Contacts of the helix formed by residues 437 - 455 (chain A) in PDB entry 6S7T
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 437 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A LYS* 4.8 3.0 - - - +
285A ARG* 5.0 4.9 + - - +
436A ILE* 1.3 77.7 - - - +
438A ASP* 1.3 84.3 + - - +
439A GLU* 2.4 31.1 + - - +
440A ARG* 3.3 41.2 + - + +
441A VAL* 3.4 17.9 + - - +
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Residues in contact with ASP 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A VAL* 4.1 19.0 - - + +
242A LYS* 6.3 0.4 - - - -
276A HIS* 2.9 29.7 + - - -
280A LEU* 4.4 16.7 - - + +
285A ARG* 3.2 32.2 + - - +
287A SER* 5.0 1.2 + - - -
289A ARG* 3.0 30.0 + - - +
290A VAL* 4.5 9.2 - - - +
437A ASN* 1.3 86.0 + - - +
439A GLU* 1.3 68.7 + - - +
441A VAL* 4.0 2.4 + - - +
442A PHE 3.9 2.3 + - - -
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Residues in contact with GLU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A GLU 4.8 3.8 - - - +
192A LEU* 3.7 16.8 - - + -
238A VAL* 3.7 28.4 - - + +
241A VAL* 4.7 6.2 - - + +
242A LYS* 2.7 42.0 + - - +
276A HIS* 4.9 1.6 - - - -
437A ASN* 2.4 36.6 + - + +
438A ASP* 1.3 85.1 - - - +
440A ARG* 1.3 64.7 + - + +
441A VAL 3.3 0.2 - - - -
442A PHE* 3.2 10.5 + - - +
443A VAL* 3.0 29.5 + - - +
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Residues in contact with ARG 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 3.1 28.0 + - + +
193A TRP* 3.1 40.0 - - - -
432A CYS* 3.5 32.5 - - - +
435A ASN* 2.9 33.4 + - - +
436A ILE* 4.5 5.2 - - + +
437A ASN* 3.3 39.5 + - + +
439A GLU* 1.3 81.6 - - + +
441A VAL* 1.3 59.1 + - - +
443A VAL* 3.2 5.8 + - - +
444A ALA* 2.9 29.6 + - - +
474A ILE* 5.9 0.2 - - - +
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Residues in contact with VAL 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A HIS* 4.4 7.6 - - + +
279A VAL* 3.6 33.4 - - + -
280A LEU* 4.9 9.0 - - + +
283A MET* 3.7 31.0 - - + -
285A ARG* 5.3 0.4 - - - +
436A ILE* 4.2 14.8 - - + -
437A ASN 3.4 16.4 - - - +
438A ASP 4.1 6.1 - - - +
440A ARG* 1.3 77.7 - - - +
442A PHE* 1.3 61.5 + - - +
444A ALA* 3.3 6.6 + - + +
445A LEU* 3.0 32.0 + - + +
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Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 5.1 5.4 - - + -
234A TYR* 3.5 45.3 - + + -
237A TRP* 4.4 12.1 - + - -
238A VAL* 3.8 28.3 - - + -
272A LEU* 3.9 27.8 - - + +
273A ILE* 5.5 2.9 - - + -
276A HIS* 3.3 50.1 - + + +
439A GLU* 3.2 11.8 + - - +
441A VAL* 1.3 79.6 - - - +
443A VAL* 1.3 68.5 + - + +
445A LEU* 3.3 3.5 + - - +
446A TYR* 2.9 36.0 + + + +
470A MET* 6.4 0.9 - - + -
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 6.1 0.4 - - + -
192A LEU* 3.3 40.2 - - + -
432A CYS* 4.1 12.3 - - - -
439A GLU 3.0 15.2 + - - +
440A ARG* 3.2 7.8 + - - +
442A PHE* 1.3 88.9 - - + +
444A ALA* 1.3 58.5 + - - +
446A TYR* 3.3 6.9 + - + +
447A ALA* 2.9 27.9 + - - +
467A VAL* 4.4 5.2 - - + +
470A MET* 4.8 9.4 - - + -
471A LEU* 3.8 29.4 - - + -
474A ILE* 5.7 0.2 - - + -
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Residues in contact with ALA 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 4.9 9.4 - - + +
432A CYS* 5.0 5.1 - - + -
433A ILE* 3.7 30.7 - - + -
440A ARG 2.9 16.1 + - - +
441A VAL* 3.7 6.7 - - + +
443A VAL* 1.3 77.5 - - - +
445A LEU* 1.3 64.4 + - + +
447A ALA* 3.3 5.8 + - - +
448A ILE* 3.0 34.9 + - + +
471A LEU* 6.2 0.2 - - - -
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Residues in contact with LEU 445 (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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272A LEU* 4.4 13.0 - - + -
275A LEU* 4.0 18.7 - - + +
276A HIS* 3.8 26.0 - - + +
279A VAL* 3.7 37.0 - - + -
441A VAL* 3.0 26.4 + - + +
442A PHE* 3.8 4.5 - - - +
444A ALA* 1.3 78.6 - - + +
446A TYR* 1.3 62.6 + - - +
448A ILE* 3.4 11.2 + - + +
449A SER* 2.9 28.7 + - - -
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Residues in contact with TYR 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A LEU* 5.5 1.6 - - + -
230A LEU* 3.3 21.0 - - - +
231A GLN* 3.6 12.0 + - - -
234A TYR* 3.8 22.0 - + - -
268A PHE* 3.4 34.5 - + - -
272A LEU* 3.8 21.5 - - + +
442A PHE* 2.9 27.3 + + + +
443A VAL* 3.6 6.1 - - - +
445A LEU* 1.3 76.3 - - - +
447A ALA* 1.3 62.0 + - - +
449A SER* 4.0 1.7 - - - -
450A ALA* 2.9 30.3 + - + +
463A THR 3.5 16.6 + - - -
