Contacts of the strand formed by residues 349 - 356 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY* 5.7 0.7 - - - -
13A ALA 5.9 0.2 - - - -
15A PHE* 4.0 26.0 - + - -
29A LYS* 6.3 0.4 - - - -
313A ILE 5.5 0.2 - - - +
314A GLY 3.9 8.1 - - - +
315A LEU* 5.5 2.8 - - - +
345A ASN 4.3 8.7 - - - -
346A PHE* 2.9 38.8 + + + +
347A LEU 4.0 2.9 - - - +
348A ARG* 1.3 92.3 - - + +
350A ILE* 1.3 61.0 + - - +
351A VAL 3.8 0.4 + - - -
365A ALA* 3.9 26.5 - - + -
366A ALA 3.3 22.0 - - - +
367A PRO* 3.5 22.9 - - + -
368A HIS* 3.8 13.7 + - - -
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Residues in contact with ILE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ILE 4.4 9.4 - - - +
314A GLY* 3.8 14.1 - - - +
349A PHE* 1.3 70.9 - - - +
351A VAL* 1.3 73.3 + - - +
352A LYS* 3.5 23.7 + - + +
365A ALA* 3.3 2.5 - - - -
366A ALA 2.8 34.6 + - - +
367A PRO 6.0 0.7 - - - -
368A HIS* 3.3 33.4 - - + +
212C TYR* 4.9 13.7 - - + +
237C LEU* 5.0 15.3 - - + -
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ILE* 3.5 40.5 - - + +
314A GLY* 2.9 25.9 + - - +
316A MET* 4.0 27.8 - - + +
346A PHE* 3.9 37.0 - - + +
350A ILE* 1.3 74.4 - - - +
352A LYS* 1.3 61.7 + - - +
353A LEU 4.0 3.1 - - - +
363A VAL* 3.8 21.8 - - + -
364A PHE 3.8 3.1 - - - -
365A ALA* 4.0 6.7 - - + -
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Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A SER* 5.0 2.8 + - - +
310A ILE* 4.0 9.2 - - - +
350A ILE* 3.6 27.6 - - + +
351A VAL* 1.3 73.3 - - - +
353A LEU* 1.3 70.5 + - + +
364A PHE* 2.8 42.7 + - + +
366A ALA* 3.8 26.0 - - + +
210C GLU* 3.9 16.0 + - - -
237C LEU* 3.5 31.9 - - + +
239C SER* 6.2 4.7 - - - -
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A PRO* 4.1 3.8 - - + +
38A VAL* 3.5 40.4 - - - +
39A HIS* 3.7 8.1 - - + +
40A LEU* 3.7 27.4 - - + +
299A TYR* 6.0 0.7 - - - -
310A ILE* 4.0 5.4 - - - -
351A VAL* 4.0 1.0 - - - +
352A LYS* 1.3 86.9 - - + +
354A VAL* 1.3 63.0 + - - +
363A VAL* 3.5 5.9 - - - +
364A PHE* 2.9 52.0 + - + +
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Residues in contact with VAL 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.1 6.4 - - - +
299A TYR* 3.6 26.5 + - + -
301A SER* 3.9 19.7 + - - -
308A ALA* 4.0 12.8 - - + +
310A ILE* 3.6 25.0 - - + +
316A MET* 3.8 25.8 - - - -
353A LEU* 1.3 77.8 - - - +
355A ALA* 1.3 66.3 + - - +
356A CYS* 4.4 0.2 - - - -
361A MET* 3.9 22.7 - - + -
362A VAL 3.3 12.8 - - - +
363A VAL* 4.0 2.7 - - + -
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Residues in contact with ALA 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.8 15.2 - - + +
41A SER* 3.8 12.6 - - - +
42A CYS* 3.6 33.6 - - - +
301A SER* 3.8 4.7 - - - -
354A VAL* 1.3 75.8 - - - +
356A CYS* 1.3 64.0 + - - +
361A MET* 3.3 5.5 - - - +
362A VAL* 2.9 33.3 + - + +
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Residues in contact with CYS 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A CYS* 3.6 13.5 - - - +
301A SER* 3.5 18.6 + - - +
302A CYS 3.3 15.1 + - - +
303A GLY* 3.3 25.5 - - - +
306A HIS* 3.4 25.8 - - - +
308A ALA* 3.8 28.9 - - - -
354A VAL* 4.4 0.4 - - - -
355A ALA* 1.3 78.2 - - - +
357A GLY* 1.3 59.2 + - - +
360A HIS 3.9 4.3 - - - -
361A MET* 3.8 7.6 - - - -
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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