Contacts of the helix formed by residues 305 - 328 (chain C) in PDB entry 3U1K
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 ASP 305 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C GLU 3.8 1.8 + - - +
304C HIS* 1.3 75.8 - - - +
306C LYS* 1.3 68.4 + - - +
307C VAL* 3.1 18.4 + - - +
308C SER* 3.0 33.7 + - - -
309C ARG* 3.1 26.3 + - - +
390C GLN* 3.1 32.5 + - - +
66D PHE* 4.3 1.2 - - - -
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Residues in contact with LYS 306 (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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305C ASP* 1.3 71.5 - - - +
307C VAL* 1.3 61.7 + - + +
309C ARG* 3.8 16.1 + - - +
310C ASP* 3.1 45.0 + - - +
390C GLN* 2.8 21.5 + - - +
434C THR* 3.7 26.5 + - - +
479C SER 2.9 28.6 + - - +
480C ASN* 4.0 19.5 - - - +
535C GLY* 6.2 4.5 - - - -
66D PHE* 3.8 20.9 - - + -
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Residues in contact with VAL 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ASP* 3.1 8.7 + - - +
306C LYS* 1.3 80.4 - - + +
308C SER* 1.3 67.2 + - - +
310C ASP* 3.2 6.5 + - + +
311C GLU* 2.8 50.5 + - + +
435C ASN* 6.5 0.4 - - + -
66D PHE* 3.7 31.9 - - + -
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Residues in contact with SER 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C GLU 4.7 0.7 + - - -
304C HIS* 2.7 29.8 + - - -
305C ASP* 3.0 34.4 + - - -
307C VAL* 1.3 78.3 - - - +
309C ARG* 1.3 55.3 + - - +
311C GLU* 3.4 11.0 + - - +
312C ALA* 2.9 30.3 + - - +
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Residues in contact with ARG 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C VAL* 3.7 21.5 - - + -
299C PHE* 4.2 19.3 - - + -
304C HIS* 3.8 40.2 + - + +
305C ASP 3.1 17.4 + - - +
306C LYS* 3.8 25.0 + - - +
308C SER* 1.3 74.9 + - - +
310C ASP* 1.3 62.3 + - - +
312C ALA* 3.4 1.6 + - - +
313C VAL* 2.9 35.0 + - + +
359C CYS* 3.6 43.5 + - - -
360C ASP* 4.5 6.5 - - - +
480C ASN* 5.2 1.6 + - - +
534C LEU* 3.8 23.4 - - - +
536C ILE* 4.5 15.1 - - + +
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Residues in contact with ASP 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C LYS* 3.1 42.0 + - - +
307C VAL* 3.2 5.9 + - - +
309C ARG* 1.3 77.5 + - - +
311C GLU* 1.3 58.3 + - + +
313C VAL* 3.8 7.5 - - - +
314C ASN* 2.9 29.5 + - - +
317C ARG* 5.5 0.7 + - - -
536C ILE* 4.8 9.2 - - - +
539C TYR* 3.7 19.3 + - - -
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Residues in contact with GLU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C VAL* 2.8 40.3 + - + +
308C SER* 3.8 9.3 - - - +
310C ASP* 1.3 75.2 - - + +
312C ALA* 1.3 59.0 + - - +
314C ASN* 3.1 6.9 + - + +
315C LYS* 2.8 30.4 + - - +
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Residues in contact with ALA 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C VAL* 3.7 23.1 - - + -
304C HIS* 3.9 16.2 - - + +
308C SER 2.9 18.3 + - - +
309C ARG 3.7 3.8 - - - +
311C GLU* 1.3 78.0 - - - +
313C VAL* 1.3 62.8 + - - +
315C LYS* 3.4 7.4 + - - +
316C ILE* 3.3 26.3 + - - +
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Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 4.4 9.9 - - + -
298C VAL* 4.0 7.6 - - + -
299C PHE* 3.6 35.0 - - + -
309C ARG* 2.9 23.1 + - + +
310C ASP* 3.8 7.4 - - - +
312C ALA* 1.3 74.1 - - - +
314C ASN* 1.3 59.5 + - - +
316C ILE* 3.2 12.3 + - - +
317C ARG* 3.0 42.9 + - - +
340C PHE* 3.8 14.8 - - + -
344C ALA* 5.0 5.8 - - + -
536C ILE* 5.3 3.6 - - + -
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Residues in contact with ASN 314 (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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310C ASP 2.9 19.2 + - - +
311C GLU* 3.1 7.6 + - + +
313C VAL* 1.3 74.7 - - - +
315C LYS* 1.3 59.5 + - - +
317C ARG* 3.1 32.7 + - - +
318C LEU* 2.9 59.2 + - - +
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Residues in contact with LYS 315 (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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294C ARG* 4.9 4.0 - - - +
311C GLU 2.8 16.5 + - - +
312C ALA* 3.6 12.1 - - - +
313C VAL 3.3 0.2 - - - -
314C ASN* 1.3 74.6 - - - +
316C ILE* 1.3 63.4 + - + +
318C LEU* 3.2 11.5 + - + +
319C ASP* 2.9 56.4 + - - +
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Residues in contact with ILE 316 (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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291C ALA* 3.9 18.4 - - + -
294C ARG* 3.6 67.1 - - + +
295C LEU* 3.8 16.6 - - + +
298C VAL* 3.9 12.8 - - + -
312C ALA 3.3 15.5 + - - +
313C VAL* 3.2 6.8 + - - +
315C LYS* 1.3 77.9 - - + +
317C ARG* 1.3 54.3 + - - +
319C ASP 3.4 0.5 + - - -
320C THR* 2.6 43.3 + - + +
340C PHE* 3.9 16.8 - - + -
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Residues in contact with ARG 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ASP 5.5 0.4 + - - -
