Contacts of the strand formed by residues 306 - 311 (chain B) in PDB entry 4JHN
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 HIS 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B HIS* 3.7 6.8 + - - -
273B GLN* 4.1 2.9 - - - +
302B CYS* 3.7 0.3 - - - -
303B GLY* 2.7 28.6 + - - -
304B GLU 3.8 0.6 - - - -
305B ASN* 1.3 81.6 + - - +
307B THR* 1.3 70.6 + - - +
318B THR* 5.2 0.4 - - + -
319B PHE 3.3 13.7 - - - +
321B ASP 4.1 6.3 - - - +
326B LYS* 3.7 31.0 + - + +
327B LEU* 3.7 23.6 - - + -
356B CYS* 3.4 34.4 - - + +
357B GLY 3.9 12.0 + - - -
360B HIS 3.6 22.2 - - - -
361B MET* 3.8 14.8 - - - +
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Residues in contact with THR 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B HIS* 3.0 17.5 + - - -
256B VAL* 3.7 20.6 - - + -
273B GLN 2.9 20.7 + - - -
301B SER 3.4 13.9 - - - +
306B HIS* 1.3 76.5 - - - +
308B ALA* 1.3 67.7 + - - +
309B LEU* 4.2 7.2 - - + -
318B THR* 3.3 7.6 - - - +
319B PHE* 2.9 64.9 + - + +
356B CYS* 5.1 0.2 - - - -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B TYR 4.2 0.2 - - - +
300B ILE* 3.7 0.9 - - - -
301B SER* 2.9 34.0 + - - +
307B THR* 1.3 75.4 - - - +
309B LEU* 1.3 68.7 + - - +
316B MET* 4.5 3.4 - - - -
317B TYR 3.3 4.9 - - - -
318B THR* 3.9 15.7 - - + -
354B VAL* 4.1 24.4 - - + +
356B CYS* 3.7 22.6 - - - -
361B MET* 4.3 0.4 - - - -
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Residues in contact with LEU 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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256B VAL* 4.5 0.7 - - + -
263B VAL* 4.2 13.2 - - + -
289B ILE* 4.7 2.0 - - + -
292B ILE* 3.5 31.9 - - + -
297B ILE* 4.1 18.2 - - + -
299B TYR 3.5 2.9 - - - -
300B ILE* 3.7 25.6 - - + -
307B THR* 4.2 13.7 - - + -
308B ALA* 1.3 83.9 - - - +
310B ILE* 1.3 63.2 + - - +
311B THR 4.2 0.4 + - - -
315B LEU 3.7 0.3 - - - +
316B MET* 3.2 7.2 - - - +
317B TYR* 2.7 47.1 + - + +
319B PHE* 3.7 26.7 - - + -
340B PRO* 4.6 3.4 - - + -
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Residues in contact with ILE 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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297B ILE* 3.6 4.8 - - - +
298B SER* 2.7 40.8 + - - +
299B TYR* 3.0 30.7 + - + -
309B LEU* 1.3 76.6 - - - +
311B THR* 1.3 66.4 + - - +
314B GLY* 4.3 2.7 - - - -
315B LEU 3.3 9.4 - - - +
316B MET* 4.8 2.5 - - + -
351B VAL* 3.4 42.2 - - + +
352B LYS 4.1 14.6 - - - +
354B VAL* 3.6 37.5 - - + +
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Residues in contact with THR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLN* 3.7 25.1 - - + +
296B THR 3.2 11.2 - - - +
297B ILE* 3.8 19.3 - - + +
298B SER* 3.2 11.3 + - - -
309B LEU 5.1 0.2 - - - +
310B ILE* 1.3 79.3 - - - +
312B ASP* 1.3 61.9 + - - +
313B ILE* 3.1 14.8 + - - +
314B GLY* 3.0 15.4 + - - -
315B LEU* 2.8 40.6 + - + +
317B TYR* 3.9 16.4 - - + -
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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