Contacts of the helix formed by residues 285 - 300 (chain C) in PDB entry 1P5Q
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 LYS 285 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C LEU* 5.6 3.0 - - - +
280C TYR* 2.7 30.7 + - + +
283C GLU* 3.2 52.3 + - + +
284C GLY* 1.3 71.1 - - - +
286C TYR* 1.3 62.7 + - - +
287C LYS 3.5 2.2 - - - -
288C GLN* 3.1 41.8 + - + +
289C ALA 2.9 15.8 + - - -
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Residues in contact with TYR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C PHE* 3.4 52.8 + + - -
284C GLY* 3.1 35.0 + - - -
285C LYS* 1.3 68.5 - - - +
287C LYS* 1.3 59.6 + - - +
289C ALA* 2.6 27.2 + - - +
290C LEU* 2.9 14.0 + - - +
328C CYS* 4.3 8.0 - - + +
331C LYS* 3.5 45.1 - - + +
332C LEU* 3.7 33.2 - - + -
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Residues in contact with LYS 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C GLU* 5.1 8.5 + - - -
197C ASN* 3.0 30.5 + - - +
285C LYS 3.5 1.0 - - - -
286C TYR* 1.3 75.1 - - - +
288C GLN* 1.3 62.1 + - - +
290C LEU* 3.0 31.5 + - + +
291C LEU* 3.3 14.9 + - + +
332C LEU* 4.2 25.1 - - + +
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Residues in contact with GLN 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C GLU* 3.0 45.1 + - + +
197C ASN* 4.2 15.0 - - + +
198C LEU* 3.6 25.7 - - - +
280C TYR* 3.7 27.2 - - + -
285C LYS* 3.1 42.4 + - - +
286C TYR 3.0 0.4 - - - -
287C LYS* 1.3 78.3 - - - +
289C ALA* 1.3 67.2 + - - +
291C LEU* 3.5 15.0 + - - +
292C GLN* 3.6 16.3 + - - +
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Residues in contact with ALA 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C GLY 4.2 4.0 - - - +
280C TYR* 3.7 6.7 - - - +
281C PHE* 4.1 18.4 - - + +
285C LYS 2.9 9.4 + - - +
286C TYR* 2.6 23.6 + - - +
288C GLN* 1.3 73.1 - - - +
290C LEU* 1.3 59.6 + - - +
292C GLN* 3.2 15.8 + - - +
293C TYR* 3.2 27.8 + - + -
328C CYS* 3.6 22.2 - - - -
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Residues in contact with LEU 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C TYR 2.9 9.2 + - - +
287C LYS* 3.0 19.9 + - + +
289C ALA* 1.3 73.4 - - - +
291C LEU* 1.3 62.5 + - + +
292C GLN 3.2 0.2 + - - -
293C TYR 3.3 0.5 + - - -
294C LYS* 2.8 51.0 + - + +
325C LEU* 3.3 28.7 - - + +
328C CYS* 3.9 18.2 - - + -
329C HIS* 3.6 32.8 - - + +
332C LEU* 3.6 28.5 - - + -
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Residues in contact with LEU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLU* 5.2 7.4 - - + +
193C GLY* 3.3 35.7 - - - +
194C GLU* 3.8 17.5 - - + +
197C ASN* 4.9 5.4 - - - +
287C LYS* 3.3 15.5 + - + +
288C GLN* 4.0 9.2 - - - +
289C ALA 3.4 0.6 - - - -
290C LEU* 1.3 80.8 - - + +
292C GLN* 1.3 67.2 + - - +
294C LYS* 4.0 13.4 - - + +
295C LYS* 3.1 28.7 + - + +
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Residues in contact with GLN 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLU* 3.4 33.9 + - - -
194C GLU* 5.4 1.8 + - - -
273C VAL* 3.1 45.7 - - - +
276C ARG* 3.5 19.9 + - - +
277C GLY* 4.0 11.7 - - - +
280C TYR* 3.8 25.9 - - + -
288C GLN 3.6 14.8 + - - +
289C ALA 3.3 7.0 - - - +
290C LEU 3.1 0.8 - - - -
291C LEU* 1.3 77.4 - - - +
293C TYR* 1.3 68.5 + - - +
295C LYS* 3.0 26.7 + - - +
296C ILE 3.3 0.3 + - - -
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Residues in contact with TYR 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C LYS* 3.7 23.4 + - + +
277C GLY* 3.2 13.8 - - - -
278C THR* 3.1 25.3 + - - -
