Contacts of the helix formed by residues 309 - 326 (chain C) in PDB entry 4BUR
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 GLY 309 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLY 3.5 2.8 - - - -
308C GLY* 1.3 76.2 - - - +
310C PHE* 1.3 65.9 + - - -
311C LEU 3.3 2.9 - - - -
312C GLY 4.2 0.6 - - - +
313C SER* 2.7 29.1 + - - -
340C MET* 3.6 11.9 - - - -
397C ALA 5.1 0.2 + - - -
700C NAD 3.4 33.5 + - - -
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Residues in contact with PHE 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C GLY* 1.3 71.6 - - - +
311C LEU* 1.3 63.2 + - - +
313C SER* 4.3 0.3 - - - -
314C GLU* 3.2 32.4 + - - +
340C MET* 3.5 24.1 - - + -
343C ILE* 3.7 31.2 - - + -
454C HIS* 3.7 21.3 - + - -
482C PHE* 3.6 28.5 - + - -
484C SER* 4.6 3.8 - - - -
486C LEU* 5.2 0.2 - - - +
492C TYR* 3.8 9.2 - - - -
700C NAD 3.1 83.9 + + + +
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Residues in contact with LEU 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C SER* 3.9 13.2 - - - -
284C PHE* 3.5 44.6 - - + +
310C PHE* 1.3 73.2 - - - +
312C GLY* 1.3 55.5 + - - +
314C GLU* 3.9 0.2 - - - -
315C LEU* 2.8 45.3 + - + +
396C ALA 5.9 0.2 - - - +
397C ALA* 3.8 15.9 - - + -
700C NAD 2.7 52.7 + - + +
1612C FAD 3.7 29.4 - - + -
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Residues in contact with GLY 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ILE* 3.7 17.8 - - - +
307C GLY 3.5 19.7 - - - -
309C GLY 3.6 2.6 + - - +
310C PHE 3.5 0.2 - - - -
311C LEU* 1.3 78.4 - - - +
313C SER* 1.3 57.0 + - - +
315C LEU* 3.2 4.5 + - - +
316C ALA* 2.8 30.0 + - - +
332C GLN* 3.5 6.9 + - - -
397C ALA* 3.6 11.3 - - - +
700C NAD 4.0 1.4 + - - -
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Residues in contact with SER 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C GLY 3.0 11.3 + - - -
309C GLY 2.7 23.0 + - - -
310C PHE 4.4 0.4 - - - -
312C GLY* 1.3 75.8 - - - +
314C GLU* 1.3 62.6 + - - +
316C ALA* 3.2 5.9 - - - +
317C CYS* 3.2 27.0 + - - -
332C GLN* 3.4 7.9 - - - +
339C ASN* 2.9 27.4 + - - +
340C MET* 4.0 6.1 - - - -
356C VAL* 5.0 1.2 - - - +
486C LEU* 3.7 23.3 - - - -
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Residues in contact with GLU 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C SER* 3.2 35.0 + - - +
177C LYS* 3.2 23.4 + - + -
310C PHE* 3.2 16.5 + - - +
311C LEU* 3.9 2.5 - - - +
313C SER* 1.3 75.3 - - - +
315C LEU* 1.3 63.1 + - - +
317C CYS* 3.3 5.7 + - - +
318C ALA* 3.2 21.5 + - - +
484C SER* 2.8 24.7 + - - +
485C ASP 3.7 12.0 + - - +
486C LEU* 3.7 19.3 - - + -
700C NAD 3.2 29.0 + - - -
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Residues in contact with LEU 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C SER* 4.4 14.8 - - - +
180C TRP* 4.6 11.4 - - + +
284C PHE* 4.0 41.5 - - + -
293C LEU* 4.5 12.3 - - + -
305C ILE* 3.7 12.1 - - + -
311C LEU* 2.8 35.0 + - + +
312C GLY* 3.5 6.5 - - - +
314C GLU* 1.3 72.3 - - - +
316C ALA* 1.3 59.8 + - - +
318C ALA* 3.4 3.7 + - + +
319C LEU* 3.0 37.6 + - + +
395C VAL* 3.7 31.9 - - + -
397C ALA* 5.4 0.7 - - + -
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Residues in contact with ALA 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ILE* 3.5 14.3 - - + +
312C GLY 2.8 16.6 + - - +
313C SER* 3.2 11.0 - - - +
315C LEU* 1.3 72.4 - - - +
317C CYS* 1.3 57.0 + - - +
319C LEU* 3.2 2.8 + - - +
320C GLY 2.8 25.6 + - - -
330C VAL* 4.2 2.1 - - - +
332C GLN* 3.6 23.3 - - + +
356C VAL* 4.4 4.5 - - + -
361C VAL* 3.4 28.2 - - + +
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Residues in contact with CYS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C PHE* 5.4 6.1 - - + -
313C SER 3.2 14.8 + - - -
314C GLU* 3.3 6.7 + - - +
316C ALA* 1.3 78.4 - - - +
318C ALA* 1.3 62.6 + - - +
320C GLY* 3.4 1.6 + - - -
321C ARG* 3.2 27.7 + - - +
356C VAL* 4.3 14.6 - - - -
359C GLU* 4.2 25.7 - - + +
