Contacts of the helix formed by residues 286 - 312 (chain C) in PDB entry 1T2K
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 286 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLU* 2.9 32.3 + - + +
283C LYS* 2.9 23.4 + - - +
285C LYS* 1.3 76.5 - - + +
287C LEU* 1.3 63.6 + - - +
289C ALA* 3.5 4.5 + - - +
290C GLN* 2.9 33.2 + - - +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C LYS* 2.8 37.3 + - + +
284C VAL* 3.9 2.0 - - - +
286C THR* 1.3 83.3 + - - +
288C LYS* 1.3 61.7 + - - +
290C GLN* 4.2 3.9 - - - +
291C ASN* 2.9 32.9 + - - +
366D ALA* 3.5 15.0 - - + +
369D LEU* 3.2 24.1 - - + +
370D SER* 3.0 44.0 - - - +
373D ASN* 4.5 8.0 - - + +
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C VAL* 3.1 19.3 + - + +
285C LYS* 4.3 3.6 - - - +
286C THR 3.5 0.2 - - - -
287C LEU* 1.3 77.0 - - - +
289C ALA* 1.3 58.8 + - - +
291C ASN* 3.3 14.1 + - - +
292C SER* 3.1 29.4 + - - -
365D LYS* 4.2 19.3 - - + +
369D LEU* 3.5 26.7 - - + +
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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
----------------------------------------------------------
285C LYS 3.4 17.0 + - - +
286C THR* 3.8 4.5 - - - +
287C LEU 3.2 0.2 - - - -
288C LYS* 1.3 76.9 - - - +
290C GLN* 1.3 66.4 + - - +
292C SER* 3.1 18.1 + - - -
293C GLU* 3.6 10.0 + - - +
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Residues in contact with GLN 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C THR* 2.9 19.1 + - - +
287C LEU* 4.2 2.9 - - - +
289C ALA* 1.3 77.4 - - - +
291C ASN* 1.3 63.1 + - - +
293C GLU* 3.2 31.0 + - - +
294C LEU* 3.2 25.4 + - + +
373D ASN* 3.5 29.9 + - - +
377D GLN* 4.0 16.6 + - - -
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Residues in contact with ASN 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU 2.9 20.4 + - - +
288C LYS* 3.3 21.1 + - - +
290C GLN* 1.3 75.7 - - - +
292C SER* 1.3 90.7 + - - +
294C LEU* 3.3 8.1 + - - +
295C ALA* 3.0 20.3 + - - +
369D LEU* 5.0 9.9 - - + +
372D LEU* 4.2 19.6 - - - +
373D ASN* 4.0 20.4 + - + +
376D LEU* 3.6 13.4 - - + +
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Residues in contact with SER 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C LYS* 3.1 11.7 + - - -
289C ALA* 3.1 15.6 + - - -
291C ASN* 1.3 86.7 - - - +
293C GLU* 1.3 55.6 + - - +
295C ALA* 3.2 14.7 + - - +
296C SER* 2.8 26.1 + - - -
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Residues in contact with GLU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C ALA 3.6 9.6 + - - +
290C GLN* 3.2 20.7 + - - +
291C ASN 3.2 0.2 - - - -
292C SER* 1.3 81.0 + - - +
294C LEU* 1.3 75.7 + - + +
296C SER* 3.3 13.8 + - - -
297C THR* 3.2 28.5 + - + +
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C GLN* 3.4 27.8 - - - +
291C ASN* 3.6 7.4 - - - +
292C SER 3.2 0.4 - - - -
293C GLU* 1.3 97.7 - - + +
295C ALA* 1.3 59.3 + - - +
296C SER 3.2 0.4 - - - -
297C THR* 2.8 26.5 + - + +
298C ALA* 2.8 17.3 + - - +
373D ASN* 4.3 8.7 - - - +
376D LEU* 3.6 27.0 - - + +
377D GLN* 3.8 42.2 - - + +
380D VAL* 4.4 6.3 - - + +
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ASN* 3.0 11.6 + - - +
292C SER* 3.2 11.8 + - - +
294C LEU* 1.3 76.5 - - - +
296C SER* 1.3 57.4 + - - +
298C ALA* 3.3 6.5 - - - +
299C ASN* 3.0 29.1 + - - +
376D LEU* 3.2 19.8 - - + +
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Residues in contact with SER 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C SER 2.8 16.8 + - - -
293C GLU* 3.3 10.3 + - - -
294C LEU 3.2 0.2 - - - -
295C ALA* 1.3 74.3 - - - +
297C THR* 1.3 56.0 + - - +
299C ASN* 3.2 8.5 + - - +
300C MET* 2.8 34.4 + - - +
303C GLU* 5.3 0.2 - - - +
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Residues in contact with THR 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C GLU* 3.2 21.7 + - + +
294C LEU* 2.8 29.4 + - + +
296C SER* 1.3 74.8 - - - +
298C ALA* 1.3 63.5 + - - +
300C MET* 3.8 22.6 - - + +
301C LEU* 3.1 34.6 + - - +
380D VAL* 3.9 14.7 - - - +
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Residues in contact with ALA 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C LEU 2.8 15.1 + - - +
295C ALA* 3.3 13.9 - - - +
297C THR* 1.3 78.4 + - - +
299C ASN* 1.3 58.8 + - - +
301C LEU* 3.7 3.3 + - - -
302C ARG* 3.1 29.4 + - - +
376D LEU* 5.1 11.2 - - + -
379D GLU* 5.5 8.7 - - + -
380D VAL* 4.6 13.9 - - + +
383D LEU* 3.9 9.8 - - + +
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Residues in contact with ASN 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ALA 3.0 15.4 + - - +
296C SER* 3.2 11.2 + - - +
298C ALA* 1.3 78.1 - - - +
