Contacts of the helix formed by residues 368 - 384 (chain A) in PDB entry 6TPN
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 SER 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A MET* 3.6 20.9 - - - -
364A TYR 3.1 17.1 + - - +
366A PHE 3.7 1.2 - - - -
367A LEU* 1.3 80.6 - - - +
369A GLY* 1.3 58.9 + - - +
370A LYS* 3.6 7.3 + - - +
371A PHE* 3.4 24.6 + - - -
372A ARG* 3.0 28.4 + - - +
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Residues in contact with GLY 369 (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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367A LEU 4.3 0.6 - - - -
368A SER* 1.3 68.4 + - - +
370A LYS* 1.3 64.1 + - - +
372A ARG* 3.6 28.0 - - - +
373A GLU* 3.1 33.1 + - - +
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Residues in contact with LYS 370 (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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82A ASN* 5.3 3.4 - - - +
84A HIS* 3.1 38.0 + - - +
85A MET* 3.6 26.3 - - - +
87A THR* 5.1 5.9 - - - +
90A ASN* 5.5 3.8 - - - +
368A SER* 3.3 7.5 + - - +
369A GLY* 1.3 77.8 - - - +
371A PHE* 1.3 58.9 - - + +
373A GLU* 4.5 2.2 - - - +
374A GLU* 3.4 29.6 + - - +
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Residues in contact with PHE 371 (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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75A VAL* 4.2 19.7 - - + -
78A ALA* 4.5 2.9 - - + -
79A VAL* 4.2 17.7 - - + -
85A MET* 3.7 22.7 - - + -
90A ASN* 3.9 25.1 - - - -
93A ILE* 4.1 26.5 - - + -
305A MET* 5.0 2.7 - - + -
364A TYR* 3.4 41.7 - + + +
368A SER* 3.3 19.9 + - - +
369A GLY 3.3 0.4 - - - -
370A LYS* 1.3 77.6 - - + +
372A ARG* 1.3 56.5 + - - +
374A GLU* 3.3 1.5 + - - +
375A PHE* 2.7 62.1 + + + -
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Residues in contact with ARG 372 (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 TYR 4.3 0.4 + - - -
365A ASN* 3.3 49.9 + - - +
366A PHE* 3.8 13.5 + - - +
367A LEU 5.0 0.6 - - - -
368A SER 3.0 15.1 + - - +
369A GLY* 3.3 27.4 + - - +
371A PHE* 1.3 76.3 - - - +
373A GLU* 1.3 73.0 + - - +
375A PHE* 3.3 4.4 + - - +
376A LYS* 3.0 36.9 + - + +
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Residues in contact with GLU 373 (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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369A GLY* 3.1 17.9 + - - +
370A LYS* 4.5 2.7 - - - +
372A ARG* 1.3 91.0 + - - +
374A GLU* 1.3 59.2 + - + +
376A LYS* 3.1 35.7 + - - +
377A ALA* 2.9 29.0 + - - +
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Residues in contact with GLU 374 (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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78A ALA* 3.7 32.5 - - + +
81A LYS* 4.6 11.8 - - - +
82A ASN* 4.0 31.2 + - - +
85A MET* 4.3 12.3 - - + -
370A LYS 3.4 18.7 + - - +
371A PHE 3.3 3.0 + - - +
372A ARG 3.3 0.2 - - - -
373A GLU* 1.3 75.4 - - + +
375A PHE* 1.3 66.2 + - - +
377A ALA* 4.0 11.4 - - - +
378A ALA* 3.1 23.9 + - - +
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Residues in contact with PHE 375 (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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71A GLY* 4.6 3.1 - - - -
74A LEU* 3.7 48.4 - - + +
75A VAL* 3.8 21.5 - - + -
78A ALA* 4.6 1.6 - - + -
361A PRO* 3.5 26.5 - - + -
364A TYR* 4.3 2.0 - - + -
365A ASN* 3.3 34.1 - - + +
371A PHE* 2.7 46.4 + + + +
372A ARG 3.5 4.7 - - - +
374A GLU* 1.3 75.3 - - - +
376A LYS* 1.3 62.7 + - + +
378A ALA* 3.5 3.5 + - + +
379A PHE* 3.1 37.4 + - + +
