Contacts of the helix formed by residues 298 - 311 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B GLU 3.4 4.4 + - - -
297B ALA* 1.3 68.9 - - - +
299B LEU* 1.3 57.5 + - - +
300B SER* 3.1 13.7 - - - -
301B LEU* 2.8 71.4 + - + +
302B TYR* 2.8 12.5 + - - +
438B PHE* 4.5 0.2 - - - -
442B MET* 4.5 7.7 - - + +
334H THR* 3.8 9.6 - - - +
406H PHE* 4.6 9.9 - - + -
410H ARG* 2.7 40.1 + - - +
452H LYS 4.2 6.7 - - - +
453H LEU 4.8 1.9 + - - -
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Residues in contact with LEU 299 (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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296B GLU* 5.8 0.7 - - - +
297B ALA* 3.1 10.4 + - + +
298B ASP* 1.3 71.6 - - - +
300B SER* 1.3 62.8 + - - +
302B TYR* 3.6 17.4 - - + +
303B ASN* 3.0 38.6 + - - +
336H SER* 3.6 17.3 - - - +
382H THR* 3.2 26.7 - - - +
383H GLY* 4.8 4.0 - - - +
384H GLN* 3.5 35.2 - - + +
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Residues in contact with SER 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ASP* 3.1 12.9 + - - -
299B LEU* 1.3 79.8 - - - +
301B LEU* 1.3 62.0 + - - +
303B ASN* 3.6 5.3 + - - +
304B GLU* 3.2 22.3 + - - +
334H THR* 4.2 23.6 - - - +
335H PHE 6.1 3.4 - - - -
336H SER* 6.6 0.2 - - - -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ASP* 2.8 25.9 + - + +
300B SER* 1.3 74.8 - - - +
302B TYR* 1.3 64.9 - - - +
304B GLU* 3.3 14.1 + - - +
305B PHE* 3.0 24.3 + - - +
320B PHE* 5.5 0.9 - - - -
323B LYS* 4.0 22.4 - - + -
438B PHE* 3.8 4.6 - - + -
442B MET* 3.4 36.1 - - + -
445B ARG* 3.7 25.8 - - - +
452H LYS* 3.7 24.2 - - + +
453H LEU* 4.3 3.6 - - + -
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Residues in contact with TYR 302 (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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297B ALA* 4.5 7.9 - - + -
298B ASP 2.8 12.0 + - - +
299B LEU* 3.6 23.8 - - + +
300B SER 3.3 0.2 - - - -
301B LEU* 1.3 77.4 - - - +
303B ASN* 1.3 66.7 + - - +
305B PHE* 3.2 2.4 + - - +
306B ARG* 2.9 58.5 + - + +
434B VAL* 4.3 12.8 - - + -
435B ASP* 2.4 30.8 + - - -
438B PHE* 3.4 45.1 - + + -
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Residues in contact with ASN 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 3.0 28.9 + - - +
300B SER* 4.0 4.9 - - - +
302B TYR* 1.3 83.6 - - - +
304B GLU* 1.3 65.8 + - - +
306B ARG* 4.0 9.0 - - - +
307B LEU* 3.1 27.0 + - - +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B SER 3.2 12.3 + - - +
301B LEU* 3.6 16.7 - - - +
302B TYR 3.3 0.2 - - - -
303B ASN* 1.3 79.0 - - - +
305B PHE* 1.3 62.4 + - - +
307B LEU* 3.7 5.3 - - - +
308B TRP* 3.2 21.3 + - - +
319B PRO* 3.2 29.2 - - + +
320B PHE* 3.8 33.8 - - + +
323B LYS* 3.2 32.8 + - - +
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Residues in contact with PHE 305 (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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301B LEU 3.0 16.1 + - - +
302B TYR* 3.7 2.9 - + - +
304B GLU* 1.3 73.8 - - - +
306B ARG* 1.3 63.0 + - + +
307B LEU 3.0 2.0 - - - -
308B TRP* 2.8 42.6 + + - +
309B LYS* 2.8 26.3 + - + +
320B PHE* 3.8 34.9 - + + -
424B ILE* 4.5 4.7 - - + -
434B VAL* 3.8 19.5 - - + -
437B MET* 3.9 20.0 - - + -
438B PHE* 3.5 53.2 - + + -
441B VAL* 3.9 17.7 - - + -
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Residues in contact with ARG 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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302B TYR* 2.9 49.2 + - + +
303B ASN* 4.1 9.0 - - - +
305B PHE* 1.3 83.3 - - - +
307B LEU* 1.3 59.8 + - - +
309B LYS* 3.9 4.8 + - + +
310B ASP* 3.3 28.3 + - - +
434B VAL* 2.9 52.7 - - + +
435B ASP* 4.6 1.2 + - - +
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Residues in contact with LEU 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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303B ASN 3.1 17.9 + - - +
304B GLU* 3.7 4.9 - - - +
305B PHE 3.0 0.4 - - - -
306B ARG* 1.3 76.4 - - - +
308B TRP* 1.3 64.5 + - - +
310B ASP* 3.2 19.5 + - + +
311B GLU* 3.6 6.6 + - - +
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Residues in contact with TRP 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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304B GLU 3.2 11.2 + - - +
305B PHE* 2.8 20.7 + + - +
307B LEU* 1.3 73.4 - - - +
309B LYS* 1.3 66.6 + - - +
311B GLU 3.1 6.0 - - - +
312B PRO* 2.9 38.9 - - + +
313B THR* 3.0 51.1 + - + +
314B MET* 5.1 1.3 - - - -
318B CYS* 4.1 14.1 - - + -
320B PHE* 3.7 43.4 - + + -
321B LEU* 4.7 2.1 - - + +
421B ILE* 3.7 51.4 - - + -
424B ILE* 4.0 24.7 - - + -
425B GLN* 5.0 1.6 - - + -
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B PHE* 2.8 34.5 + - + +
306B ARG 4.0 4.7 - - - +
308B TRP* 1.3 83.8 - - + +
310B ASP* 1.3 73.1 + - - +
312B PRO* 2.9 22.2 - - - +
424B ILE* 5.0 6.7 - - + +
434B VAL* 3.2 42.4 - - + -
437B MET* 4.2 24.8 - - + +
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Residues in contact with ASP 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ARG* 3.3 19.8 + - - +
307B LEU* 3.2 11.2 + - + +
308B TRP 3.1 1.0 - - - -
309B LYS* 1.3 96.1 + - - +
311B GLU* 1.3 63.9 + - + +
312B PRO* 3.4 2.6 - - - +
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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
----------------------------------------------------------
307B LEU 3.6 5.7 + - - +
308B TRP* 3.1 10.3 + - - +
310B ASP* 1.3 82.9 - - + +
312B PRO* 1.3 67.0 - - - +
313B THR* 3.7 8.7 + - - +
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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