313C VAL* 3.0 28.4 + - - +
314C ASN* 3.1 34.1 + - - +
316C ILE* 1.3 77.2 - - - +
318C LEU* 1.3 59.8 + - - +
320C THR* 3.2 0.2 + - - -
321C GLU* 2.7 74.3 + - + +
337C ILE* 5.1 4.9 + - - +
340C PHE* 3.5 31.9 - - + -
341C ASN* 3.0 28.9 + - - +
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ASN* 2.9 41.4 + - - +
315C LYS* 3.8 11.4 - - + +
317C ARG* 1.3 82.1 - - + +
319C ASP* 1.3 63.0 + - - +
320C THR 3.2 0.5 + - - -
321C GLU* 4.5 10.7 - - + +
322C GLU* 3.3 23.2 + - - +
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Residues in contact with ASP 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG* 3.0 29.3 + - - +
315C LYS* 2.9 54.0 + - - +
316C ILE 3.9 1.6 - - - +
318C LEU* 1.3 76.5 - - - +
320C THR* 1.3 60.3 + - + +
322C GLU* 4.1 5.3 - - - +
323C GLN* 3.1 30.4 + - - +
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Residues in contact with THR 320 (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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287C THR* 5.7 0.7 - - - -
290C LEU* 4.3 19.1 - - + +
291C ALA* 4.1 14.8 - - + -
294C ARG* 5.1 5.4 - - - +
316C ILE* 2.6 36.5 + - + +
317C ARG 3.2 3.6 + - - -
319C ASP* 1.3 83.2 - - + +
321C GLU* 1.3 63.6 + - - +
322C GLU 3.1 1.6 - - - -
323C GLN* 3.1 10.1 + - - +
324C LEU* 2.8 44.0 + - - +
340C PHE* 3.4 20.4 - - - -
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Residues in contact with GLU 321 (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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317C ARG* 2.7 55.7 + - + +
318C LEU* 4.5 10.2 - - + +
320C THR* 1.3 73.9 + - - +
322C GLU* 1.3 60.8 + - - +
324C LEU* 3.5 3.4 + - + +
325C LYS* 3.1 29.2 + - + +
336C ILE* 3.6 27.2 - - + +
337C ILE* 3.5 38.3 - - - +
340C PHE* 3.9 11.8 - - + +
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Residues in contact with GLU 322 (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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318C LEU 3.3 17.4 + - - +
319C ASP* 4.1 7.6 - - - +
320C THR 3.1 0.2 - - - -
321C GLU* 1.3 79.6 - - - +
323C GLN* 1.3 64.1 + - + +
325C LYS* 3.3 18.7 + - - +
326C GLU* 3.3 43.0 + - - +
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Residues in contact with GLN 323 (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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286C TYR* 4.8 7.0 + - + +
290C LEU* 3.8 40.2 - - + +
319C ASP* 3.1 26.0 + - - +
320C THR* 3.1 10.3 + - - +
322C GLU* 1.3 74.2 - - + +
324C LEU* 1.3 60.6 + - - +
325C LYS 3.1 1.3 - - - -
326C GLU* 3.2 17.4 + - - +
327C LYS* 2.9 30.4 + - - +
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Residues in contact with LEU 324 (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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283C ILE* 3.5 27.6 - - + +
286C TYR* 3.6 23.1 - - + -
287C THR* 3.5 26.0 - - + +
290C LEU* 4.2 15.0 - - + -
320C THR* 2.8 39.8 + - - +
321C GLU* 3.8 6.7 - - + +
323C GLN* 1.3 77.1 - - - +
325C LYS* 1.3 53.3 + - - +
327C LYS* 4.3 2.0 - - - -
328C PHE* 2.7 50.7 + - + +
336C ILE* 3.8 24.1 - - + +
340C PHE* 6.3 0.2 - - + -
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Residues in contact with LYS 325 (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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321C GLU* 3.1 17.0 + - + +
322C GLU* 3.4 21.6 + - - +
323C GLN 3.1 0.4 - - - -
324C LEU* 1.3 74.9 - - - +
326C GLU* 1.3 64.0 + - + +
328C PHE 4.7 1.6 - - - -
329C PRO* 3.4 26.9 - - - +
331C ALA 6.1 0.2 - - - +
333C PRO* 5.6 11.4 - - + -
336C ILE* 4.0 19.3 - - + -
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322C GLU* 3.3 39.9 - - - +
323C GLN* 3.2 17.1 + - - +
325C LYS* 1.3 77.4 - - + +
327C LYS* 1.3 62.2 + - - +
329C PRO* 3.6 12.0 - - - +
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Residues in contact with LYS 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C GLU* 6.0 0.4 - - - -
286C TYR* 4.0 38.0 - - + +
323C GLN 2.9 16.8 + - - +
324C LEU 3.7 3.1 - - - +
326C GLU* 1.3 79.5 - - - +
328C PHE* 1.3 94.8 + - + +
329C PRO* 3.3 6.9 - - - +
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Residues in contact with PHE 328 (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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282C GLU* 4.0 38.8 - - + -
283C ILE* 3.9 23.1 - - + -
286C TYR* 3.9 17.7 - + + -
324C LEU* 2.7 49.0 + - + +
325C LYS* 3.7 4.4 - - - +
327C LYS* 1.3 109.8 - - + +
329C PRO* 1.3 59.8 - - - +
330C GLU 3.1 2.9 - - - -
331C ALA* 2.8 38.8 + - + +
336C ILE* 4.6 4.0 - - + +
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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) + - + + + + + -
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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