Contacts of the helix formed by residues 301 - 317 (chain A) in PDB entry 3BJI
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 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A PHE* 3.0 46.9 + - - +
228A LEU* 4.3 11.7 - - - +
297A VAL* 2.9 14.1 + - + +
298A ALA 3.2 7.5 - - - +
299A ALA 3.3 0.6 - - - -
300A ALA* 1.3 86.4 - - + +
302A GLU* 1.3 59.9 + - - +
303A ASP* 3.0 33.7 + - - +
304A VAL* 2.9 30.9 + - + +
305A GLN 3.0 8.8 + - - -
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Residues in contact with GLU 302 (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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298A ALA 4.1 1.5 + - - +
299A ALA 5.1 1.9 + - - +
300A ALA 4.1 1.4 + - - -
301A ARG* 1.3 69.9 - - - +
303A ASP* 1.3 62.4 + - - +
304A VAL 3.1 0.9 - - - -
305A GLN* 3.6 17.4 - - + +
306A MET* 2.9 39.1 + - + +
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Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A PHE* 4.0 18.5 - - + -
301A ARG* 3.0 51.3 + - - +
302A GLU* 1.3 76.6 + - - +
304A VAL* 1.3 60.5 + - - -
306A MET* 3.6 9.6 + - - +
307A LYS* 3.2 26.2 + - - +
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Residues in contact with VAL 304 (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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224A LEU* 4.2 13.0 - - + -
227A PHE* 4.0 22.0 - - + -
228A LEU* 3.8 26.2 - - + -
294A LEU* 5.6 1.8 - - + -
297A VAL* 3.7 21.8 - - + -
298A ALA* 4.2 6.3 - - - -
301A ARG* 2.9 26.8 + - + +
303A ASP* 1.3 79.0 + - - +
305A GLN* 1.3 59.8 + - - +
307A LYS* 3.2 5.8 + - - +
308A LEU* 2.9 46.5 + - + +
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Residues in contact with GLN 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ALA* 4.1 24.2 - - + +
299A ALA* 5.1 2.9 - - - -
301A ARG 3.0 5.1 + - - -
302A GLU* 3.6 22.2 - - + +
304A VAL* 1.3 79.7 - - - +
306A MET* 1.3 65.8 + - + +
308A LEU* 3.5 11.3 - - - +
309A GLU* 3.3 24.2 + - + +
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Residues in contact with MET 306 (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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302A GLU* 2.9 35.3 + - + +
303A ASP* 3.7 9.0 - - - +
304A VAL 3.2 0.2 - - - -
305A GLN* 1.3 78.2 - - + +
307A LYS* 1.3 70.0 + - - +
309A GLU* 2.9 12.1 + - + +
310A GLU* 2.8 20.9 + - - +
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Residues in contact with LYS 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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223A PRO* 5.1 6.5 - - + -
224A LEU* 4.6 10.1 - - + -
227A PHE* 3.5 37.0 - - + -
303A ASP 3.2 15.1 + - - +
304A VAL* 3.2 6.7 + - - +
306A MET* 1.3 78.1 - - - +
308A LEU* 1.3 52.6 + - - +
310A GLU* 2.9 23.3 + - + +
311A CYS* 2.6 51.2 + - - +
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Residues in contact with LEU 308 (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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220A PHE* 4.6 6.4 - - + -
224A LEU* 3.4 42.2 - - + -
294A LEU* 4.0 26.2 - - + -
298A ALA* 4.6 11.0 - - + -
304A VAL* 2.9 29.0 + - + +
305A GLN* 3.5 11.0 - - - +
306A MET 3.1 0.2 - - - -
307A LYS* 1.3 76.9 - - - +
309A GLU* 1.3 61.7 + - - +
311A CYS* 3.2 5.6 + - + +
312A SER* 3.1 24.4 + - - -
322A LEU* 4.6 17.9 - - + +
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A GLN* 3.3 12.4 + - + +
306A MET* 2.9 12.7 + - + +
308A LEU* 1.3 73.6 - - - +
310A GLU* 1.3 71.2 + - - +
311A CYS 3.2 0.3 + - - -
312A SER* 3.3 8.0 + - - -
313A GLN* 3.2 26.7 + - - +
