Contacts of the helix formed by residues 377 - 392 (chain A) in PDB entry 6T8B
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 LYS 377 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372A PRO* 6.3 0.2 - - - -
375A GLY 4.2 0.4 + - - -
376A VAL* 1.3 88.6 - - - +
378A VAL* 1.3 63.9 + - - +
379A SER* 3.2 23.2 + - - +
380A ARG* 3.8 18.8 + - + +
381A ILE* 4.5 2.8 + - - +
350B PHE* 4.0 12.9 - - + -
383B ASN* 5.1 12.6 - - - +
384B LEU* 3.6 22.7 - - + +
387B ASP* 3.4 19.7 - - - +
4G T 3.4 26.9 + - - +
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Residues in contact with VAL 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PRO* 5.2 2.5 - - + -
376A VAL 5.0 0.4 - - - +
377A LYS* 1.3 72.8 - - - +
379A SER* 1.3 62.5 + - - +
380A ARG 3.2 1.3 - - - -
381A ILE* 3.3 11.0 + - + +
382A SER* 2.9 30.0 + - - +
399A VAL* 5.9 0.4 - - + -
401A GLU* 4.3 32.5 - - + +
409A VAL* 3.9 19.3 - - + -
386B LYS* 4.3 13.7 - - + -
387B ASP* 3.4 21.8 + - - +
390B ARG* 3.5 29.4 - - - +
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Residues in contact with SER 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A LYS* 3.7 23.0 - - - +
378A VAL* 1.3 79.7 - - - +
380A ARG* 1.3 70.0 + - - +
382A SER* 4.3 5.8 - - - -
383A ASN* 2.7 40.4 + - - +
4G T 4.9 8.4 + - - -
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Residues in contact with ARG 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A PHE 5.7 0.9 + - - -
351A GLY 4.1 19.0 + - - -
352A VAL* 3.6 25.5 - - + +
375A GLY 5.4 3.0 + - - -
376A VAL* 4.0 33.6 - - - +
377A LYS* 3.8 15.3 + - + +
379A SER* 1.3 87.4 + - - +
381A ILE* 1.3 64.0 + - + +
383A ASN* 3.8 3.8 - - - +
384A LEU* 2.9 34.4 + - + +
377F LYS* 5.8 0.2 + - - -
3G A 5.6 9.7 + - - +
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Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.7 29.8 - - + -
352A VAL* 3.5 34.5 - - + -
370A ILE* 4.8 18.8 - - + -
372A PRO* 6.0 5.2 - - + -
376A VAL* 5.6 0.4 - - + -
377A LYS 4.8 7.0 - - - +
378A VAL* 3.3 11.5 + - + +
380A ARG* 1.3 76.1 - - - +
382A SER* 1.3 58.8 + - - +
384A LEU* 4.3 4.3 - - + -
385A ALA* 2.9 30.8 + - - +
388A LEU* 4.9 6.5 - - + -
399A VAL* 3.6 31.2 - - + -
409A VAL* 5.1 4.0 - - + -
411A ILE* 4.8 6.5 - - + -
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Residues in contact with SER 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A VAL 2.9 19.2 + - - -
379A SER* 3.8 7.4 - - - -
381A ILE* 1.3 77.1 - - - +
383A ASN* 1.3 63.6 + - - +
385A ALA* 4.1 9.5 - - - +
399A VAL* 4.2 22.5 + - - +
401A GLU* 3.7 21.6 + - - +
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Residues in contact with ASN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A SER* 2.7 33.2 + - - +
380A ARG* 3.9 4.0 - - - +
382A SER* 1.3 81.7 + - - +
384A LEU* 1.3 56.9 + - - +
385A ALA 3.4 2.8 + - - -
386A LYS* 4.6 6.6 + - - +
377F LYS* 5.3 11.0 + - - +
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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
----------------------------------------------------------
347A LEU* 3.8 29.6 - - + -
350A PHE* 3.8 42.2 - - + +
352A VAL* 4.5 10.5 - - + -
380A ARG* 2.9 33.1 + - + +
381A ILE* 4.5 7.0 - - + +
383A ASN* 1.3 75.1 - - - +
385A ALA* 1.3 59.4 + - - +
386A LYS* 3.1 3.1 + - - +
387A ASP* 3.2 15.7 + - + +
388A LEU* 2.9 27.8 + - + +
377F LYS* 4.4 24.2 - - - +
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Residues in contact with ALA 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ILE 2.9 16.3 + - - +
382A SER 4.1 9.2 - - - +
