Contacts of the helix formed by residues 359 - 368 (chain A) in PDB entry 1NBF
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 ASN 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A LYS* 3.4 1.3 - - - +
358A LYS* 1.3 81.9 - - - +
360A ILE* 1.3 63.8 + - - +
361A PHE* 2.8 24.9 - - + +
362A GLU* 2.8 36.8 + - - +
363A SER 3.1 15.2 + - - -
425A PHE* 3.3 15.1 - - - -
426A GLU* 3.1 27.7 - - + +
428A PRO* 6.2 0.4 - - + -
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Residues in contact with ILE 360 (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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352A LEU* 3.6 21.3 - - + -
359A ASN* 1.3 73.4 - - - +
361A PHE* 1.3 66.9 + - + +
363A SER* 3.4 2.5 - - - -
364A PHE* 3.0 41.5 + - + -
404A LEU* 3.7 18.2 - - + -
425A PHE* 3.4 12.9 - - + -
426A GLU 2.9 12.3 + - - +
427A PHE* 3.8 9.6 - - + -
428A PRO* 3.8 13.2 - - + -
431A LEU* 3.4 30.1 - - + -
516A LEU* 3.7 30.3 - - + -
518A TYR* 4.2 7.0 - - + +
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Residues in contact with PHE 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ASN* 2.8 23.2 - - + +
360A ILE* 1.3 80.7 - - + +
362A GLU* 1.3 65.2 + - + +
363A SER 3.1 1.3 - - - -
364A PHE* 3.3 5.0 + - - +
365A VAL* 2.9 31.7 + - + +
428A PRO* 3.8 26.9 - - + -
430A GLN 4.6 0.7 - - - -
431A LEU* 3.8 15.5 - - + -
432A PRO* 3.6 40.6 - - + -
433A LEU* 5.9 0.2 - - + -
436A PHE* 4.2 13.4 - + + -
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Residues in contact with GLU 362 (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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356A GLY 3.9 4.9 - - - +
357A LYS* 3.6 19.9 - - + +
358A LYS* 2.9 45.4 + - - +
359A ASN* 2.8 31.2 - - - +
361A PHE* 1.3 73.7 - - + +
363A SER* 1.3 56.5 + - - +
365A VAL* 3.4 10.2 + - - +
366A ASP* 2.9 28.8 + - - +
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Residues in contact with SER 363 (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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352A LEU* 3.2 26.9 - - - +
353A SER 2.7 32.2 + - - -
357A LYS* 4.3 5.1 - - - +
359A ASN 3.1 13.4 + - - -
360A ILE* 3.4 10.8 - - - -
361A PHE 3.1 0.4 - - - -
362A GLU* 1.3 76.9 - - - +
364A PHE* 1.3 59.8 + - - +
366A ASP* 3.1 7.3 + - - +
367A TYR* 2.9 25.6 + - - +
425A PHE* 4.0 11.3 - - - -
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Residues in contact with PHE 364 (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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350A ILE* 4.0 19.1 - - + -
352A LEU* 3.8 33.4 - - + -
360A ILE* 3.0 39.0 + - + +
361A PHE* 3.3 0.9 + - - +
363A SER* 1.3 72.4 - - - +
365A VAL* 1.3 67.0 + - - +
367A TYR* 3.0 16.1 + - + +
368A VAL* 3.0 19.2 + - - +
395A PHE* 4.1 20.0 - + - -
398A LEU* 5.1 1.8 - - + -
402A LEU* 4.8 0.2 - - + -
404A LEU* 4.2 19.5 - - + -
431A LEU* 4.7 2.2 - - + -
433A LEU* 3.9 35.2 - - + -
436A PHE* 3.6 40.6 - + + -
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Residues in contact with VAL 365 (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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361A PHE* 2.9 24.8 + - + +
362A GLU* 3.5 9.9 - - - +
364A PHE* 1.3 77.1 - - - +
366A ASP* 1.3 61.6 + - - +
368A VAL* 3.4 7.2 - - + +
369A ALA* 3.1 22.2 + - + +
435A GLU* 6.2 0.4 - - + -
436A PHE* 3.8 20.0 - - + -
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Residues in contact with ASP 366 (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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353A SER* 3.5 23.1 + - - -
357A LYS* 3.6 28.4 + - + -
362A GLU 2.9 13.9 + - - +
363A SER* 3.3 9.8 - - - +
364A PHE 3.1 0.2 - - - -
365A VAL* 1.3 77.8 - - - +
367A TYR* 1.3 66.4 + - - +
369A ALA* 3.3 23.0 + - - +
306D LYS* 4.9 8.0 + - - -
310D GLY* 5.0 8.5 - - - +
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Residues in contact with TYR 367 (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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328A MET* 3.4 16.4 - - - +
350A ILE* 3.7 20.9 - - + +
351A GLN* 3.4 29.6 + - + -
352A LEU* 4.5 6.5 - - + -
353A SER 5.7 1.8 - - - -
363A SER 2.9 12.5 + - - +
364A PHE* 3.0 13.2 + - - +
366A ASP* 1.3 79.9 + - - +
368A VAL* 1.3 60.8 + - + +
369A ALA 3.3 3.5 + - - +
393A VAL* 4.0 35.9 + - + +
395A PHE* 3.8 29.4 - + + -
306D LYS* 4.7 24.5 + - + +
368D HIS* 3.4 29.9 + + - -
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Residues in contact with VAL 368 (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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364A PHE 3.0 16.8 + - - +
365A VAL* 3.4 11.9 - - + +
367A TYR* 1.3 75.9 - - - +
369A ALA* 1.3 66.0 + - - +
370A VAL* 3.5 6.6 + - - +
392A GLY* 4.7 0.5 - - - -
393A VAL 3.1 32.1 + - - +
394A LYS* 4.4 24.6 + - + +
395A PHE* 4.3 15.9 - - + -
436A PHE* 3.9 36.1 - - + +
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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
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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