Contacts of the helix formed by residues 302 - 320 (chain A) in PDB entry 1BG1
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 ARG 302 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL* 5.6 0.4 - - + +
281A ILE* 3.8 20.2 + - + +
284A LEU* 4.5 4.9 - - + -
285A GLU* 3.2 62.7 + - - +
297A PRO 4.5 0.2 + - - -
298A ILE* 2.9 31.2 + - + +
299A VAL* 6.1 0.6 - - - +
301A HIS* 1.3 76.9 - - - +
303A PRO* 1.3 86.5 - - + +
305A LEU* 3.0 14.7 + - + +
306A GLU* 2.9 55.0 + - - +
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Residues in contact with PRO 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A VAL* 3.6 19.7 - - - +
300A GLN 4.8 0.7 - - - -
301A HIS* 3.3 6.1 - - - +
302A ARG* 1.3 114.7 - - + +
304A MET* 1.3 57.3 + - + +
306A GLU* 3.4 5.3 + - + +
307A GLU* 3.0 27.9 + - - +
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Residues in contact with MET 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A HIS* 2.9 13.0 + - - +
303A PRO* 1.3 77.7 - - + +
305A LEU* 1.3 65.5 + - + +
307A GLU* 3.5 32.0 - - - +
308A ARG* 3.0 49.2 + - + +
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 4.3 22.2 - - + +
221A LEU* 4.0 28.7 - - + -
222A ALA* 3.9 26.9 - - + +
225A LEU* 3.5 25.6 - - + +
281A ILE* 3.7 18.9 - - + +
284A LEU* 4.7 3.6 - - + -
301A HIS* 3.2 15.9 + - + +
302A ARG* 3.4 20.6 - - - +
304A MET* 1.3 79.3 - - + +
306A GLU* 1.3 59.0 + - - +
308A ARG* 3.4 5.4 + - - +
309A ILE* 3.0 30.5 + - - +
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ARG* 3.7 24.1 + - - +
281A ILE* 3.9 13.1 - - + +
282A LYS* 3.6 27.5 - - - +
285A GLU* 5.8 0.7 - - - -
302A ARG* 2.9 37.3 + - - +
303A PRO* 3.4 10.3 - - + +
305A LEU* 1.3 73.4 - - - +
307A GLU* 1.3 66.6 + - - +
309A ILE* 3.1 8.3 - - - +
310A VAL* 2.9 47.3 + - - +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A PRO 3.0 13.5 + - - +
304A MET* 3.5 35.0 - - - +
306A GLU* 1.3 78.0 - - - +
308A ARG* 1.3 61.7 + - - +
310A VAL* 3.6 5.2 + - - +
311A GLU* 3.1 30.5 + - + +
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Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ALA* 3.3 38.8 + - - +
225A LEU* 3.6 23.1 - - + +
226A SER* 3.5 15.0 + - - -
229A GLU* 2.8 48.6 + - - +
304A MET* 3.0 40.9 + - - +
305A LEU* 3.8 5.2 - - - +
307A GLU* 1.3 79.7 - - + +
309A ILE* 1.3 65.4 + - - +
311A GLU* 3.4 4.9 + - - +
312A LEU* 3.1 30.1 + - - +
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LEU* 3.9 20.4 - - + +
228A MET* 4.2 5.6 - - - -
274A GLN* 3.5 48.9 - - + +
277A THR* 4.3 5.2 - - + -
278A ARG* 3.8 33.9 - - + +
281A ILE* 4.2 11.9 - - + -
305A LEU 3.0 17.0 + - - +
306A GLU* 3.1 19.5 - - - +
308A ARG* 1.3 75.6 - - - +
310A VAL* 1.3 69.1 + - + +
312A LEU* 3.3 7.4 + - + +
313A PHE* 3.0 24.0 + - + +
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ARG* 4.0 18.8 - - - +
306A GLU* 2.9 40.6 + - - +
307A GLU* 3.9 4.9 - - - +
309A ILE* 1.3 79.8 - - + +
311A GLU* 1.3 57.7 + - - +
313A PHE* 4.0 5.1 - - - +
314A ARG* 2.9 46.8 + - - +
450A LEU* 3.7 29.1 - - + +
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 3.1 21.2 + - + +
308A ARG* 3.8 6.3 - - - +
309A ILE 3.3 0.2 - - - -
310A VAL* 1.3 75.1 - - - +
312A LEU* 1.3 67.3 + - + +
314A ARG* 3.7 15.6 + - - +
315A ASN* 3.0 54.1 + - - +
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 4.0 7.0 - - + +
228A MET* 3.9 19.7 - - + -
229A GLU* 3.6 49.6 - - + +
232A GLN* 2.8 47.6 + - + +
274A GLN* 3.7 11.7 - - - +
308A ARG 3.1 21.4 + - - +
309A ILE* 3.6 18.6 - - + +
311A GLU* 1.3 80.0 - - + +
313A PHE* 1.3 56.7 + - - +
315A ASN* 4.8 1.1 - - - +
