Contacts of the strand formed by residues 316 - 320 (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 MET 316 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C ALA* 4.4 7.0 - - - -
309C LEU 3.2 14.4 - - - +
310C ILE* 4.6 1.6 - - + -
314C GLY 4.1 0.4 + - - -
315C LEU* 1.3 78.1 - - - +
317C TYR* 1.3 68.7 + - - +
318C THR* 4.4 1.6 - - + -
328C GLY 5.6 0.2 - - - +
342C LEU* 3.7 7.1 - - - +
343C CYS* 2.8 56.1 + - + +
346C PHE* 4.1 14.4 - - + +
351C VAL* 4.0 29.0 - - + +
354C VAL* 3.8 27.4 - - - -
361C MET* 4.1 11.9 - - + -
363C VAL* 3.7 29.4 - - + -
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Residues in contact with TYR 317 (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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291C ASN* 6.0 0.7 - - - -
292C ILE* 4.5 13.5 - - + -
295C GLN* 2.6 35.9 + - + -
297C ILE* 5.0 6.1 - - + -
307C THR 4.0 0.2 - - - +
308C ALA* 3.4 2.8 - - - -
309C LEU* 2.8 45.0 + - + +
311C THR* 3.6 24.0 - - + -
315C LEU* 4.6 3.2 - - + +
316C MET* 1.3 76.6 - - - +
318C THR* 1.3 64.8 + - - +
319C PHE* 4.7 1.5 - - - -
340C PRO* 4.0 29.2 - - + -
341C THR 3.3 6.7 - - - +
342C LEU* 3.5 48.9 - - + +
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Residues in contact with THR 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C HIS* 5.2 0.2 - - + -
307C THR 3.2 13.7 - - - +
308C ALA* 3.9 15.0 - - + -
316C MET* 4.4 2.7 - - + -
317C TYR* 1.3 79.6 - - - +
319C PHE* 1.3 65.1 + - - +
327C LEU* 2.8 40.1 + - - +
329C LEU* 3.5 18.4 - - - +
337C HIS* 4.6 0.9 - - - +
341C THR* 2.9 33.0 + - - -
343C CYS* 3.7 10.9 - - - -
361C MET* 4.1 13.9 - - + -
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Residues in contact with PHE 319 (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* 5.6 0.2 - - + -
265C THR* 4.7 2.7 - - + -
272C GLY 3.5 6.5 - - - +
273C GLN* 3.2 22.8 - - - -
274C LEU 3.6 4.9 - - - -
275C GLY* 3.4 27.4 - - - -
289C ILE* 3.7 19.5 - - + -
306C HIS* 3.3 4.5 - - - +
307C THR* 2.9 55.2 + - + -
309C LEU* 3.7 31.6 - - + -
317C TYR 4.8 0.2 - - - -
318C THR* 1.3 83.0 - - - +
320C GLY* 1.3 60.9 + - - +
327C LEU* 3.7 6.5 - - - +
337C HIS* 3.4 16.2 - - - +
339C ILE 3.6 13.7 - - - +
340C PRO* 3.5 19.7 - - + -
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Residues in contact with GLY 320 (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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271C PHE 3.1 17.4 - - - +
272C GLY 3.6 0.8 + - - -
273C GLN* 3.5 17.0 - - - -
305C ASN 3.7 5.8 - - - -
319C PHE* 1.3 74.7 - - - +
321C ASP* 1.3 65.4 + - - -
322C GLY 3.4 1.6 + - - -
327C LEU* 3.5 5.2 - - - +
336C ASN* 3.4 0.3 - - - -
337C HIS 2.8 34.6 + - - -
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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