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Residues in contact with LYS 376 (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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365A ASN* 5.8 1.1 - - - +
372A ARG* 3.0 26.5 + - + +
373A GLU* 3.1 43.9 + - - +
375A PHE* 1.3 76.9 - - + +
377A ALA* 1.3 58.7 + - - +
379A PHE* 3.9 4.7 - - - +
380A SER* 2.9 34.1 + - - +
387A HIS* 4.8 4.5 - - + +
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Residues in contact with ALA 377 (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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81A LYS* 5.4 0.7 + - - -
373A GLU 2.9 16.1 + - - +
374A GLU* 4.1 16.4 - - - +
375A PHE 3.3 0.2 - - - -
376A LYS* 1.3 78.7 - - - +
378A ALA* 1.3 58.2 + - - +
380A SER* 3.7 1.4 + - - -
381A TRP* 3.2 25.8 + - - +
387A HIS* 4.2 30.0 + - + +
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Residues in contact with ALA 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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74A LEU* 3.7 29.2 - - + +
77A VAL* 4.8 11.0 - - + -
78A ALA* 6.1 1.3 - - + +
81A LYS* 4.8 15.7 - - + +
374A GLU 3.1 18.0 + - - +
375A PHE* 4.1 1.6 - - - +
377A ALA* 1.3 76.9 - - - +
379A PHE* 1.3 59.8 + - - +
381A TRP* 3.6 7.2 + - + +
382A TRP* 3.1 29.3 + - - +
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Residues in contact with PHE 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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70A ILE* 4.2 13.0 - - + -
74A LEU* 3.6 28.5 - - + -
375A PHE* 3.1 29.0 + - + +
376A LYS* 3.9 6.3 - - - +
377A ALA 3.4 0.2 - - - -
378A ALA* 1.3 75.2 - - - +
380A SER* 1.3 63.8 + - - +
382A TRP* 3.2 26.4 + + - -
383A TRP* 3.1 56.3 + + + +
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Residues in contact with SER 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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376A LYS* 2.9 13.9 + - - +
379A PHE* 1.3 76.0 - - - +
381A TRP* 1.3 50.2 + - - +
384A LEU* 3.0 20.8 + - - +
385A GLY 2.6 28.1 + - - -
386A VAL* 3.4 16.3 + - - +
387A HIS* 2.7 43.7 - - - -
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Residues in contact with TRP 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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81A LYS* 4.6 16.6 - - - +
377A ALA 3.2 18.3 + - - +
378A ALA* 4.0 6.3 - - - +
379A PHE 3.3 0.2 - - - -
380A SER* 1.3 76.7 - - - +
382A TRP* 1.3 82.1 - + + +
383A TRP 4.4 0.2 - - - -
385A GLY* 3.1 23.9 + - - +
386A VAL 4.4 1.6 - - - +
387A HIS* 4.6 1.2 + - - +
388A HIS* 3.2 65.2 + + + +
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Residues in contact with TRP 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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70A ILE* 3.6 34.1 - - + -
74A LEU* 5.5 8.1 - - + -
378A ALA 3.1 20.2 + - - +
379A PHE* 3.2 34.3 + + - +
381A TRP* 1.3 94.4 - + + +
383A TRP* 1.3 97.9 + + - +
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Residues in contact with TRP 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 PHE* 3.1 52.0 + + + +
382A TRP* 1.3 117.5 - + - +
384A LEU* 1.3 69.1 + - + +
385A GLY 3.8 0.2 - - - -
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Residues in contact with LEU 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 SER* 3.0 19.3 + - - +
383A TRP* 1.3 85.9 - - + +
385A GLY* 1.3 63.2 + - - +
386A VAL* 3.9 25.4 - - + +
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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