Contacts of the strand formed by residues 297 - 302 (chain D) 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 ILE 297 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D LEU* 3.7 35.0 - - + +
259D THR 5.3 0.7 - - - +
260D GLU 5.7 0.7 - - - +
263D VAL* 3.7 18.2 - - + -
292D ILE* 3.8 19.7 - - + +
295D GLN* 3.8 14.7 + - + +
296D THR* 1.3 79.3 - - - +
298D SER* 1.3 62.9 + - - +
299D TYR 3.6 22.4 - - - +
300D ILE* 4.0 6.7 - - + -
309D LEU* 4.0 22.2 - - + -
310D ILE 3.6 3.6 - - - +
311D THR* 3.9 24.0 - - + -
317D TYR* 5.0 3.6 - - + -
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Residues in contact with SER 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247D GLN* 3.2 16.6 - - - +
258D LEU* 3.7 7.0 - - - +
296D THR* 3.7 1.8 + - - -
297D ILE* 1.3 73.4 - - - +
299D TYR* 1.3 61.3 + - - +
310D ILE* 2.7 18.6 + - - -
311D THR 3.9 16.4 - - - -
312D ASP* 4.1 11.0 - - - -
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Residues in contact with TYR 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D LEU 5.7 0.7 + - - -
194D TRP* 4.2 21.7 - + - -
247D GLN* 3.6 17.7 - - - +
258D LEU* 4.6 0.2 - - - -
297D ILE* 3.6 4.4 - - - +
298D SER* 1.3 83.6 - - - +
300D ILE* 1.3 83.5 + - - +
301D SER* 3.9 5.0 + - - -
309D LEU* 3.5 4.2 - - - -
310D ILE* 2.9 46.6 + - + -
353D LEU* 6.1 0.2 - - - -
354D VAL* 3.7 41.3 + - + -
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Residues in contact with ILE 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194D TRP* 5.7 0.7 - - - -
247D GLN* 3.2 24.4 + - + +
248D VAL* 3.9 2.0 - - - +
249D ALA* 3.7 19.1 - - + +
256D VAL* 3.4 46.7 - - + +
258D LEU* 3.7 28.9 - - + +
263D VAL* 4.6 3.6 - - + -
297D ILE* 4.0 11.0 - - + -
299D TYR* 1.3 99.6 + - - +
301D SER* 1.3 60.2 - - - +
308D ALA 3.7 2.9 - - - -
309D LEU* 3.7 22.2 - - + -
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Residues in contact with SER 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D ALA* 4.2 4.0 - - - -
299D TYR* 3.9 7.4 + - - -
300D ILE* 1.3 76.3 - - - +
302D CYS* 1.3 65.5 + - - +
307D THR* 3.4 8.0 - - - +
308D ALA 2.9 33.0 + - - +
354D VAL* 3.9 25.6 + - - -
355D ALA* 3.8 6.1 - - - -
356D CYS* 3.5 29.7 + - - -
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Residues in contact with CYS 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D ALA* 3.4 28.7 - - + +
250D CYS 3.9 20.2 - - - +
251D GLY* 4.0 2.7 - - - +
254D HIS* 3.6 15.7 - - - -
256D VAL* 3.2 37.9 - - - -
301D SER* 1.3 78.2 + - - +
303D GLY* 1.3 63.7 - - - +
306D HIS 3.7 2.5 - - - -
307D THR* 4.4 0.7 - - - -
356D CYS* 3.3 16.2 - - - +
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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