Contacts of the strand formed by residues 306 - 311 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C HIS* 3.8 3.0 + - - -
273C GLN* 4.0 4.0 - - - +
302C CYS* 3.4 2.4 - - - -
303C GLY* 2.8 27.2 + - - +
305C ASN* 1.3 80.6 + - - +
307C THR* 1.3 71.5 + - - +
318C THR* 5.2 0.4 - - + -
319C PHE 3.3 14.4 - - - +
321C ASP 4.0 5.8 - - - +
326C LYS* 3.6 39.1 + - + +
327C LEU* 3.6 23.8 - - + -
356C CYS* 3.5 38.2 - - + +
357C GLY 3.8 12.3 + - - -
360C HIS 3.7 16.6 - - - -
361C MET* 3.9 9.3 - - - +
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Residues in contact with THR 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C HIS* 3.0 17.0 + - - -
256C VAL* 3.7 21.1 - - + -
273C GLN 3.0 20.6 + - - -
301C SER 3.4 13.0 - - - +
302C CYS* 4.2 0.7 - - - +
306C HIS* 1.3 77.3 - - - +
308C ALA* 1.3 68.9 + - - +
309C LEU* 4.3 7.0 - - + -
317C TYR 4.6 0.2 - - - -
318C THR* 3.2 8.1 - - - -
319C PHE* 2.9 62.7 + - + +
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Residues in contact with ALA 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C TYR 4.1 0.2 - - - +
300C ILE* 3.6 0.5 - - - -
301C SER* 2.8 34.4 + - - +
307C THR* 1.3 75.6 - - - +
309C LEU* 1.3 68.9 + - - +
316C MET* 4.4 3.4 - - - -
317C TYR 3.4 4.9 - - - +
318C THR* 3.9 15.3 - - + -
354C VAL* 4.1 25.3 - - + +
356C CYS* 3.7 22.6 - - - -
361C MET* 4.3 0.4 - - - -
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Residues in contact with LEU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C VAL* 4.5 0.4 - - + -
263C VAL* 4.3 15.3 - - + -
292C ILE* 4.2 26.2 - - + -
297C ILE* 4.0 25.1 - - + -
299C TYR 3.5 2.7 - - - -
300C ILE* 3.6 24.5 - - + -
307C THR* 4.3 13.9 - - + -
308C ALA* 1.3 84.7 - - - +
310C ILE* 1.3 63.9 + - - +
315C LEU 3.8 0.2 - - - +
316C MET* 3.2 6.8 - - - +
317C TYR* 2.8 46.4 + - + +
319C PHE* 3.7 25.4 - - + -
340C PRO* 4.6 2.7 - - + -
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Residues in contact with ILE 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ILE* 3.5 5.0 - - - +
298C SER* 2.8 32.3 + - - +
299C TYR* 2.9 29.7 + - + +
309C LEU* 1.3 76.4 - - - +
311C THR* 1.3 74.1 + - - +
314C GLY* 4.4 2.2 - - - -
315C LEU 3.4 8.1 - - - +
316C MET* 4.6 3.1 - - + -
351C VAL* 3.6 42.2 - - + +
352C LYS 4.1 12.3 - - - +
353C LEU 4.1 2.9 - - - -
354C VAL* 3.6 39.3 - - + +
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Residues in contact with THR 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C GLN* 3.7 19.5 - - + +
296C THR 3.3 11.9 - - - -
297C ILE* 3.8 11.4 - - + +
298C SER* 3.3 9.7 + - - -
310C ILE* 1.3 80.6 - - - +
312C ASP* 1.3 67.5 + - - +
313C ILE* 3.4 16.0 + - - +
314C GLY 3.1 11.3 + - - -
315C LEU* 2.8 38.0 + - + +
317C TYR* 3.6 30.1 - - + -
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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
------------------------------------------------------------
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