281C PHE* 5.2 3.5 - - + +
289C ALA* 3.2 35.9 + - + -
292C GLN* 1.3 72.5 - - - +
294C LYS* 1.3 71.5 + - - +
296C ILE* 2.7 32.4 + - + +
297C VAL* 3.2 10.9 + - - +
321C SER* 4.2 9.1 + - - +
324C ASN* 3.3 47.9 + - + -
325C LEU* 3.6 29.8 - - + -
327C MET* 5.3 2.9 - - + +
328C CYS* 4.3 7.4 - - - -
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Residues in contact with LYS 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C LEU* 2.8 48.1 + - + +
291C LEU* 4.0 12.6 - - + +
293C TYR* 1.3 73.5 - - - +
295C LYS* 1.3 66.0 + - - +
297C VAL* 3.1 8.3 + - - +
298C SER* 2.9 23.1 + - - -
325C LEU* 4.2 15.5 - - + -
329C HIS* 5.2 10.9 - - - -
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Residues in contact with LYS 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C GLY* 3.8 22.3 + - - -
191C GLU* 3.1 31.0 + - - -
255C ALA* 4.8 7.9 - - - +
273C VAL* 4.4 6.5 - - + -
276C ARG* 4.5 11.1 - - - +
291C LEU* 3.1 24.7 + - - +
292C GLN* 3.0 27.0 + - - +
293C TYR 2.9 0.4 + - - -
294C LYS* 1.3 75.4 - - - +
296C ILE* 1.3 61.9 + - - +
298C SER* 3.0 8.3 + - - -
299C TRP* 2.9 60.9 + - + +
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Residues in contact with ILE 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C SER* 3.4 39.9 - - - +
273C VAL* 3.6 14.6 - - + -
274C LYS* 3.7 26.9 - - + +
292C GLN 3.3 0.2 + - - -
293C TYR* 2.7 22.2 + - + +
295C LYS* 1.3 76.9 - - - +
297C VAL* 1.3 64.8 + - - +
299C TRP* 3.2 3.3 + - - +
300C LEU* 3.1 44.5 + - + +
317C LEU* 4.4 11.2 - - + +
318C ARG* 4.7 0.9 - - - +
321C SER* 2.8 33.9 - - - +
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Residues in contact with VAL 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C TYR 3.2 3.3 + - - +
294C LYS* 3.1 10.8 + - - +
296C ILE* 1.3 81.4 - - + +
298C SER* 1.3 67.4 + - - +
300C LEU 3.6 4.0 - - - +
301C GLU* 3.5 27.4 + - + +
318C ARG* 4.8 13.5 - - + +
321C SER* 3.8 23.1 - - - -
322C HIS* 3.6 37.7 - - + +
325C LEU* 4.6 7.0 - - + -
344C LYS* 5.8 2.2 - - - +
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Residues in contact with SER 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C SER* 5.3 1.4 + - - -
294C LYS 2.9 13.1 + - - -
295C LYS* 3.4 11.7 - - - -
297C VAL* 1.3 79.5 - - - +
299C TRP* 1.3 70.2 + - - +
301C GLU* 3.1 28.4 + - - +
302C TYR 4.8 0.3 + - - -
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Residues in contact with TRP 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ALA* 6.2 2.5 - - + -
256C LYS* 4.2 14.1 + - + -
257C GLU 4.9 1.0 + - - -
258C SER* 3.9 20.2 + - - -
261C MSE 3.3 30.8 - - + +
266C LYS* 3.0 36.1 - - + +
269C GLN* 3.5 33.4 - - + -
270C SER* 3.5 22.9 - - - +
273C VAL* 3.4 34.1 - - + -
295C LYS* 2.9 51.3 + - + +
296C ILE* 3.7 2.7 - - - +
298C SER* 1.3 81.1 + - - +
300C LEU* 1.3 58.4 + - - +
301C GLU 3.3 3.0 + - - -
302C TYR 5.0 0.3 + - - -
303C GLU* 3.9 4.0 + - - +
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C LYS* 4.4 10.8 - - + -
267C LEU* 3.6 18.2 - - + -
270C SER* 3.7 17.7 - - - +
296C ILE* 3.1 37.6 + - + +
297C VAL 3.6 4.7 - - - +
299C TRP* 1.3 76.6 - - - +
301C GLU* 1.3 56.1 + - - +
302C TYR 4.0 0.2 - - - -
303C GLU* 4.8 5.8 - - - -
306C PHE* 3.5 27.1 - - + -
314C ALA* 4.0 4.0 - - + +
317C LEU* 3.9 21.1 - - + -
318C ARG* 2.5 57.7 + - + +
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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
------------------------------------------------------------
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