316A LEU* 2.9 15.2 + - - +
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Residues in contact with PHE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ALA* 4.2 22.2 - - + -
274A GLN* 3.2 21.0 + - + +
275A LEU* 3.6 45.3 - - + -
278A ARG* 6.4 1.3 - - - -
309A ILE* 3.0 14.7 + - + +
310A VAL* 4.0 5.4 - - - +
312A LEU* 1.3 75.8 - - - +
314A ARG* 1.3 67.4 + - - +
316A LEU* 3.0 4.4 + - + +
317A MET* 2.9 46.5 + - + +
353A VAL* 5.6 0.2 - - + -
355A PHE* 4.1 7.6 - + - -
447A HIS* 4.3 14.1 - + + -
450A LEU* 3.8 25.4 - - + -
452A ILE* 3.8 21.3 - - + -
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Residues in contact with ARG 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A VAL* 2.9 41.0 + - + +
311A GLU* 3.7 17.7 + - - +
313A PHE* 1.3 78.4 - - - +
315A ASN* 1.3 66.6 + - - +
317A MET* 3.4 3.1 + - - +
318A LYS* 3.2 46.5 + - - +
450A LEU* 3.9 15.7 - - + +
451A LYS 2.7 31.5 + - - +
452A ILE* 3.8 24.3 - - + +
453A ASP 5.3 0.4 - - - +
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Residues in contact with ASN 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLN* 3.8 13.8 - - - +
311A GLU* 3.0 51.1 + - - +
312A LEU* 5.0 0.8 - - - +
314A ARG* 1.3 79.0 - - - +
316A LEU* 1.3 63.0 + - - +
318A LYS* 3.5 15.5 + - - +
319A SER* 2.8 30.0 + - - +
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A GLN* 3.4 17.6 - - - +
235A LEU* 4.3 5.6 - - + -
236A THR* 4.3 16.4 - - + -
267A ILE* 3.8 26.7 - - + +
270A LEU* 4.0 14.8 - - + -
271A ALA* 3.6 36.1 - - + +
274A GLN* 3.5 22.4 - - - +
312A LEU 2.9 18.1 + - - +
313A PHE* 3.0 6.7 + - + +
315A ASN* 1.3 75.8 - - - +
317A MET* 1.3 64.0 + - - +
319A SER* 3.2 5.9 + - - -
320A ALA* 3.0 24.7 + - - +
353A VAL* 4.7 2.5 - - + -
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Residues in contact with MET 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A PHE* 2.9 43.9 + - + +
314A ARG 3.6 7.9 - - - +
316A LEU* 1.3 75.7 - - - +
318A LYS* 1.3 62.7 + - - +
320A ALA* 3.2 19.1 + - - +
321A PHE 3.5 5.2 + - - -
351A LEU* 3.8 30.0 - - + +
353A VAL* 3.8 28.7 - - - -
355A PHE* 5.3 1.6 - - + -
358A LEU* 4.8 5.6 - - + -
445A VAL* 4.1 32.3 - - + -
447A HIS* 6.1 1.1 - - + -
452A ILE* 3.8 16.6 - - + -
454A LEU* 3.7 17.4 - - + +
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Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ARG* 3.2 40.7 + - - +
315A ASN* 3.8 15.2 + - - +
316A LEU 3.3 0.2 - - - -
317A MET* 1.3 77.8 - - - +
319A SER* 1.3 60.2 + - - +
321A PHE* 3.6 16.4 + - - +
452A ILE* 4.1 5.6 - - + +
453A ASP* 3.5 30.8 + - - +
454A LEU* 3.9 13.9 - - + +
455A GLU 4.6 8.5 - - - +
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A THR* 3.7 36.3 + - - +
240A LEU* 3.4 23.7 - - - +
244A LYS* 5.1 3.3 + - - +
267A ILE* 5.4 0.9 - - - -
315A ASN* 2.8 18.6 + - - +
316A LEU* 3.2 4.5 + - - -
318A LYS* 1.3 75.5 - - - +
320A ALA* 1.3 63.7 + - - +
321A PHE 3.2 1.0 + - - +
322A VAL* 3.5 11.1 - - - +
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Residues in contact with ALA 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ILE* 4.1 7.8 - - + +
316A LEU 3.0 12.6 + - - +
317A MET 3.2 12.5 + - - +
319A SER* 1.3 77.7 - - - +
321A PHE* 1.3 57.1 + - - +
322A VAL 3.4 0.5 + - - -
350A ARG 3.1 6.1 - - - +
351A LEU* 4.0 4.7 - - + -
352A LEU* 2.9 54.7 + - + +
353A VAL* 3.8 22.4 - - + -
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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
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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