300C MET* 1.3 55.1 + - - +
302C ARG* 3.1 19.5 + - - +
303C GLU* 2.8 46.8 + - - +
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Residues in contact with MET 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C SER 2.8 18.9 + - - +
297C THR* 3.3 20.6 + - + +
299C ASN* 1.3 72.8 - - - +
301C LEU* 1.3 88.7 + - + +
303C GLU* 3.4 23.4 + - - +
304C GLN* 3.2 30.1 + - - +
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C THR* 3.1 17.8 + - - +
298C ALA* 4.1 0.7 - - - +
300C MET* 1.3 103.8 - - + +
302C ARG* 1.3 61.7 + - - +
304C GLN* 3.2 31.4 + - - +
305C VAL* 3.3 6.9 + - - +
380D VAL* 3.8 21.8 - - + +
383D LEU* 3.9 22.2 - - + -
384D ARG* 3.2 40.6 - - + +
387D VAL* 3.9 15.3 - - + +
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Residues in contact with ARG 302 (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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298C ALA 3.1 20.1 + - - +
299C ASN* 3.1 21.5 + - - +
301C LEU* 1.3 75.1 - - - +
303C GLU* 1.3 64.4 + - - +
305C VAL* 3.3 21.1 + - + +
306C ALA* 3.5 6.1 + - - +
383D LEU* 3.6 15.0 - - + +
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Residues in contact with GLU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C SER 5.3 0.3 - - - +
299C ASN* 2.8 32.3 + - + +
300C MET* 3.4 27.0 + - - +
302C ARG* 1.3 72.4 - - - +
304C GLN* 1.3 59.3 + - + +
306C ALA* 3.2 10.7 + - - +
307C GLN* 2.9 25.9 + - - +
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Residues in contact with GLN 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C MET* 3.2 35.0 + - - +
301C LEU* 3.2 21.4 + - - +
303C GLU* 1.3 76.2 - - + +
305C VAL* 1.3 56.1 + - - +
307C GLN* 3.7 24.0 - - - +
308C LEU* 2.5 44.9 + - + +
387D VAL* 4.1 23.2 - - + +
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Residues in contact with VAL 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C LEU 3.3 10.0 + - - +
302C ARG* 3.3 18.2 + - + +
304C GLN* 1.3 76.5 - - - +
306C ALA* 1.3 65.2 + - + +
308C LEU* 4.5 4.1 - - - +
309C LYS* 3.3 23.5 + - + +
383D LEU* 4.7 10.8 - - + -
386D GLU* 3.7 35.7 - - + +
387D VAL* 4.7 6.9 - - + +
390D LEU* 6.0 3.3 - - + +
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Residues in contact with ALA 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ARG 3.5 6.0 + - - +
303C GLU* 3.2 10.2 + - - +
304C GLN 3.1 0.6 - - - -
305C VAL* 1.3 85.4 - - + +
307C GLN* 1.3 60.1 + - - +
309C LYS* 3.5 5.9 + - - +
310C GLN* 3.3 26.3 + - - +
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Residues in contact with GLN 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C GLU 2.9 14.5 + - - +
304C GLN* 2.8 32.3 + - - +
306C ALA* 1.3 75.2 - - - +
308C LEU* 1.3 73.6 + - + +
310C GLN* 3.4 7.2 + - - +
311C LYS* 3.2 30.2 + - + +
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C GLN* 2.5 29.7 + - + +
305C VAL* 4.5 3.8 - - - +
307C GLN* 1.3 84.8 - - + +
309C LYS* 1.3 56.2 + - - +
311C LYS* 3.7 11.6 - - + +
312C VAL* 2.6 41.0 + - + +
387D VAL* 4.1 17.0 - - + +
390D LEU* 3.7 18.8 - - + -
391D LYS* 3.3 39.0 - - + -
395D LEU* 4.7 10.3 - - + -
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Residues in contact with LYS 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C VAL* 3.3 19.8 + - + +
306C ALA* 3.5 7.4 - - - +
307C GLN 3.3 0.6 - - - -
308C LEU* 1.3 78.3 - - - +
310C GLN* 1.3 62.8 + - + +
312C VAL* 3.8 11.8 - - + +
313C MET* 2.9 37.8 + - + +
390D LEU* 4.9 10.8 - - + +
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Residues in contact with GLN 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ALA 3.3 15.7 + - - +
307C GLN* 3.4 8.3 + - - +
308C LEU 3.2 0.4 - - - -
309C LYS* 1.3 84.3 - - - +
311C LYS* 1.3 62.3 + - + +
313C MET* 4.1 4.1 - - - +
314C ASN* 3.6 19.9 + - - +
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Residues in contact with LYS 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLN* 3.2 22.8 + - + +
308C LEU* 3.2 15.3 + - + +
310C GLN* 1.3 80.8 - - + +
312C VAL* 1.3 61.3 + - - +
314C ASN* 3.7 17.7 + - - +
395D LEU* 3.7 29.1 - - + +
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Residues in contact with VAL 312 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C LEU 2.6 25.9 + - - +
309C LYS* 3.8 17.0 - - + +
311C LYS* 1.3 68.6 - - - +
313C MET* 1.3 69.6 + - + +
314C ASN* 3.1 10.7 + - - +
390D LEU* 4.2 19.3 - - + -
394D LEU* 3.1 56.5 - - + +
395D LEU* 3.8 15.6 - - + +
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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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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