Contacts of the helix formed by residues 435 - 457 (chain A) in PDB entry 5NTI
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 GLU 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A CYS* 3.8 25.0 + - - +
348A ASP* 2.9 17.5 + - - +
434A GLN* 1.3 82.8 - - + +
436A LYS* 1.3 63.9 + - - +
437A ARG* 3.2 3.1 - - - -
438A LYS* 3.0 52.3 + - + +
439A VAL* 3.4 10.3 + - - +
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Residues in contact with LYS 436 (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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428A ALA 3.4 28.2 + - - +
429A HIS* 4.8 14.4 + - - +
430A ARG 5.8 1.7 + - - +
433A LEU* 4.0 23.8 + - + +
434A GLN 3.6 2.6 + - - -
435A GLU* 1.3 74.2 - - - +
437A ARG* 1.3 56.5 + - - +
439A VAL* 3.2 8.1 + - - +
440A GLU* 2.9 49.0 + - - +
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Residues in contact with ARG 437 (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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435A GLU 3.0 1.2 + - - -
436A LYS* 1.3 75.5 - - - +
438A LYS* 1.3 68.6 + - - +
440A GLU* 3.2 19.0 + - + +
441A GLN* 3.1 36.0 + - + +
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Residues in contact with LYS 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLU* 2.8 35.1 + - + +
344A LEU* 3.6 31.9 - - + +
345A CYS* 3.7 4.4 - - - +
435A GLU* 3.0 41.6 + - + +
437A ARG* 1.3 84.0 - - - +
439A VAL* 1.3 60.7 + - - +
441A GLN* 3.5 6.8 + - + +
442A LEU* 3.3 22.2 + - - +
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 4.2 20.2 - - + -
348A ASP* 4.2 15.7 - - + +
352A LEU* 4.3 13.0 - - + -
426A ILE* 4.0 16.7 - - + +
428A ALA* 3.8 25.6 - - + +
433A LEU* 4.1 25.8 - - + -
435A GLU 3.6 13.9 - - - +
436A LYS 3.2 7.2 + - - +
437A ARG 3.2 0.4 - - - -
438A LYS* 1.3 74.3 - - - +
440A GLU* 1.3 58.7 + - - +
442A LEU* 3.4 2.4 + - - +
443A GLN* 2.9 29.5 + - - +
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Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ALA* 3.5 21.9 - - + +
436A LYS* 2.9 41.7 + - - +
437A ARG* 3.2 26.3 + - + +
439A VAL* 1.3 76.1 - - - +
441A GLN* 1.3 56.4 + - - +
443A GLN* 3.5 7.0 + - - +
444A TYR* 3.0 29.1 + - - +
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Residues in contact with GLN 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TYR* 4.7 14.6 + - - +
437A ARG* 3.1 25.4 + - + +
438A LYS* 3.8 11.4 - - + +
439A VAL 3.3 0.2 - - - -
440A GLU* 1.3 75.1 - - - +
442A LEU* 1.3 59.6 + - - +
444A TYR* 3.4 13.9 + - - +
445A ASN* 3.0 48.1 + - - +
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Residues in contact with LEU 442 (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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273A LEU* 5.2 3.6 - - + -
338A LEU* 6.3 0.4 - - + -
339A SER 3.4 21.5 - - - +
340A GLY* 3.6 33.0 - - - +
341A PHE 3.9 3.4 - - - +
344A LEU* 4.1 16.2 - - + -
426A ILE* 4.0 25.1 - - + -
438A LYS 3.3 14.3 + - - +
439A VAL* 3.9 3.6 - - - +
441A GLN* 1.3 76.0 - - - +
443A GLN* 1.3 66.1 + - - +
445A ASN* 3.3 11.3 + - + +
446A LEU* 3.0 37.1 + - + +
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Residues in contact with GLN 443 (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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423A LEU* 3.7 7.0 - - + +
426A ILE* 3.4 25.5 - - + +
427A ASN* 3.5 7.6 - - - +
428A ALA* 2.7 38.6 + - - +
429A HIS* 4.7 11.0 + - - -
439A VAL 2.9 19.0 + - - +
440A GLU* 3.7 7.5 + - - +
442A LEU* 1.3 77.3 - - - +
444A TYR* 1.3 56.3 + - - +
446A LEU* 3.3 6.6 + - - +
447A GLU* 2.9 52.1 + - - +
469A LYS* 4.6 12.5 + - - +
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Residues in contact with TYR 444 (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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440A GLU 3.0 18.7 + - - +
441A GLN* 3.7 13.9 - - - +
443A GLN* 1.3 76.8 - - - +
445A ASN* 1.3 62.2 + - - +
447A GLU* 3.1 27.2 + - + +
448A LEU* 2.8 62.8 + - + +
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Residues in contact with ASN 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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264A TYR 5.9 0.6 - - - +
265A ALA* 3.7 28.7 + - - +
270A ILE* 3.9 1.9 - - + +
273A LEU* 3.4 23.1 - - + +
441A GLN* 3.0 41.2 + - - +
442A LEU* 3.7 11.7 - - + +
444A TYR* 1.3 76.9 - - - +
446A LEU* 1.3 57.6 + - - +
448A LEU* 3.2 23.4 + - - +
449A ALA 2.8 23.0 + - - -
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Residues in contact with LEU 446 (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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273A LEU* 4.1 18.4 - - + -
277A VAL* 3.7 30.1 - - + -
338A LEU* 5.0 5.2 - - + -
339A SER 5.1 2.7 - - - +
419A LEU* 4.9 3.9 - - + +
422A ALA* 4.2 17.7 - - + +
423A LEU* 3.8 15.4 - - + +
426A ILE* 3.6 36.1 - - + -
442A LEU* 3.0 33.8 + - + +
443A GLN* 3.6 4.5 - - - +
445A ASN* 1.3 73.0 - - - +
447A GLU* 1.3 56.4 + - - +