485C ASP 5.6 0.7 - - - +
486C LEU* 3.7 37.2 - - - -
487C GLY* 3.8 11.9 - - - +
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Residues in contact with ALA 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C SER 4.1 11.7 - - - +
180C TRP* 3.9 37.3 - - + +
181C PHE* 4.5 15.6 - - + -
314C GLU 3.2 11.8 + - - +
315C LEU* 3.8 8.5 - - + +
317C CYS* 1.3 77.9 - - - +
319C LEU* 1.3 65.9 - - + +
321C ARG* 3.3 5.5 + - - +
322C LYS* 3.3 25.2 + - - +
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Residues in contact with LEU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C TRP* 3.8 34.1 - - + -
293C LEU* 4.5 15.0 - - + -
297C SER* 4.0 19.3 - - - -
303C ILE* 4.1 30.5 - - + -
305C ILE* 3.8 24.9 - - + -
315C LEU* 3.0 20.6 + - + +
318C ALA* 1.3 77.5 - - + +
320C GLY* 1.3 57.7 + - - +
322C LYS* 3.4 5.9 + - + +
323C ALA* 2.9 29.8 + - - +
330C VAL* 3.4 22.1 - - + +
395C VAL* 5.1 0.7 - - + -
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Residues in contact with GLY 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ALA 2.8 16.2 + - - -
317C CYS 3.8 2.2 - - - -
318C ALA 3.2 0.2 - - - -
319C LEU* 1.3 77.6 - - - +
321C ARG* 1.3 55.8 + - - +
323C ALA* 3.4 8.7 + - - +
324C ARG* 3.1 27.7 + - - +
330C VAL* 4.1 5.1 - - - +
359C GLU 3.4 20.7 - - - +
360C GLY* 4.4 9.4 - - - +
361C VAL* 4.5 3.8 - - - -
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Residues in contact with ARG 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C PHE* 3.3 58.5 + - + +
317C CYS 3.2 13.8 + - - +
318C ALA* 3.3 8.5 + - - +
320C GLY* 1.3 74.3 - - - +
322C LYS* 1.3 66.0 + - + +
323C ALA 3.1 0.7 + - - -
324C ARG* 3.5 24.3 + - - +
325C ALA* 4.0 7.3 + - - +
359C GLU* 4.4 18.2 - - - +
487C GLY* 6.4 0.4 - - - -
488C PRO* 6.1 3.8 - - - +
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Residues in contact with LYS 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C TRP* 3.9 38.0 - - + +
294C GLU* 3.4 33.0 + - - +
297C SER* 3.4 27.6 + - - +
298C ARG* 4.7 7.0 - - + +
318C ALA 3.3 12.7 + - - +
319C LEU* 3.8 11.7 - - + +
321C ARG* 1.3 79.6 - - + +
323C ALA* 1.3 60.9 + - - +
325C ALA* 3.7 17.1 + - + +
326C LEU* 4.1 12.0 + - - +
328C THR* 4.8 1.1 + - - -
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Residues in contact with ALA 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C LEU 2.9 18.1 + - - +
320C GLY* 3.5 8.3 - - - +
321C ARG 3.1 0.4 - - - -
322C LYS* 1.3 74.0 - - - +
324C ARG* 1.3 59.3 + - - +
325C ALA 3.2 2.4 + - - -
326C LEU 3.6 1.0 + - - -
327C GLY* 2.9 27.4 + - - -
328C THR* 3.2 35.2 + - - +
330C VAL* 3.6 20.4 - - + +
360C GLY 5.1 4.3 - - - +
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Residues in contact with ARG 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C GLY 3.1 15.9 + - - +
321C ARG* 3.6 21.3 - - - +
322C LYS 3.5 0.2 - - - -
323C ALA* 1.3 75.2 - - - +
325C ALA* 1.3 64.5 + - - +
327C GLY* 3.5 8.6 + - - +
358C ARG* 3.5 26.7 + - - +
359C GLU* 3.8 13.6 + - - +
360C GLY* 4.0 15.0 - - - +
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Residues in contact with ALA 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ARG 4.0 4.9 + - - +
322C LYS* 3.7 14.5 + - + +
323C ALA 3.2 0.6 - - - -
324C ARG* 1.3 82.1 - - - +
326C LEU* 1.3 69.6 + - + +
327C GLY 3.8 0.5 + - - -
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Residues in contact with LEU 326 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C SER 5.2 3.4 - - - +
298C ARG* 4.3 30.5 - - + +
300C VAL 5.9 0.9 - - - +
301C LYS* 5.4 3.5 + - - +
322C LYS 4.1 10.3 + - - +
323C ALA 3.6 2.4 + - - -
325C ALA* 1.3 88.1 - - + +
327C GLY* 1.3 53.7 + - - +
328C THR* 2.9 38.7 + - + +
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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
------------------------------------------------------------
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