Contacts of the helix formed by residues 298 - 311 (chain Q) in PDB entry 4UJ3
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 298 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296Q GLU 3.3 5.7 + - - +
297Q ALA* 1.3 68.0 - - - +
299Q LEU* 1.3 64.4 + - - +
300Q SER* 2.9 28.4 + - - -
301Q LEU* 3.1 30.1 + - + +
302Q TYR* 3.0 22.1 + - - +
438Q PHE* 4.5 4.5 - - - -
442Q MET* 4.9 5.2 - - + +
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Residues in contact with LEU 299 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296Q GLU* 6.0 1.8 - - - +
297Q ALA* 3.2 12.3 + - + +
298Q ASP* 1.3 72.2 + - - +
300Q SER* 1.3 63.3 + - - +
302Q TYR* 3.9 9.1 - - + +
303Q ASN* 3.1 38.0 + - - +
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Residues in contact with SER 300 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298Q ASP* 2.9 13.6 + - - -
299Q LEU* 1.3 82.2 - - - +
301Q LEU* 1.3 67.1 + - - +
303Q ASN* 3.7 3.9 + - - +
304Q GLU* 3.3 20.2 + - - +
323Q LYS* 6.0 1.6 - - - -
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Residues in contact with LEU 301 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298Q ASP* 3.1 27.4 + - + +
300Q SER* 1.3 82.4 - - - +
302Q TYR* 1.3 59.6 + - - +
304Q GLU* 3.3 25.7 + - - +
305Q PHE* 2.9 30.8 + - - +
320Q PHE* 5.4 0.3 - - - -
323Q LYS* 3.5 27.6 - - + -
438Q PHE* 3.8 13.0 - - + -
442Q MET* 3.7 23.3 - - + -
445Q ARG* 4.1 16.8 - - - +
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Residues in contact with TYR 302 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297Q ALA* 4.5 11.9 - - + -
298Q ASP 3.0 16.0 + - - +
299Q LEU* 3.9 11.9 - - + +
300Q SER 3.4 0.2 - - - -
301Q LEU* 1.3 77.8 - - - +
303Q ASN* 1.3 64.9 + - - +
305Q PHE* 3.3 2.2 + + - +
306Q ARG* 2.7 74.0 + - + +
434Q VAL* 4.1 5.5 - - + +
435Q ASP* 2.7 31.4 + - - -
438Q PHE* 3.6 45.0 - + + -
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Residues in contact with ASN 303 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299Q LEU* 3.1 24.9 + - - +
300Q SER* 4.1 4.4 - - - +
302Q TYR* 1.3 86.3 - - - +
304Q GLU* 1.3 60.3 + - - +
306Q ARG* 3.7 7.7 - - - +
307Q LEU* 2.9 39.5 + - + +
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Residues in contact with GLU 304 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300Q SER 3.3 13.1 + - - +
301Q LEU* 3.4 30.0 - - - +
302Q TYR 3.3 0.2 - - - -
303Q ASN* 1.3 79.3 - - - +
305Q PHE* 1.3 61.0 + - - +
307Q LEU* 3.6 6.3 + - - +
308Q TRP* 3.2 22.0 + - - +
319Q PRO* 3.3 30.0 - - + +
320Q PHE* 3.9 27.1 - - + +
323Q LYS* 2.9 28.3 + - - +
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Residues in contact with PHE 305 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301Q LEU 2.9 16.4 + - - +
302Q TYR* 3.8 3.1 - + - +
304Q GLU* 1.3 71.6 - - - +
306Q ARG* 1.3 62.8 + - + +
307Q LEU 3.1 2.2 - - - -
308Q TRP* 3.0 19.2 + + - +
309Q LYS* 2.7 44.3 + - + +
320Q PHE* 3.4 40.8 - + + -
424Q ILE* 4.4 8.3 - - + -
434Q VAL* 3.9 17.7 - - + -
437Q MET* 3.8 26.7 - - + -
438Q PHE* 3.5 43.5 - + + -
441Q VAL* 3.7 18.6 - - + -
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Residues in contact with ARG 306 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302Q TYR* 2.7 54.6 + - + +
303Q ASN* 3.7 9.4 - - - +
305Q PHE* 1.3 78.6 - - - +
307Q LEU* 1.3 60.9 + - + +
309Q LYS* 3.8 12.7 - - - +
310Q ASP* 3.8 29.8 + - - +
434Q VAL* 3.1 44.8 - - - +
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Residues in contact with LEU 307 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303Q ASN* 2.9 20.7 + - + +
304Q GLU* 3.8 5.8 - - - +
306Q ARG* 1.3 76.4 - - + +
308Q TRP* 1.3 63.4 + - - +
310Q ASP* 3.3 21.4 + - + +
311Q GLU* 4.0 3.5 + - - +
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Residues in contact with TRP 308 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304Q GLU 3.2 14.4 + - - +
305Q PHE* 3.0 17.4 + + - +
307Q LEU* 1.3 76.9 - - - +
309Q LYS* 1.3 69.2 + - - +
311Q GLU 3.2 6.9 - - - +
312Q PRO* 3.1 33.3 - - + -
313Q THR* 3.3 51.4 + - + +
318Q CYS* 3.9 16.7 - - + -
319Q PRO* 6.2 0.4 - - + -
320Q PHE* 3.5 46.6 - + + -
321Q LEU* 4.5 2.2 - - + +
421Q ILE* 3.8 42.2 - - + -
424Q ILE* 4.3 19.7 - - + -
425Q GLN* 5.3 0.4 - - - -
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Residues in contact with LYS 309 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305Q PHE* 2.7 36.6 + - + +
306Q ARG* 3.8 9.4 - - - +
307Q LEU 3.2 0.2 - - - -
308Q TRP* 1.3 85.0 - - + +
310Q ASP* 1.3 78.4 + - - +
311Q GLU 3.4 0.5 + - - -
312Q PRO* 3.4 14.2 - - - +
424Q ILE* 4.7 6.2 - - + +
429Q VAL* 5.4 5.7 + - - +
434Q VAL* 4.3 29.4 - - + -
437Q MET* 4.2 29.3 - - + +
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Residues in contact with ASP 310 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306Q ARG* 3.8 25.8 + - - +
307Q LEU* 3.3 13.5 + - + +
308Q TRP 3.2 1.2 - - - -
309Q LYS* 1.3 96.9 + - - +
311Q GLU* 1.3 69.7 + - + +
312Q PRO* 3.7 2.6 - - - +
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Residues in contact with GLU 311 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307Q LEU 4.0 3.1 + - - +
308Q TRP* 3.2 11.2 + - - +
310Q ASP* 1.3 88.1 - - + +
312Q PRO* 1.3 71.2 - - - +
313Q THR* 3.6 8.5 + - - +
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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