449A ALA* 3.5 5.9 - - + +
450A PHE* 2.7 34.3 + - - +
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Residues in contact with GLU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A LEU* 3.6 19.8 - - + +
443A GLN* 2.9 44.2 + - - +
444A TYR* 3.2 31.5 - - + +
446A LEU* 1.3 74.3 - - - +
448A LEU* 1.3 59.9 + - + +
450A PHE* 3.5 4.0 - - - +
451A HIS* 2.8 55.9 + - + +
469A LYS* 5.5 2.6 + - - -
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Residues in contact with LEU 448 (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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265A ALA* 5.0 7.4 - - + +
270A ILE* 3.8 25.0 - - + +
444A TYR* 2.8 52.8 + - + +
445A ASN* 3.3 28.5 - - - +
447A GLU* 1.3 72.8 - - + +
449A ALA* 1.3 57.5 + - - +
451A HIS* 4.1 8.1 - - + +
452A HIS* 2.8 33.3 + - - +
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Residues in contact with ALA 449 (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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270A ILE* 3.8 8.2 - - - +
273A LEU* 3.8 22.0 - - + -
274A VAL* 3.4 31.2 - - + +
419A LEU* 4.1 12.6 - - + +
445A ASN 2.8 16.8 + - - +
446A LEU* 3.5 10.3 - - + +
448A LEU* 1.3 71.5 - - - +
450A PHE* 1.3 63.8 + - - +
452A HIS* 3.7 0.2 - - - +
453A HIS* 3.1 21.0 + - - +
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Residues in contact with PHE 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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412A PHE* 5.1 1.1 - + - -
416A GLU* 3.7 23.3 - - + -
419A LEU* 3.3 27.7 - - + +
420A TYR* 4.0 17.7 - + + -
423A LEU* 3.4 28.7 - - + -
446A LEU 2.7 21.2 + - - +
447A GLU 3.3 4.9 + - - +
449A ALA* 1.3 74.4 - - - +
451A HIS* 1.3 65.9 + + - +
453A HIS* 3.3 1.6 + - - +
454A LEU* 3.1 48.4 + - + +
462A ILE* 4.5 12.8 - - + -
463A LEU* 3.7 30.1 - - + -
466A LEU* 4.0 16.4 - - + -
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Residues in contact with HIS 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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447A GLU* 2.8 46.9 + - + +
448A LEU* 4.1 8.3 + - + +
450A PHE* 1.3 77.7 - + - +
452A HIS* 1.3 62.1 + - - +
454A LEU* 3.9 4.0 - - - +
455A SER* 3.0 21.5 + - - -
460A GLN* 3.2 23.2 + - - +
463A LEU* 3.5 42.8 - - + +
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Residues in contact with HIS 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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267A LEU* 3.5 30.7 - - + +
270A ILE* 3.9 13.7 - - + -
271A GLU* 3.4 26.5 - - + +
274A VAL* 4.4 14.6 - - + -
448A LEU 2.8 18.9 + - - +
449A ALA 3.7 3.8 - - - +
450A PHE 3.3 0.2 - - - -
451A HIS* 1.3 78.0 - - - +
453A HIS* 1.3 63.4 + - - +
455A SER* 3.1 20.9 + - - -
456A LYS* 3.3 45.9 + - + +
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Residues in contact with HIS 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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274A VAL* 4.0 20.7 - - + +
413A SER* 4.9 1.8 + - - -
415A ASP* 3.6 35.4 - - + +
416A GLU* 4.5 17.5 + - + +
419A LEU* 3.7 30.5 - - + +
449A ALA 3.1 9.1 + - - +
450A PHE 3.8 0.9 - - - +
452A HIS* 1.3 83.7 - - - +
454A LEU* 1.3 56.7 + - + +
456A LYS* 3.4 10.5 + - - +
457A THR* 2.8 51.2 + - + +
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Residues in contact with LEU 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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416A GLU* 3.7 23.6 - - + +
450A PHE* 3.1 45.8 + - + +
451A HIS* 3.9 4.5 - - - +
452A HIS 3.3 0.2 - - - -
453A HIS* 1.3 81.0 - - + +
455A SER* 1.3 55.1 + - - +
457A THR* 2.9 7.0 + - - +
458A HIS 2.9 9.4 + - - -
459A ARG* 2.8 54.6 + - + +
460A GLN* 3.9 12.8 - - + +
462A ILE* 3.8 13.5 - - + -
463A LEU* 3.8 34.3 - - + -
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Residues in contact with SER 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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451A HIS 3.0 8.5 + - - -
452A HIS* 3.1 16.5 + - - -
454A LEU* 1.3 75.8 - - - +
456A LYS* 1.3 66.4 + - - +
458A HIS* 3.3 22.0 + - - +
460A GLN* 3.3 30.7 - - - +
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Residues in contact with LYS 456 (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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271A GLU* 3.3 22.5 + - - +
452A HIS* 3.3 41.7 + - + +
453A HIS* 3.6 13.2 - - - +
454A LEU 3.3 0.2 - - - -
455A SER* 1.3 83.3 + - - +
457A THR* 1.3 62.2 + - + +
458A HIS* 3.4 6.9 + - - -
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Residues in contact with THR 457 (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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416A GLU* 4.6 1.3 + - - -
453A HIS* 2.8 44.4 + - + +
454A LEU* 2.9 13.5 + - - -
456A LYS* 1.3 79.8 - - + +
458A HIS* 1.3 69.9 + - - +
459A ARG* 3.4 19.7 - - - +
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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