Contacts of the helix formed by residues 305 - 318 (chain B) in PDB entry 3Q6N
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 THR 305 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303B ASP 4.4 1.5 + - - +
304B ILE* 1.3 81.9 - - - +
306B ASN* 1.3 65.9 + - - +
307B GLU* 3.8 8.5 + - - +
308B GLU* 3.3 35.4 + - - +
309B TYR* 3.2 19.9 + - - -
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Residues in contact with ASN 306 (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 THR* 1.3 73.9 - - - +
307B GLU* 1.3 57.3 + - - +
309B TYR* 3.1 10.7 + - - +
310B GLY* 2.8 27.7 + - - -
322B ASP* 4.0 18.4 + - - -
323B HIS* 3.3 25.9 + - - -
326B VAL* 5.5 1.2 - - - +
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Residues in contact with GLU 307 (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 THR* 3.3 8.3 + - - +
306B ASN* 1.3 77.9 - - - +
308B GLU* 1.3 58.9 + - + +
310B GLY* 3.4 1.9 + - - +
311B GLU* 2.9 48.7 + - + +
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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
----------------------------------------------------------
298B THR* 5.4 4.8 + - - +
304B ILE* 3.5 31.8 - - + +
305B THR* 3.3 26.3 + - - +
306B ASN 3.2 0.6 - - - -
307B GLU* 1.3 77.2 - - - +
309B TYR* 1.3 66.3 + - - +
311B GLU* 3.0 8.7 + - - +
312B PHE* 2.9 22.8 + - - +
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Residues in contact with TYR 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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298B THR* 5.0 4.0 - - - -
302B ASP* 3.7 12.6 + - - -
304B ILE* 3.3 38.8 - - + +
305B THR 3.2 17.6 + - - -
306B ASN* 3.1 12.9 + - - +
308B GLU* 1.3 76.9 - - - +
310B GLY* 1.3 57.1 + - - +
312B PHE* 3.2 4.8 + - + +
313B TYR* 2.8 30.7 + - - +
323B HIS* 3.7 14.1 - - + +
326B VAL* 4.2 19.7 - - + -
328B HIS* 2.8 32.7 + + + +
340B LEU* 3.4 34.8 - - + -
342B PHE* 3.4 16.5 - + + -
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Residues in contact with GLY 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ASN 2.8 18.9 + - - -
307B GLU* 3.7 2.7 - - - -
309B TYR* 1.3 73.5 - - - +
311B GLU* 1.3 61.4 + - - +
313B TYR* 3.1 3.5 + - - +
314B LYS* 3.0 32.4 + - - +
322B ASP* 3.9 12.1 - - - -
323B HIS* 3.4 20.6 + - - -
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Residues in contact with GLU 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 GLU* 2.9 39.6 + - + +
308B GLU* 3.0 9.4 + - - +
310B GLY* 1.3 71.2 - - - +
312B PHE* 1.3 64.6 + - - +
314B LYS* 3.4 27.6 + - - +
315B SER* 3.2 22.9 + - - -
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Residues in contact with PHE 312 (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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298B THR* 3.3 33.7 - - + +
299B ARG* 3.9 11.0 - - - -
308B GLU 2.9 12.8 + - - +
309B TYR* 3.6 8.5 - - - +
311B GLU* 1.3 75.3 - - - +
313B TYR* 1.3 63.7 + - - +
315B SER* 3.1 12.9 + - - -
316B LEU* 3.0 50.1 + - + +
340B LEU* 3.6 22.2 - - + -
342B PHE* 3.6 21.3 - + - -
388B VAL* 3.9 24.2 - - + -
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Residues in contact with TYR 313 (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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309B TYR 2.8 17.3 + - - +
310B GLY 3.4 3.1 - - - +
312B PHE* 1.3 78.6 - - - +
314B LYS* 1.3 64.3 + - - +
316B LEU* 3.1 13.6 + - + +
317B THR* 3.0 43.6 + - + +
319B ASP* 3.0 36.2 + - + +
321B GLU 3.4 14.4 - - - -
322B ASP* 3.8 3.4 - - - -
323B HIS* 3.5 27.4 - - + -
342B PHE* 3.5 47.8 - + + -
344B PRO* 3.5 28.2 - - + +
386B ARG* 4.3 11.4 + - + +
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Residues in contact with LYS 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 GLY 3.0 20.9 + - - +
311B GLU* 3.5 28.3 + - - +
313B TYR* 1.3 79.3 - - - +
315B SER* 1.3 56.7 + - - +
317B THR* 4.3 1.8 - - - -
318B ASN* 2.9 33.3 + - - -
319B ASP 3.4 17.5 + - - +
320B TRP* 3.4 23.8 + - - +
321B GLU 3.8 16.4 - - - +
322B ASP* 4.2 14.1 - - - +
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Residues in contact with SER 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 GLU 3.2 10.7 + - - -
312B PHE* 3.1 17.9 + - - -
314B LYS* 1.3 79.2 - - - +
316B LEU* 1.3 65.7 + - - +
317B THR 3.4 0.5 + - - -
318B ASN* 3.9 11.3 - - - +
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Residues in contact with LEU 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 PHE* 3.0 44.7 + - + +
313B TYR* 3.1 4.7 + - - +
315B SER* 1.3 82.6 + - - +
317B THR* 1.3 67.2 + - + +
318B ASN* 5.1 0.7 - - - -
342B PHE* 4.6 7.6 - - + -
362B LYS* 3.9 42.5 - - + +
386B ARG* 4.8 3.1 + - - -
387B GLY* 3.8 31.4 - - - +
388B VAL* 4.3 8.5 - - + -
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B TYR* 3.0 32.0 + - + +
316B LEU* 1.3 90.5 - - + +
318B ASN* 1.3 72.2 + - - +
319B ASP* 3.3 21.8 + - - +
386B ARG* 3.8 57.2 + - + +
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Residues in contact with ASN 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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314B LYS 2.9 11.2 + - - +
315B SER* 3.9 11.3 - - - +
316B LEU 5.1 0.3 - - - -
317B THR* 1.3 81.4 + - - +
319B ASP* 1.3 64.7 + - - +
320B TRP* 3.8 2.6 + - - -
315C SER 5.2 7.8 + - - -
362C LYS* 4.5 17.3 - - - +
364C TYR* 5.4 3.6 + - - -
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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