Contacts of the helix formed by residues 306 - 319 (chain B) in PDB entry 3CB4
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 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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301B PRO* 4.1 10.6 - - + +
303B SER* 3.0 30.1 + - - +
304B SER 2.8 1.0 + - - -
305B ASP* 1.3 84.2 - - - +
307B TYR* 1.3 64.7 + - - +
308B GLU 3.1 3.3 + - - -
309B ALA* 3.2 9.5 + - - +
310B PHE* 2.9 24.6 + - - +
360B ASP 5.6 2.0 - - - +
361B LEU* 3.8 23.2 - - + +
362B ASP* 5.2 10.5 + - - +
243C LYS* 5.2 10.9 + - - +
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Residues in contact with TYR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PRO* 4.3 12.6 - - + +
304B SER* 3.0 16.6 + - - +
305B ASP 3.6 0.4 - - - -
306B ASP* 1.3 76.9 - - - +
308B GLU* 1.3 64.8 + - + +
310B PHE* 3.6 2.6 - + - +
311B ARG* 2.8 68.8 + - - +
328B PRO* 4.7 8.0 - - - +
336B PHE* 3.4 51.5 - + + +
337B GLY* 3.8 7.2 + - - -
338B PHE* 3.5 35.5 - + - -
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ASP 4.8 10.5 - - - +
306B ASP 3.1 0.6 - - - -
307B TYR* 1.3 86.4 - - + +
309B ALA* 1.3 57.8 + - - +
311B ARG* 3.2 34.2 + - - +
312B ASP* 2.9 36.7 + - - +
219C LYS* 5.7 4.0 + - - -
236C ARG* 4.6 4.9 + - - +
244C GLN 6.0 2.0 - - - +
246C ASP* 3.8 44.9 - - + +
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ASP 5.9 0.2 - - - +
306B ASP* 3.2 12.9 + - - +
308B GLU* 1.3 76.7 - - - +
310B PHE* 1.3 60.3 + - - +
312B ASP* 3.4 7.9 + - - +
313B ALA* 2.8 31.0 + - - +
359B TYR* 5.3 6.8 - - + +
361B LEU* 4.2 16.5 - - + +
244C GLN 5.8 4.0 - - - +
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Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B LEU* 3.5 48.5 - - + -
300B PHE 4.3 2.5 - - - -
301B PRO* 3.8 22.7 - - + -
306B ASP 2.9 17.8 + - - +
307B TYR* 3.6 5.2 - - - +
309B ALA* 1.3 73.6 - - - +
311B ARG* 1.3 64.0 + - - +
313B ALA* 3.3 1.6 + - - +
314B LEU* 3.2 43.1 + - + +
337B GLY* 4.8 0.4 - - - -
338B PHE* 3.5 24.9 - + + -
355B LEU* 4.0 16.4 - - + -
361B LEU* 3.8 25.4 - - + +
363B LEU* 3.8 22.0 - - + -
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Residues in contact with ARG 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B TYR* 2.8 46.7 + - + +
308B GLU* 3.2 28.5 + - - +
310B PHE* 1.3 72.6 - - - +
312B ASP* 1.3 68.3 + - - +
314B LEU* 3.6 4.8 + - - +
315B GLY* 3.2 17.8 + - - -
326B TYR* 5.0 5.7 + - + -
338B PHE* 3.6 27.7 - - + -
203C TYR* 4.2 2.8 + - - +
219C LYS* 5.7 4.9 - - - +
236C ARG* 4.8 18.0 - - - +
246C ASP* 5.3 0.2 + - - -
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Residues in contact with ASP 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLU* 2.9 21.3 + - - +
309B ALA* 3.7 7.5 - - - +
310B PHE 3.2 0.2 - - - -
311B ARG* 1.3 83.3 + - - +
313B ALA* 1.3 58.6 + - - +
315B GLY 3.4 0.7 + - - -
