8 9.9 - - + -
268P LYS* 6.3 0.9 - - + -
295P LYS 4.3 5.4 - - - +
296P LEU* 3.2 21.3 + - + +
297P GLU 4.8 0.2 - - - -
298P GLU* 1.3 84.8 - - + +
300P PRO* 1.3 62.0 - - - +
301P LYS* 3.1 23.9 + - - +
302P TYR* 3.4 40.3 + - + +
303P LYS* 3.4 6.6 + - - +
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Residues in contact with PRO 300 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297P GLU 5.1 2.2 - - - +
298P GLU 3.1 14.6 - - - +
299P ILE* 1.3 83.9 - - - +
301P LYS* 1.3 69.6 + - + +
302P TYR 3.2 0.8 + - - -
303P LYS* 4.2 22.2 - - - +
304P ASP* 2.5 37.9 + - - +
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Residues in contact with LYS 301 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299P ILE* 3.1 21.2 - - - +
300P PRO* 1.3 90.9 - - + +
302P TYR* 1.3 75.4 + - + +
304P ASP* 4.7 0.4 - - - +
305P LEU* 4.2 4.9 + - - +
324P TYR* 3.9 12.9 - - - -
327P GLU* 2.9 54.6 - - + +
330P LYS* 5.2 8.9 + - - +
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Residues in contact with TYR 302 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268P LYS* 3.3 52.9 + - + -
271P VAL* 4.5 20.3 - - + +
272P LEU* 4.7 14.5 - - + +
296P LEU* 4.6 5.8 - - + -
299P ILE* 3.4 30.9 + - + +
301P LYS* 1.3 97.3 + - + +
303P LYS* 1.3 57.8 + - - +
304P ASP 3.0 2.5 - - - -
305P LEU* 2.7 41.2 + - + +
306P LEU* 2.9 12.5 + - - +
327P GLU* 3.2 26.5 + - + +
328P LEU* 4.2 22.1 - - + +
330P LYS 5.1 1.2 + - - -
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Residues in contact with LYS 303 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296P LEU* 3.8 34.5 - - + +
297P GLU* 3.0 47.8 - - - +
299P ILE 3.4 5.6 + - - +
300P PRO* 4.2 18.6 + - + +
302P TYR* 1.3 76.4 - - - +
304P ASP* 1.3 84.8 + - - +
306P LEU* 3.4 5.1 + - - +
307P LYS* 2.9 30.5 + - + +
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Residues in contact with ASP 304 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300P PRO* 2.5 27.0 - - - +
301P LYS 4.8 1.3 - - - +
302P TYR 3.0 0.8 - - - -
303P LYS* 1.3 102.1 + - - +
305P LEU* 1.3 65.7 + - - +
307P LYS* 3.1 9.3 + - - +
308P LEU* 3.0 26.7 + - - +
324P TYR* 3.7 17.0 - - + +
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Residues in contact with LEU 305 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271P VAL* 5.9 4.3 - - + +
272P LEU* 4.5 13.7 - - + -
275P ILE* 4.4 19.5 - - + +
301P LYS 4.2 5.5 + - - +
302P TYR* 2.7 41.4 + - + +
304P ASP* 1.3 76.1 - - - +
306P LEU* 1.3 55.5 + - - -
308P LEU* 3.7 7.8 + - + +
309P PHE* 3.3 31.4 - - + -
320P LEU* 3.9 18.6 - - + -
324P TYR* 3.7 34.8 + - + -
327P GLU* 6.0 0.2 - - - +
328P LEU* 5.0 10.3 - - + -
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Residues in contact with LEU 306 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271P VAL* 3.9 16.1 - - + +
274P VAL* 3.8 18.4 - - + -
275P ILE* 3.8 25.6 - - + -
287P VAL* 4.3 13.9 - - + +
290P ILE* 4.6 5.6 - - + -
291P SER* 3.5 30.5 - - - +
296P LEU* 4.1 23.6 - - + -
302P TYR 2.9 9.3 + - - +
303P LYS* 3.7 7.9 - - - +
305P LEU* 1.3 72.7 - - - +
307P LYS* 1.3 60.1 + - - +
308P LEU 3.1 2.0 - - - -
309P PHE* 3.0 7.6 + - + +
310P THR* 3.0 33.7 + - + +
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Residues in contact with LYS 307 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303P LYS* 2.9 22.2 + - + +
304P ASP* 3.1 11.4 + - - +
306P LEU* 1.3 75.7 - - - +
308P LEU* 1.3 61.7 + - - +
310P THR* 3.6 11.6 + - - +
311P THR* 3.4 33.4 + - + +
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Residues in contact with LEU 308 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304P ASP 3.0 14.5 + - - +
305P LEU* 3.7 10.1 - - - +
306P LEU 3.1 0.6 - - - -
307P LYS* 1.3 79.9 - - - +
309P PHE* 1.3 62.0 + - - +
310P THR 3.5 0.2 + - - -
311P THR* 3.6 17.1 + - - +
313P GLU 4.5 4.9 - - - +
315P MET* 3.6 35.4 - - + +
320P LEU* 4.4 9.4 - - + -
324P TYR* 3.8 32.3 - - + +
361P HIS* 4.1 5.5 + - - -
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Residues in contact with PHE 309 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275P ILE* 3.6 57.0 - - + -
279P PHE* 5.0 12.6 - + + -
305P LEU* 3.3 32.1 - - + +
306P LEU* 3.0 8.5 + - + +
308P LEU* 1.3 78.2 - - - +
310P THR* 1.3 65.3 + - + +
311P THR 4.0 0.2 - - - -
315P MET* 3.7 34.3 - - + -
320P LEU* 5.0 2.2 - - + -
354P LEU* 4.7 2.7 - - + -
357P ARG* 4.6 7.6 - - + -
358P VAL* 3.7 30.1 - - + -
361P HIS* 3.2 31.9 - + + -
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Residues in contact with THR 310 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287P VAL* 4.4 25.1 - - + +
288P HIS* 4.8 12.8 - - + +
291P SER* 4.3 18.4 - - - +
306P LEU* 3.0 23.2 + - + +
307P LYS* 3.6 18.9 + - - +
309P PHE* 1.3 76.7 - - + +
311P THR* 1.3 76.4 + - - +
312P MET* 4.4 7.1 - - - +
361P HIS* 4.9 1.0 - - - -
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Residues in contact with THR 311 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316O SER* 6.5 0.4 - - - -
307P LYS* 3.4 35.1 + - + +
308P LEU* 3.6 13.9 + - - +
310P THR* 1.3 86.8 - - - +
312P MET* 1.3 60.3 + - - +
313P GLU* 3.4 22.3 + - - +
361P HIS* 3.8 10.4 + - - -
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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