Contacts of the strand formed by residues 349 - 356 (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 PHE 349 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D MET* 4.0 22.4 - - + -
15D PHE* 3.9 24.5 - + - -
29D LYS* 5.5 0.9 - - - -
314D GLY 3.9 8.0 - - - +
315D LEU* 5.2 4.2 - - - +
345D ASN 4.5 7.2 - - - -
346D PHE* 2.8 38.0 + + + +
347D LEU 4.3 2.6 - - - +
348D ARG* 1.3 94.0 - - + +
350D ILE* 1.3 64.2 + - - +
351D VAL 3.9 0.4 - - - -
365D ALA* 4.0 24.9 - - + -
366D ALA 3.3 8.1 - - - +
367D PRO* 3.5 38.1 - - + -
368D HIS* 4.0 7.9 + - - -
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Residues in contact with ILE 350 (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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313D ILE 3.5 19.1 - - - +
314D GLY* 3.9 14.6 - - - +
349D PHE* 1.3 74.7 - - - +
351D VAL* 1.3 66.2 + - - +
352D LYS* 3.4 33.3 + - + +
365D ALA* 3.2 3.0 - - - -
366D ALA* 2.7 40.5 + - + +
367D PRO 5.7 0.9 - - - +
368D HIS* 3.4 32.1 - - + +
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Residues in contact with VAL 351 (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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310D ILE* 3.6 42.9 - - + +
314D GLY* 2.9 30.8 + - - +
316D MET* 4.0 25.8 - - + +
346D PHE* 4.1 29.8 - - + -
349D PHE 5.2 0.2 - - - +
350D ILE* 1.3 72.6 - - - +
352D LYS* 1.3 62.6 + - - +
353D LEU 4.1 3.1 - - - +
363D VAL* 3.7 26.0 - - + -
364D PHE 3.8 3.1 - - - -
365D ALA* 4.1 4.0 - - + -
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Residues in contact with LYS 352 (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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310D ILE* 4.1 9.4 - - - +
350D ILE* 3.7 38.1 - - + +
351D VAL* 1.3 73.7 - - - +
353D LEU* 1.3 72.8 + - + +
364D PHE* 2.8 38.5 + - + +
366D ALA* 4.4 16.8 - - + +
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Residues in contact with LEU 353 (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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37D PRO 4.1 1.8 - - - +
38D VAL* 3.6 38.6 - - - +
39D HIS* 3.8 4.9 - - - +
40D LEU* 3.4 35.2 - - + +
299D TYR* 6.1 0.4 - - - -
310D ILE* 4.1 5.6 - - - -
351D VAL* 3.8 0.7 - - - +
352D LYS* 1.3 88.5 - - + +
354D VAL* 1.3 62.2 + - - +
363D VAL* 3.4 9.4 - - - +
364D PHE* 2.9 44.8 + - + -
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Residues in contact with VAL 354 (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* 4.8 5.9 - - - +
299D TYR* 3.7 24.6 + - + -
301D SER* 3.9 21.1 + - - -
308D ALA* 4.1 11.7 - - + +
310D ILE* 3.6 27.9 - - + +
316D MET* 3.7 25.1 - - - -
353D LEU* 1.3 76.8 - - - +
355D ALA* 1.3 66.7 + - - +
356D CYS* 4.5 0.2 - - - -
361D MET* 4.0 22.2 - - + -
362D VAL 3.4 11.7 - - - +
363D VAL* 4.5 2.7 - - + -
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Residues in contact with ALA 355 (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* 3.8 25.3 - - + +
41D SER* 3.8 2.7 - - - -
42D CYS* 3.5 31.3 - - - +
301D SER* 3.8 4.7 - - - -
354D VAL* 1.3 76.2 - - - +
356D CYS* 1.3 63.5 + - - +
361D MET* 3.4 4.9 - - - +
362D VAL 2.9 33.7 + - - +
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Residues in contact with CYS 356 (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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42D CYS* 3.6 14.0 + - - +
301D SER* 3.5 20.4 + - - -
302D CYS 3.3 15.5 + - - +
303D GLY* 3.4 23.0 - - - +
306D HIS* 3.5 27.8 - - - +
308D ALA* 3.7 29.6 - - - -
354D VAL* 4.5 0.7 - - - -
355D ALA* 1.3 78.8 - - - +
357D GLY* 1.3 59.7 + - - +
360D HIS 3.9 3.4 - - - -
361D MET* 3.9 7.2 - - - -
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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