466A PRO* 4.0 4.5 - - - +
467A VAL* 3.7 31.6 - - + -
470A MET* 5.0 9.9 - - + -
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Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A PHE* 4.2 5.2 - - + -
429A LEU* 4.2 14.4 - - + -
443A VAL 2.9 16.9 + - - +
444A ALA* 3.6 6.3 - - - +
446A TYR* 1.3 77.5 - - - +
448A ILE* 1.3 64.1 + - - +
450A ALA* 3.9 0.9 - - - +
451A VAL* 3.0 30.2 + - - +
464A LEU* 4.9 0.3 - - - +
467A VAL* 3.9 15.0 - - + +
471A LEU* 3.7 28.3 - - + -
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Residues in contact with ILE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LEU* 4.6 4.9 - - + -
433A ILE* 6.2 0.2 - - + -
444A ALA* 3.0 27.7 + - + +
445A LEU* 4.0 11.7 - - + +
447A ALA* 1.3 74.9 - - - +
449A SER* 1.3 65.5 + - - +
451A VAL* 3.4 6.7 + - - +
452A TYR* 3.0 23.0 + - + +
223H ALA* 3.8 31.0 - - + -
226H PHE* 3.6 27.6 - - + -
227H VAL* 4.6 13.9 - - + -
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Residues in contact with SER 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A PHE* 3.6 14.8 - - - -
272A LEU* 5.3 6.1 - - - -
275A LEU* 5.6 8.0 - - - +
445A LEU 2.9 19.0 + - - -
446A TYR* 4.0 2.9 - - - -
448A ILE* 1.3 78.4 - - - +
450A ALA* 1.3 58.6 + - - +
452A TYR* 3.4 4.3 + - - +
453A PHE* 3.0 60.6 + - - -
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Residues in contact with ALA 450 (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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268A PHE* 4.9 6.9 - - + -
446A TYR* 2.9 29.9 + - + +
447A ALA 3.9 0.9 - - - +
449A SER* 1.3 73.0 - - - +
451A VAL* 1.3 66.2 + - - +
453A PHE* 4.5 4.5 - - - +
454A ALA* 2.9 28.2 + - - +
463A THR* 4.8 6.2 - - + +
464A LEU* 3.7 33.0 - - + +
467A VAL* 4.2 7.2 - - + -
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Residues in contact with VAL 451 (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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414A PHE* 4.9 4.5 - - + -
425A PHE* 3.5 33.4 - - + -
447A ALA 3.0 22.7 + - - +
448A ILE* 3.7 5.4 - - - +
450A ALA* 1.3 76.7 - - - +
452A TYR* 1.3 63.5 + - - +
454A ALA* 3.9 1.4 - - - +
455A GLY* 3.0 20.1 + - - -
464A LEU* 4.1 15.7 - - + -
226H PHE* 5.2 2.7 - - + -
227H VAL* 4.3 22.4 - - + +
230H MET* 3.7 27.4 - - + +
231H THR* 4.4 10.3 - - - +
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Residues in contact with TYR 452 (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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387A LEU 4.0 19.9 + - - -
388A TRP* 5.4 6.9 + - - -
390A THR* 5.5 0.9 + - - -
448A ILE* 3.0 16.0 + - + +
449A SER* 3.8 5.2 - - - +
451A VAL* 1.3 77.6 - - - +
453A PHE* 1.3 88.9 + + - +
455A GLY* 3.1 14.0 + - - -
456A VAL* 3.7 12.2 + - + +
226H PHE* 4.0 18.6 - + + -
230H MET* 3.8 34.4 - - + +
235H MET* 4.5 22.2 - - + +
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Residues in contact with PHE 453 (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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268A PHE* 4.3 18.8 - + - -
387A LEU* 4.2 36.3 - - + +
449A SER* 3.0 46.5 + - - +
450A ALA* 4.1 3.8 - - - +
452A TYR* 1.3 94.9 - + - +
454A ALA* 1.3 62.0 + - - +
456A VAL* 3.4 20.9 + - + +
457A MET* 3.6 8.8 + - - +
460A LEU* 4.0 21.6 - - + +
463A THR* 6.2 1.8 - - + -
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Residues in contact with ALA 454 (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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409A THR* 3.5 11.6 + - - +
414A PHE* 4.2 6.0 - - + -
450A ALA 2.9 18.5 + - - +
451A VAL 4.0 1.3 - - - +
453A PHE* 1.3 72.1 - - - +
455A GLY* 1.3 58.1 + - - +
456A VAL 3.0 10.7 + - - -
457A MET 3.1 21.0 + - - +
460A LEU* 4.8 5.6 - - - +
461A MET* 4.1 17.9 - - + +
463A THR* 6.3 0.4 - - + -
464A LEU* 3.6 32.3 - - + -
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Residues in contact with GLY 455 (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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408A PRO* 4.6 0.3 - - - +
409A THR 4.3 16.2 + - - +
414A PHE* 3.9 18.1 - - - -
451A VAL 3.0 15.2 + - - -
452A TYR 3.1 7.5 + - - -
454A ALA* 1.3 76.3 - - - +
456A VAL* 1.3 56.7 + - - +
230H MET* 4.6 12.6 - - - -
233H GLY* 5.6 1.9 - - - -
235H MET* 3.2 24.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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