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Residues in contact with GLU 310 (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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306A MET 2.8 11.3 + - - +
307A LYS* 3.1 25.9 - - + +
309A GLU* 1.3 78.4 - - - +
311A CYS* 1.3 57.9 - - - +
313A GLN* 3.0 18.4 + - - +
314A ARG* 3.1 15.6 + - + +
50C PRO* 5.4 8.0 - - - +
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Residues in contact with CYS 311 (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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219A HIS 2.7 32.8 - - - +
220A PHE* 3.7 24.4 - - + -
223A PRO* 4.0 16.6 - - - -
224A LEU* 4.9 5.2 - - - -
307A LYS* 2.6 30.5 + - - +
308A LEU* 3.4 8.7 - - - +
310A GLU* 1.3 72.9 - - - +
312A SER* 1.3 61.9 + - - +
314A ARG* 3.7 9.7 - - - +
315A ALA* 3.3 24.6 + - - +
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Residues in contact with SER 312 (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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220A PHE* 3.8 16.4 - - - -
308A LEU 3.1 12.2 + - - -
309A GLU* 3.8 8.7 + - - +
310A GLU 3.2 0.2 + - - -
311A CYS* 1.3 74.0 - - - +
313A GLN* 1.3 54.7 + - - +
315A ALA* 3.8 1.8 - - - -
316A ASN* 3.0 21.8 + - - +
318A GLY* 2.8 32.6 + - - -
320A PHE 3.2 26.7 + - - -
321A THR* 4.7 6.1 - - - +
322A LEU 5.1 0.2 - - - -
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Residues in contact with GLN 313 (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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309A GLU* 3.2 14.9 + - - +
310A GLU* 3.0 11.3 + - - +
312A SER* 1.3 73.8 + - - +
314A ARG* 1.3 66.4 + - - +
315A ALA 2.7 5.4 + - - -
317A ASN* 3.0 50.9 + - - +
318A GLY* 3.5 12.7 - - - +
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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
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218A GLN* 3.9 12.3 + - - +
219A HIS* 3.5 42.7 + - + +
223A PRO* 4.7 13.9 - - - +
310A GLU* 3.1 9.6 + - + +
311A CYS* 3.7 13.7 - - - +
313A GLN* 1.3 78.6 - - - +
315A ALA* 1.3 57.9 + - - +
317A ASN* 5.7 0.5 + - - -
43C ASN* 2.8 52.0 + - - +
44C VAL 6.1 0.2 - - - -
45C MET* 4.5 28.8 - - - +
50C PRO* 5.0 15.3 - - + +
52C ASN* 5.6 0.2 + - - -
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Residues in contact with ALA 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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215A SER* 3.8 17.5 + - - +
219A HIS* 3.4 29.0 + - + +
220A PHE* 4.1 6.1 - - + -
311A CYS 3.3 17.3 + - - +
313A GLN 2.7 6.9 + - - -
314A ARG* 1.3 76.4 - - - +
316A ASN* 1.3 69.4 + - - +
317A ASN* 3.8 1.8 - - - -
317B ASN* 3.9 16.8 + - - +
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Residues in contact with ASN 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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215A SER* 5.7 0.2 + - - -
312A SER* 3.0 16.5 + - - +
315A ALA* 1.3 83.9 - - - +
317A ASN* 1.3 81.0 + - - +
319A ARG* 2.7 27.9 + - + +
320A PHE* 2.4 67.4 + - + +
325A LEU* 4.5 11.7 - - - +
313B GLN* 4.9 1.6 + - - -
317B ASN* 3.7 16.7 - - - +
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Residues in contact with ASN 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 GLN* 3.0 37.1 + - - +
314A ARG 5.7 0.4 + - - -
315A ALA 5.3 1.0 - - - -
316A ASN* 1.3 82.4 - - - +
318A GLY* 1.3 61.4 + - - +
319A ARG* 3.2 2.8 + - - +
313B GLN* 3.5 21.1 + - - -
317B ASN* 3.8 21.6 + - - +
318B GLY* 4.5 5.0 + - - -
52C ASN* 6.0 1.6 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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