316B LYS* 2.9 39.9 + - - +
203C TYR* 3.6 28.5 + - + -
204C LEU* 4.3 5.1 - - + +
236C ARG* 2.9 45.6 + - - -
244C GLN* 4.6 4.5 - - - +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B ALA 2.8 20.9 + - - +
310B PHE 3.6 5.4 - - - +
312B ASP* 1.3 74.0 - - - +
314B LEU* 1.3 51.5 + - - +
316B LYS* 3.2 3.4 + - - +
317B LEU* 2.8 40.5 + - - +
355B LEU* 4.0 12.3 - - + -
359B TYR* 3.6 46.2 - - + -
361B LEU* 4.4 2.7 - - + -
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B PHE* 3.2 33.7 + - + +
311B ARG 3.9 4.3 - - - +
313B ALA* 1.3 75.0 - - - +
315B GLY* 1.3 60.3 + - - +
317B LEU* 3.5 7.0 + - + +
318B SER* 2.8 31.2 + - - -
324B LEU* 4.2 18.6 - - + +
326B TYR* 3.6 36.6 - - + -
338B PHE* 3.6 44.2 - - + -
340B CYS* 4.4 12.1 - - - -
351B ILE* 5.4 2.7 - - + -
355B LEU* 4.9 12.8 - - + -
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Residues in contact with GLY 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B ARG 3.2 9.4 + - - -
314B LEU* 1.3 78.2 - - - +
316B LYS* 1.3 60.7 + - - +
318B SER* 3.2 14.9 + - - -
319B LEU* 3.4 14.2 + - - +
326B TYR* 3.6 16.2 + - - -
203C TYR* 3.5 28.7 - - - -
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B ASP* 2.9 23.6 + - - +
313B ALA 3.4 4.5 - - - +
315B GLY* 1.3 76.1 - - - +
317B LEU* 1.3 62.7 + - - +
318B SER 3.3 0.3 + - - -
319B LEU* 3.3 25.8 + - + +
320B ASN* 4.4 6.1 + - - +
359B TYR* 3.4 40.3 - - + +
201C ASP* 5.1 7.7 + - - -
203C TYR* 3.6 42.0 - - + -
204C LEU* 5.3 2.6 - - - +
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B ALA 2.8 16.2 + - - +
314B LEU* 3.9 6.1 - - + +
316B LYS* 1.3 74.1 - - - +
318B SER* 1.3 57.8 + - - +
319B LEU 3.3 0.5 + - - -
320B ASN* 3.4 4.3 + - - +
321B ASP* 3.1 33.1 + - + +
324B LEU* 4.1 12.1 - - + -
351B ILE* 4.2 30.1 - - + +
354B ARG* 3.2 39.2 + - + +
355B LEU* 3.7 27.8 - - + -
359B TYR* 3.3 36.1 - - + +
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Residues in contact with SER 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B ILE* 4.5 4.5 - - - +
266B HIS* 4.6 12.0 + - - -
314B LEU 2.8 20.1 + - - -
315B GLY* 3.3 11.2 - - - -
316B LYS 3.1 0.8 - - - -
317B LEU* 1.3 77.3 - - - +
319B LEU* 1.3 59.5 + - - +
320B ASN 3.3 0.8 + - - -
321B ASP 3.6 19.5 + - - +
324B LEU* 4.5 11.0 + - - +
326B TYR* 3.3 24.4 + - - -
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Residues in contact with LEU 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B PHE* 3.5 45.7 - - + +
202B ASN* 6.1 0.7 - - - +
264B ASP* 6.1 4.5 - - + -
265B ILE* 3.4 27.0 + - - +
315B GLY 3.5 12.3 - - - +
316B LYS* 3.6 16.6 - - + +
317B LEU 3.2 1.2 - - - -
318B SER* 1.3 78.6 - - - +
320B ASN* 1.3 63.5 + - - +
202C ASN 5.2 6.3 - - - +
203C TYR* 4.1 23.6 - - + -
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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