Contacts of the helix formed by residues 301 - 321 (chain C) in PDB entry 4BGG
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 301 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300C LEU* 1.3 76.5 - - - +
302C THR* 1.3 53.1 + - - +
303C VAL* 2.5 20.9 + - - +
304C SER* 2.9 21.5 + - - +
305C CYS* 5.1 0.7 - - - -
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Residues in contact with THR 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ASP* 1.3 66.3 - - - +
303C VAL* 1.3 63.9 + - - -
305C CYS* 3.0 28.2 + - - +
306C LEU* 3.1 6.9 + - - +
464C ASP* 6.1 0.7 - - - -
466C THR* 4.9 20.9 - - - +
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Residues in contact with VAL 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C ASP 2.5 8.8 + - - +
302C THR* 1.3 75.3 - - - +
304C SER* 1.3 59.8 + - - +
305C CYS 3.2 1.3 - - - -
306C LEU* 3.6 12.1 - - + +
307C ARG* 2.9 28.7 + - + +
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Residues in contact with SER 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C TYR* 6.0 1.8 - - - -
300C LEU* 3.6 8.7 - - - +
301C ASP* 2.9 36.6 + - - +
303C VAL* 1.3 70.6 - - - +
305C CYS* 1.3 62.3 + - - +
307C ARG* 4.0 6.5 - - - +
308C ILE* 3.2 33.7 + - - +
348C GLY* 4.8 2.1 - - - +
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Residues in contact with CYS 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C LEU* 4.1 17.6 - - + +
301C ASP 3.9 0.4 + - - -
302C THR* 3.0 18.2 + - - +
304C SER* 1.3 79.2 + - - +
306C LEU* 1.3 61.8 + - - +
308C ILE* 3.3 7.1 + - - +
309C VAL* 3.2 26.0 + - - +
414C VAL* 4.0 22.7 - - - -
415C ALA* 4.6 10.8 - - - -
466C THR* 5.5 4.3 - - + -
470C LEU* 3.9 28.0 - - - -
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Residues in contact with LEU 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C THR 3.1 6.4 + - - +
303C VAL* 3.4 19.4 + - + +
305C CYS* 1.3 78.2 - - - +
307C ARG* 1.3 58.8 + - - +
309C VAL* 3.7 8.9 - - - +
310C LEU* 2.9 37.7 + - + +
466C THR* 5.7 8.0 - - + +
470C LEU* 6.3 0.4 - - - -
495C LEU* 6.2 0.4 - - + -
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Residues in contact with ARG 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C VAL* 2.9 21.2 + - + +
304C SER* 4.0 7.0 - - - +
305C CYS 3.2 0.2 - - - -
306C LEU* 1.3 76.6 - - - +
308C ILE* 1.3 60.7 + - - +
310C LEU* 4.2 3.7 - - - +
311C SER* 3.0 29.3 + - - -
347C ASN 5.8 1.1 - - - +
348C GLY* 4.2 17.3 - - - +
349C GLN* 4.6 9.5 - - + +
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Residues in contact with ILE 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C LEU* 4.2 13.2 - - + -
294C TYR* 4.4 22.7 - - + -
295C LEU* 5.2 4.3 - - + -
300C LEU* 5.5 5.4 - - + -
304C SER* 3.2 20.5 + - - +
305C CYS* 3.6 7.9 - - - +
306C LEU 3.2 0.2 - - - -
307C ARG* 1.3 77.5 - - - +
309C VAL* 1.3 62.5 + - - +
311C SER* 2.7 21.5 + - - -
312C ILE* 3.1 23.8 + - + +
344C VAL* 5.9 2.0 - - + -
348C GLY 3.7 16.2 - - - +
350C CYS* 3.8 21.1 - - - -
414C VAL* 4.1 28.7 - - + -
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Residues in contact with VAL 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C CYS* 3.2 19.9 + - - +
306C LEU* 3.7 10.3 - - - +
308C ILE* 1.3 74.9 - - + +
310C LEU* 1.3 68.1 + - - +
312C ILE* 3.3 10.4 + - + +
313C ALA* 3.0 24.6 + - - +
407C PHE* 4.2 4.7 - - + -
410C VAL* 6.3 0.2 - - + -
411C LEU* 3.5 33.9 - - + -
414C VAL* 3.9 27.1 - - + -
470C LEU* 4.5 7.9 - - + -
495C LEU* 3.8 28.1 - - + +
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C LEU* 2.9 22.6 + - + +
307C ARG* 4.2 4.3 - - - +
309C VAL* 1.3 78.5 - - - +
311C SER* 1.3 58.3 + - - +
313C ALA* 3.3 0.7 + - + +
314C SER* 3.0 37.5 + - - +
492C LYS* 3.9 25.1 - - + +
495C LEU* 4.0 21.5 - - + +
496C THR* 3.8 32.5 - - + +
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Residues in contact with SER 311 (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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261C ASN* 3.4 37.5 - - - +
307C ARG 3.0 16.2 + - - -
308C ILE 2.7 20.3 + - - -
310C LEU* 1.3 74.2 - - - +
312C ILE* 1.3 67.5 + - - +
314C SER* 3.2 2.9 + - - -
315C GLY 3.0 18.4 + - - -
349C GLN* 3.9 14.4 - - - +
350C CYS* 3.0 26.1 + - - +
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Residues in contact with ILE 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C LEU* 4.0 19.3 - - + -
308C ILE* 3.1 32.4 + - + +
309C VAL* 3.7 11.2 - - + +
311C SER* 1.3 77.3 + - - +
313C ALA* 1.3 62.3 + - - +
315C GLY* 3.3 1.0 + - - -
316C LEU* 2.9 22.6 + - + +
337C LEU* 5.1 5.6 - - + -
342C ILE* 4.1 26.0 - - + -
