Contacts of the helix formed by residues 377 - 389 (chain A) in PDB entry 5ANC
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 LEU 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A PHE* 6.0 2.0 - - + -
367A ILE 4.1 9.0 - - - +
368A ASP* 4.4 10.5 - - - +
369A THR 4.3 11.0 - - - +
376A GLY* 1.3 67.5 - - - -
378A HIS* 1.3 103.9 + - + +
380A THR* 3.0 27.4 + - + +
381A ALA* 3.3 12.0 + - + +
14G TYR* 3.4 30.0 - - + -
15G PRO* 3.8 31.9 - - + -
16G ALA* 5.6 4.3 - - + -
17G ARG* 5.0 1.3 - - - +
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Residues in contact with HIS 378 (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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309A THR* 5.8 2.8 + - - -
310A GLU 5.9 0.4 - - - -
311A LYS* 3.8 36.5 - - + -
312A THR 5.8 2.0 - - - +
316A MET* 4.6 15.1 - - + +
367A ILE 3.3 18.4 - - - -
369A THR* 3.1 31.7 + - + +
376A GLY 3.2 8.7 + - - -
377A LEU* 1.3 109.8 + - + +
379A GLN* 1.3 72.2 + - + +
380A THR* 4.7 8.6 + - + +
381A ALA* 3.9 0.3 - - - +
382A GLU* 3.0 35.4 + - - +
395A SER* 5.7 0.5 - - - -
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Residues in contact with GLN 379 (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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298A GLN* 5.5 4.8 + - - -
309A THR* 4.8 8.6 + - - +
310A GLU* 3.3 36.6 + - - +
311A LYS* 5.9 2.0 - - + -
378A HIS* 1.3 86.9 - - + +
380A THR* 1.3 64.3 + - + +
382A GLU* 3.4 17.3 + - - +
383A ASP* 2.9 39.3 + - - +
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Residues in contact with THR 380 (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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309A THR* 4.7 15.0 - - + +
377A LEU* 3.0 25.7 + - + +
378A HIS* 5.2 7.9 - - + +
379A GLN* 1.3 79.7 - - + +
381A ALA* 1.3 66.2 + - - +
383A ASP* 3.0 23.4 + - - +
384A LYS* 3.1 31.7 + - - +
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Residues in contact with ALA 381 (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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376A GLY* 4.0 6.7 - - - +
377A LEU* 3.3 36.7 + - + +
378A HIS 4.1 0.2 - - - +
380A THR* 1.3 77.6 + - - +
382A GLU* 1.3 55.1 + - - +
384A LYS* 4.5 9.0 - - - +
385A THR* 2.7 45.0 + - + +
395A SER* 4.8 2.5 - - - +
14G TYR* 4.0 15.5 - - + +
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Residues in contact with GLU 382 (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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316A MET* 4.5 8.0 - - + +
378A HIS 3.0 17.8 + - - +
379A GLN* 3.4 29.2 + - + +
381A ALA* 1.3 76.1 - - - +
383A ASP* 1.3 61.3 + - - +
385A THR* 2.8 14.2 + - - -
386A LYS* 3.1 15.9 + - - +
394A ARG* 3.4 25.7 + - + +
395A SER* 4.0 15.6 + - - +
396A THR* 3.9 21.0 - - - +
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Residues in contact with ASP 383 (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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379A GLN* 2.9 27.4 - - - +
380A THR* 3.0 10.8 + - - +
382A GLU* 1.3 79.2 - - - +
384A LYS* 1.3 62.9 + - + +
386A LYS* 3.2 9.5 + - - +
387A TYR* 2.9 61.6 + - + +
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Residues in contact with LYS 384 (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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380A THR* 3.1 28.6 + - - +
381A ALA* 4.2 7.0 - - - +
383A ASP* 1.3 79.6 - - + +
385A THR* 1.3 59.0 + - + +
387A TYR* 3.2 19.7 + - + +
388A PHE* 2.9 28.4 + - - +
3G THR* 4.9 17.0 + - - +
12G LYS* 4.9 18.8 - - + +
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Residues in contact with THR 385 (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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376A GLY* 6.6 0.2 - - - -
381A ALA* 2.7 28.2 + - + +
382A GLU 2.8 13.7 + - - -
384A LYS* 1.3 81.2 - - + +
386A LYS* 1.3 55.5 + - - +
388A PHE* 3.2 11.3 + - + +
389A GLY 2.9 28.8 + - - +
393A SER* 3.0 31.9 + - - +
394A ARG 3.2 14.1 + - - -
395A SER* 3.7 7.1 + - - +
14G TYR* 6.0 1.8 - - - +
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Residues in contact with LYS 386 (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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382A GLU 3.1 14.9 + - - +
383A ASP* 3.2 11.0 + - - +
385A THR* 1.3 82.6 + - - +
387A TYR* 1.3 69.2 - - + +
389A GLY* 3.1 23.7 + - - -
390A VAL* 3.8 23.1 + - + +
393A SER 3.8 3.6 - - - -
394A ARG* 3.8 31.0 - - + +
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Residues in contact with TYR 387 (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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383A ASP* 2.9 53.1 + - + +
384A LYS* 3.3 19.1 - - + +
386A LYS* 1.3 83.3 - - + +
388A PHE* 1.3 64.7 + - - +
389A GLY* 3.4 1.2 + - - -
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Residues in contact with PHE 388 (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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384A LYS 2.9 12.7 + - - +
385A THR* 3.4 13.2 - - - +
387A TYR* 1.3 78.5 - - - +
389A GLY* 1.3 56.3 + - - +
392A LYS* 3.3 54.2 + - + -
393A SER* 6.2 2.5 - - - -
10G GLU* 6.4 1.6 - - - -
11G PHE* 5.8 7.0 - + - -
53G MET* 3.6 26.2 - - + -
54G VAL 5.6 0.7 - - - -
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Residues in contact with GLY 389 (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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385A THR 2.9 6.5 + - - +
386A LYS* 3.1 13.1 + - - +
387A TYR 4.1 1.6 - - - -
388A PHE* 1.3 80.0 - - - +
390A VAL* 1.3 59.5 - - - -
391A LYS* 3.5 3.4 - - - -
392A LYS* 4.3 11.8 - - - +
393A SER 2.9 26.2 + - - +
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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