Contacts of the helix formed by residues 371 - 382 (chain S) in PDB entry 5L4K
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 371 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366S ALA 4.3 6.2 + - - +
369S THR* 3.4 26.7 + - - +
370S GLY* 1.3 76.7 - - - +
372S LEU* 1.3 67.8 + - - +
373S ALA* 3.3 12.6 + - - +
374S LYS* 3.1 46.7 + - - +
375S PHE* 3.9 13.3 + - - +
402S VAL* 4.3 7.7 + - - +
425S LYS 4.0 15.9 - - - +
426S LEU* 3.9 9.2 - - - +
427S GLN* 4.1 6.8 - - + +
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Residues in contact with LEU 372 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371S ASN* 1.3 74.0 - - - +
373S ALA* 1.3 66.8 + - - +
375S PHE* 3.1 8.3 + - + +
376S ASN* 3.0 28.6 + - - +
399S ARG* 3.4 49.6 - - + +
402S VAL* 3.6 28.5 - - + -
403S ILE* 3.6 34.3 - - + -
426S LEU 3.4 9.7 + - - +
427S GLN 4.0 15.0 - - - +
428S LEU* 5.0 6.5 - - + -
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Residues in contact with ALA 373 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371S ASN* 3.3 10.5 + - - +
372S LEU* 1.3 79.5 - - - +
374S LYS* 1.3 66.7 + - + +
376S ASN* 3.2 8.5 + - - +
377S GLN* 3.1 34.3 + - - +
427S GLN* 3.7 30.0 + - + +
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Residues in contact with LYS 374 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365S GLN 5.5 1.3 - - - +
366S ALA* 4.0 14.1 - - + -
369S THR* 4.6 16.6 + - + +
371S ASN* 3.1 31.8 + - - +
373S ALA* 1.3 81.6 - - + +
375S PHE* 1.3 62.6 + - - +
377S GLN* 3.8 12.5 - - - +
378S VAL* 3.0 27.7 + - - +
47Y ASN* 5.2 10.5 + - - +
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Residues in contact with PHE 375 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363S LEU* 3.8 26.5 - - + -
366S ALA* 3.8 17.7 - - + +
367S VAL* 4.4 8.3 - - + -
371S ASN 3.9 9.5 + - - +
372S LEU* 3.1 13.0 + - + +
374S LYS* 1.3 79.2 - - - +
376S ASN* 1.3 65.6 + - - +
378S VAL* 3.3 4.7 - - - +
379S LEU* 2.9 48.8 + - + +
395S ILE* 4.0 10.5 - - + -
396S ILE 4.8 0.4 - - - -
398S LEU* 3.6 27.8 - - + -
399S ARG* 3.5 44.4 - - + -
402S VAL* 4.2 20.6 - - + -
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Residues in contact with ASN 376 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372S LEU* 3.0 23.6 + - - +
373S ALA* 3.6 7.7 + - - +
375S PHE* 1.3 80.1 - - - +
377S GLN* 1.3 63.8 + - + +
379S LEU* 3.7 3.2 - - - -
380S ASP* 2.9 25.7 + - - +
399S ARG* 3.2 37.5 + - - +
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Residues in contact with GLN 377 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373S ALA* 3.1 25.7 + - - +
374S LYS* 3.8 12.9 + - - +
376S ASN* 1.3 76.5 - - + +
378S VAL* 1.3 57.4 + - - +
380S ASP* 3.1 7.6 + - - +
381S GLN* 3.1 39.4 + - - +
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Residues in contact with VAL 378 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359S PRO 4.8 1.8 - - - +
362S LEU* 3.3 50.0 - - + +
363S LEU* 4.0 17.0 - - + +
366S ALA* 4.2 4.5 - - + -
374S LYS 3.0 21.3 + - - +
375S PHE* 3.3 12.6 - - - +
377S GLN* 1.3 72.8 - - - +
379S LEU* 1.3 66.8 + - - +
380S ASP 3.0 5.7 + - - -
381S GLN* 3.6 8.2 + - - +
382S PHE* 3.4 36.6 + - + +
386S PHE* 4.4 2.0 - - + -
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Residues in contact with LEU 379 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363S LEU* 4.3 6.5 - - + -
375S PHE* 2.9 36.5 + - + +
376S ASN* 3.7 3.8 - - - +
378S VAL* 1.3 77.6 - - - +
380S ASP* 1.3 57.4 + - - +
383S GLY* 3.6 13.6 - - - -
386S PHE* 3.5 31.2 - - + -
392S TYR* 4.3 19.7 + - + +
395S ILE* 3.4 35.7 - - + -
396S ILE* 4.5 19.7 - - + -
399S ARG* 6.1 1.1 - - + -
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Residues in contact with ASP 380 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376S ASN 2.9 17.4 + - - +
377S GLN* 3.2 8.1 - - - +
378S VAL 3.0 0.2 - - - -
379S LEU* 1.3 78.8 - - - +
381S GLN* 1.3 75.4 + - - +
382S PHE 3.5 0.2 + - - -
383S GLY* 3.6 6.9 + - - -
384S GLU 5.1 0.5 + - - -
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Residues in contact with GLN 381 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377S GLN* 3.1 26.9 + - + +
378S VAL* 3.6 4.6 + - - +
380S ASP* 1.3 85.1 + - - +
382S PHE* 1.3 85.2 + - + +
383S GLY 3.6 0.3 + - - -
384S GLU* 4.6 6.6 + - - +
385S LYS* 5.5 2.6 - - - -
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Residues in contact with PHE 382 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358S MET* 5.4 1.6 - - + -
359S PRO* 3.6 34.5 - - + -
362S LEU* 3.9 21.5 - - + -
378S VAL* 3.4 18.6 + - + +
381S GLN* 1.3 102.7 - - + +
383S GLY* 1.3 66.0 + - - +
384S GLU* 3.1 3.8 - - - -
385S LYS* 2.9 46.7 + - + +
386S PHE* 3.2 32.8 + + + -
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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