350C CYS* 4.1 14.6 - - + -
351C CYS* 6.5 0.4 - - - +
352C ILE* 3.8 17.3 - - + +
407C PHE* 3.5 26.7 - - + -
410C VAL* 4.2 9.9 - - + -
414C VAL* 5.2 0.2 - - + -
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Residues in contact with ALA 313 (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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309C VAL 3.0 17.4 + - - +
310C LEU* 3.7 4.5 - - - +
311C SER 3.2 0.2 - - - -
312C ILE* 1.3 78.1 - - - +
314C SER* 1.3 55.9 + - - +
316C LEU* 3.8 4.7 - - - +
317C ALA* 2.8 31.5 + - - +
407C PHE* 4.1 14.6 - - + -
488C ALA* 4.5 5.6 - - - +
491C ILE* 4.2 10.1 - - + -
492C LYS* 4.2 15.9 - - + +
495C LEU* 4.0 17.3 - - + -
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Residues in contact with SER 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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259C HIS* 4.0 9.4 + - - -
261C ASN* 3.6 18.8 - - - -
310C LEU* 3.0 23.0 + - - +
311C SER* 3.6 1.4 - - - -
312C ILE 3.2 0.2 - - - -
313C ALA* 1.3 74.3 - - - +
315C GLY* 1.3 60.5 + - - +
317C ALA* 3.5 1.4 + - - +
318C HIS* 2.9 29.6 + - - +
492C LYS* 3.5 36.0 + - - +
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Residues in contact with GLY 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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259C HIS* 4.4 6.3 - - - -
261C ASN* 3.8 28.8 - - - +
262C ILE* 4.1 4.4 - - - +
311C SER 3.0 11.1 + - - -
312C ILE 3.7 2.7 - - - -
314C SER* 1.3 77.6 - - - +
316C LEU* 1.3 61.9 + - - +
318C HIS* 3.2 3.5 + - - +
319C LEU* 3.0 25.7 + - - +
352C ILE* 3.8 8.1 - - - -
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Residues in contact with LEU 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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312C ILE* 2.9 16.1 + - + +
313C ALA* 3.9 5.2 - - - +
315C GLY* 1.3 75.4 - - - +
317C ALA* 1.3 64.1 + - - +
319C LEU* 3.0 17.5 + - + +
320C HIS* 2.9 50.0 + - + +
334C HIS* 4.9 1.6 - - + -
337C LEU* 4.1 27.6 - - + -
352C ILE* 3.6 9.0 - - + +
403C ASP* 3.9 17.0 - - + +
404C ILE* 4.3 18.8 - - + -
407C PHE* 4.2 21.8 - - + -
488C ALA* 4.2 6.3 - - + -
491C ILE* 6.1 0.2 - - + -
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Residues in contact with ALA 317 (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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313C ALA 2.8 19.3 + - - +
314C SER 3.9 3.6 - - - +
316C LEU* 1.3 76.7 - - - +
318C HIS* 1.3 63.9 + - - +
320C HIS* 3.9 1.8 - - - +
321C ILE* 3.0 29.1 + - - +
488C ALA* 3.7 28.4 - - + +
489C LEU* 4.2 10.1 - - + +
492C LYS* 4.5 14.4 - - + +
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Residues in contact with HIS 318 (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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257C LEU* 4.3 12.0 - - + +
258C ARG 4.0 15.0 + - - -
259C HIS* 3.4 36.3 + + + +
262C ILE* 3.9 18.2 - - + -
314C SER 2.9 19.0 + - - +
315C GLY* 3.6 4.5 - - - +
316C LEU 3.2 0.2 - - - -
317C ALA* 1.3 78.4 - - - +
319C LEU* 1.3 61.3 + - - +
321C ILE* 3.7 8.7 - - - +
323C ILE* 5.9 4.5 - - + -
329C LYS* 3.7 30.3 - - + +
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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
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257C LEU* 4.0 24.0 - - + -
262C ILE* 3.6 23.1 - - + -
315C GLY 3.0 17.4 + - - +
316C LEU* 3.0 11.4 + - + +
318C HIS* 1.3 79.2 - - - +
320C HIS* 1.3 57.4 + - + +
321C ILE 4.2 1.0 - - - +
329C LYS* 5.0 0.4 - - - +
330C PRO 4.3 1.2 - - - +
331C ALA* 3.7 2.3 - - - -
332C ILE* 2.7 58.8 + - + +
334C HIS* 4.4 22.4 - - + +
352C ILE* 4.5 17.9 - - + -
355C LEU* 4.3 21.3 - - + -
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Residues in contact with HIS 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C LEU* 2.9 34.1 + - + +
317C ALA* 3.3 6.3 + - - +
319C LEU* 1.3 78.7 - - + +
321C ILE* 1.3 56.9 + - - +
322C GLU 3.7 0.5 + - - -
331C ALA* 3.1 21.4 - - - +
332C ILE 3.2 20.4 - - - +
333C ALA* 4.3 0.2 - - - -
400C LYS* 3.6 63.1 + - + +
403C ASP* 2.9 29.2 + - + -
404C ILE* 4.4 9.4 - - + +
488C ALA* 3.7 16.3 + - + +
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Residues in contact with ILE 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 ALA* 3.0 18.2 + - + +
318C HIS* 3.7 13.1 - - - +
319C LEU 3.5 0.8 - - - +
320C HIS* 1.3 77.3 - - - +
322C GLU* 1.3 65.5 + - - +
323C ILE* 3.5 3.9 + - + +
329C LYS* 3.8 11.8 - - - +
330C PRO 4.0 2.8 - - - +
331C ALA* 4.4 1.1 - - - -
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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