Contacts of the helix formed by residues 298 - 311 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296T GLU 3.3 4.9 + - - +
297T ALA* 1.3 67.2 - - - +
299T LEU* 1.3 54.2 + - - +
300T SER* 3.1 22.3 + - - -
301T LEU* 2.8 39.4 + - + +
302T TYR* 2.7 32.0 + - - +
438T PHE* 4.4 4.7 - - - -
442T MET* 4.8 5.6 - - + +
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Residues in contact with LEU 299 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296T GLU* 6.1 0.7 - - - +
297T ALA* 3.2 15.4 + - + +
298T ASP* 1.3 74.4 + - - +
300T SER* 1.3 57.2 + - - +
302T TYR* 3.9 12.8 - - + -
303T ASN* 2.8 44.7 + - - +
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Residues in contact with SER 300 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298T ASP* 3.1 15.0 + - - -
299T LEU* 1.3 79.5 - - - +
301T LEU* 1.3 60.7 + - - +
303T ASN* 4.1 3.9 - - - +
304T GLU* 3.0 32.3 + - - +
323T LYS* 5.8 2.9 + - - -
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Residues in contact with LEU 301 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298T ASP* 2.8 30.3 + - + +
300T SER* 1.3 80.6 - - - +
302T TYR* 1.3 65.5 + - - +
304T GLU* 3.8 13.6 - - - +
305T PHE* 3.0 26.2 + - - +
320T PHE* 5.6 0.7 - - - -
323T LYS* 3.6 33.9 - - + +
438T PHE* 3.7 14.1 - - + -
442T MET* 3.6 23.8 - - + -
445T ARG* 3.9 18.6 - - - +
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Residues in contact with TYR 302 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297T ALA* 4.4 16.4 - - + -
298T ASP 2.7 17.6 + - - +
299T LEU* 3.2 18.8 + - + +
301T LEU* 1.3 74.5 - - - +
303T ASN* 1.3 69.8 + - - +
305T PHE* 3.4 3.6 + + - +
306T ARG* 2.8 72.2 + - + +
434T VAL* 4.4 4.3 - - + +
435T ASP* 3.1 30.9 + - - -
438T PHE* 3.8 34.7 - + + -
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Residues in contact with ASN 303 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299T LEU* 2.8 30.0 + - - +
300T SER* 4.1 3.3 - - - +
302T TYR* 1.3 85.4 - - - +
304T GLU* 1.3 67.8 + - - +
306T ARG* 3.9 6.4 - - - +
307T LEU* 3.1 25.3 + - - +
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Residues in contact with GLU 304 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300T SER* 3.0 20.8 + - - +
301T LEU* 3.8 18.2 - - - +
303T ASN* 1.3 77.0 - - - +
305T PHE* 1.3 59.4 + - - +
307T LEU* 3.8 5.2 + - - +
308T TRP* 3.4 19.2 + - - +
319T PRO* 3.3 32.8 - - + +
320T PHE* 4.0 24.9 + - + +
323T LYS* 3.0 33.8 + - - +
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Residues in contact with PHE 305 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301T LEU 3.0 19.8 + - - +
302T TYR* 3.6 4.9 - + - +
304T GLU* 1.3 74.4 - - - +
306T ARG* 1.3 64.0 + - + +
307T LEU 3.0 2.2 - - - -
308T TRP* 2.9 10.2 + + - +
309T LYS* 2.8 42.2 + - + +
320T PHE* 3.8 35.4 - + + -
421T ILE* 6.0 0.2 - - + -
424T ILE* 4.4 14.4 - - + -
434T VAL* 3.8 25.8 - - + -
437T MET* 4.0 14.6 - - + -
438T PHE* 3.8 42.8 - + + -
441T VAL* 3.7 20.6 - - + -
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Residues in contact with ARG 306 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302T TYR* 2.8 59.7 + - + +
303T ASN* 4.0 7.6 - - - +
305T PHE* 1.3 82.3 - - + +
307T LEU* 1.3 60.6 + - - +
309T LYS* 3.6 8.8 - - + +
310T ASP* 3.6 26.8 + - - +
434T VAL* 3.4 37.8 - - + +
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Residues in contact with LEU 307 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303T ASN 3.1 15.8 + - - +
304T GLU* 3.9 5.8 - - - +
305T PHE 3.0 0.6 - - - -
306T ARG* 1.3 75.8 - - - +
308T TRP* 1.3 65.3 + - - +
310T ASP* 3.0 19.5 + - + +
311T GLU* 3.5 9.2 + - - +
319T PRO* 5.9 6.7 - - + -
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Residues in contact with TRP 308 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304T GLU 3.4 12.3 + - - +
305T PHE* 2.9 15.1 + + - +
307T LEU* 1.3 80.3 - - - +
309T LYS* 1.3 68.5 + - - +
311T GLU 3.1 5.8 - - - +
312T PRO* 3.0 34.0 - - + +
313T THR* 3.1 50.6 + - + +
314T MET* 5.3 0.7 - - - -
318T CYS* 4.0 15.3 - - + -
319T PRO* 6.1 0.4 - - + -
320T PHE* 3.6 44.7 - + + -
321T LEU* 4.5 1.7 - - + +
421T ILE* 3.7 49.8 - - + -
424T ILE* 4.0 28.3 - - + -
425T GLN* 5.1 1.1 - - + -
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Residues in contact with LYS 309 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305T PHE* 2.8 30.8 + - + +
306T ARG* 3.6 15.5 - - + +
307T LEU 3.1 0.2 - - - -
308T TRP* 1.3 87.6 - - - +
310T ASP* 1.3 73.1 + - - +
312T PRO* 3.3 16.9 - - - +
424T ILE* 4.6 7.4 - - + +
429T VAL 5.9 0.8 + - - -
434T VAL* 4.2 27.8 - - + -
437T MET* 4.6 22.1 - - + +
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Residues in contact with ASP 310 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306T ARG* 3.6 17.7 + - - +
307T LEU* 3.0 15.0 + - + +
309T LYS* 1.3 93.8 - - - +
311T GLU* 1.3 69.8 + - + +
312T PRO* 3.6 3.0 - - - +
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Residues in contact with GLU 311 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307T LEU 3.5 5.7 + - - +
308T TRP* 3.1 10.0 + - - +
310T ASP* 1.3 89.7 - - + +
312T PRO* 1.3 69.1 - - - +
313T THR* 3.5 9.4 + - - +
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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