383A ASN 3.4 2.0 - - - -
384A LEU* 1.3 78.0 - - - +
386A LYS* 1.3 57.7 + - - +
388A LEU* 3.6 8.7 - - - +
389A ALA* 2.8 28.9 + - - +
397A VAL* 3.9 23.1 - - + +
399A VAL* 3.7 22.4 - - + +
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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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383A ASN 4.6 5.1 + - - +
384A LEU* 3.1 1.9 - - - +
385A ALA* 1.3 79.4 - - - +
387A ASP* 1.3 59.4 + - - +
389A ALA* 3.1 11.8 + - + +
390A ARG* 3.0 27.3 + - - +
395A ILE 5.6 2.9 + - - +
396A SER* 5.6 9.3 - - - +
378F VAL* 4.5 18.6 - - + -
401F GLU* 5.2 12.1 - - - +
402F VAL* 3.7 29.8 - - + +
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Residues in contact with ASP 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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350A PHE* 3.7 24.1 - - + -
384A LEU* 3.2 13.1 + - + +
386A LYS* 1.3 73.8 - - - +
388A LEU* 1.3 60.9 + - - +
390A ARG* 2.6 40.4 + - - +
391A SER* 2.9 28.4 + - - -
377F LYS* 3.1 38.0 - - - +
378F VAL* 3.1 23.5 + - - +
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 3.6 39.3 - - + +
346A LYS* 4.5 7.2 - - + -
347A LEU* 3.6 33.7 - - + +
350A PHE* 5.3 2.7 - - + -
381A ILE* 4.9 7.9 - - + -
384A LEU* 2.9 22.7 + - + +
385A ALA* 3.6 7.4 - - - +
387A ASP* 1.3 75.2 - - - +
389A ALA* 1.3 63.1 + - - +
391A SER* 2.8 25.6 + - - +
392A LEU* 3.3 13.4 + - + +
397A VAL* 4.6 14.6 - - + -
411A ILE* 3.9 17.9 - - + -
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ALA 2.8 14.9 + - - +
386A LYS* 3.1 15.9 + - + +
388A LEU* 1.3 77.0 - - - +
390A ARG* 1.3 51.6 + - - +
392A LEU* 2.7 28.7 - - - +
394A VAL* 3.3 16.4 + - - +
395A ILE 4.6 3.8 - - - +
396A SER* 4.0 11.9 - - - +
397A VAL* 3.5 35.2 - - + +
402F VAL* 6.4 0.7 - - + -
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Residues in contact with ARG 390 (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 PHE* 5.3 1.8 - - - -
386A LYS* 3.0 12.9 + - + +
387A ASP* 2.6 43.1 + - - +
388A LEU 3.3 0.4 - - - -
389A ALA* 1.3 75.9 - - - +
391A SER* 1.3 59.4 + - - +
392A LEU 2.8 11.1 - - - +
394A VAL 5.1 1.1 - - - -
372F PRO* 4.1 20.8 - - - +
376F VAL 4.1 12.7 + - - -
377F LYS 4.8 0.2 - - - -
378F VAL* 3.2 21.2 - - - +
401F GLU 3.9 12.7 + - - +
402F VAL* 5.4 10.5 - - + +
403F ILE 5.6 0.9 - - - +
406F LYS 5.0 2.7 - - - +
407F THR* 3.2 19.4 - - - -
408F THR* 3.3 34.9 - - - +
409F VAL* 3.5 20.4 - - - +
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Residues in contact with SER 391 (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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342A LEU* 4.7 6.9 - - - +
346A LYS* 3.4 52.0 - - - +
350A PHE* 5.5 4.3 - - - -
387A ASP 2.9 14.0 + - - -
388A LEU* 2.8 27.8 + - - +
390A ARG* 1.3 77.7 - - - +
392A LEU* 1.3 62.4 + - - +
407F THR* 3.5 12.8 - - - +
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Residues in contact with LEU 392 (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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339A MET* 4.0 28.7 - - + +
342A LEU* 3.6 37.9 - - + +
343A LEU* 3.8 28.3 - - + +
368A PHE* 5.7 0.2 - - + -
388A LEU* 3.3 14.4 + - + +
389A ALA* 2.7 16.8 - - - +
390A ARG* 2.8 13.5 - - - +
391A SER* 1.3 84.1 + - - +
393A ALA* 1.3 60.3 + - - +
394A VAL* 3.1 18.7 + - + +
397A VAL* 5.1 1.1 - - + -
413A ILE* 3.8 28.9 - - + -
406F LYS 5.4 0.3 - - - +
407F THR* 3.3 2.9 - - - +
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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