Contacts of the helix formed by residues 435 - 457 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B GLU 5.0 0.2 - - - +
344B LEU* 4.7 0.8 - - + -
345B CYS* 3.6 29.0 + - - +
348B ASP* 2.8 18.7 + - - +
434B GLN* 1.3 91.0 + - + +
436B LYS* 1.3 63.8 + - - +
437B ARG 3.3 3.1 - - - -
438B LYS* 3.2 43.9 + - + +
439B VAL* 3.2 15.9 + - - +
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Residues in contact with LYS 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B ALA* 3.3 29.4 - - - +
429B HIS* 4.5 20.0 + - - +
433B LEU* 4.6 20.1 - - + +
434B GLN 3.6 3.8 + - - -
435B GLU* 1.3 75.4 - - - +
437B ARG* 1.3 56.6 + - - +
439B VAL* 3.3 6.1 + - - +
440B GLU* 2.9 51.4 + - + +
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Residues in contact with ARG 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B GLU 3.3 1.0 - - - -
436B LYS* 1.3 78.9 - - - +
438B LYS* 1.3 61.5 + - - +
440B GLU* 3.5 20.8 + - - +
441B GLN* 3.2 24.5 + - - +
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Residues in contact with LYS 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLU* 3.3 40.6 + - - +
344B LEU* 4.0 15.8 - - + +
435B GLU* 3.2 42.7 + - + +
437B ARG* 1.3 79.2 - - - +
439B VAL* 1.3 61.1 + - - +
441B GLN* 3.5 7.2 + - - +
442B LEU* 3.3 20.4 + - - +
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Residues in contact with VAL 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B LEU* 3.9 25.6 - - + -
348B ASP* 4.3 12.8 - - + +
352B LEU* 4.2 10.5 - - + -
426B ILE* 4.0 18.4 - - + -
427B ASN 4.2 3.1 - - - -
428B ALA* 3.8 25.6 - - + +
433B LEU* 4.3 20.0 - - + -
435B GLU 3.2 14.4 + - - +
436B LYS 3.3 6.0 + - - +
438B LYS* 1.3 72.4 - - - +
440B GLU* 1.3 61.7 + - - +
442B LEU* 3.4 3.9 + - - +
443B GLN* 2.9 28.2 + - - +
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Residues in contact with GLU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B ALA* 3.7 20.2 - - + +
429B HIS* 5.4 7.5 + - + -
436B LYS* 2.9 36.2 + - + +
437B ARG* 3.5 27.7 + - + +
439B VAL* 1.3 77.0 - - - +
441B GLN* 1.3 57.2 + - - +
443B GLN* 3.2 7.0 + - - +
444B TYR* 2.8 31.6 + - - +
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Residues in contact with GLN 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR* 4.9 16.4 + - - +
437B ARG* 3.2 14.7 + - - +
438B LYS* 3.8 7.2 - - + +
439B VAL 3.3 0.2 - - - -
440B GLU* 1.3 77.9 - - - +
442B LEU* 1.3 58.3 + - - +
444B TYR* 3.9 12.2 - - - +
445B ASN* 3.0 64.9 + - - +
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Residues in contact with LEU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B LEU* 5.4 4.9 - - + -
338B LEU* 5.9 0.2 - - + -
339B SER 3.3 22.2 - - - +
340B GLY* 3.8 31.4 - - - +
341B PHE* 3.9 2.0 - - + +
344B LEU* 4.1 13.7 - - + -
426B ILE* 3.8 34.5 - - + -
438B LYS 3.3 11.1 + - - +
439B VAL* 3.8 7.4 - - - +
440B GLU 3.3 0.2 - - - -
441B GLN* 1.3 74.5 - - - +
443B GLN* 1.3 60.5 + - - +
445B ASN* 3.4 9.9 + - + +
446B LEU* 2.9 46.4 + - + +
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Residues in contact with GLN 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B LEU* 3.7 6.0 - - + +
426B ILE* 3.6 24.3 - - + +
427B ASN* 3.6 5.2 - - - +
428B ALA* 2.7 38.6 + - - +
429B HIS* 4.5 15.5 + - - -
439B VAL 2.9 17.7 + - - +
440B GLU* 3.4 7.1 + - - +
442B LEU* 1.3 77.0 - - - +
444B TYR* 1.3 55.8 - - - +
446B LEU* 3.2 5.6 + - - +
447B GLU* 2.8 56.6 + - - +
469B LYS* 5.8 4.7 + - - +
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Residues in contact with TYR 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B GLU 2.8 20.6 + - - +
441B GLN* 3.9 12.1 - - - +
443B GLN* 1.3 72.7 - - - +
445B ASN* 1.3 63.7 + - - +
447B GLU* 3.3 23.8 + - + +
448B LEU* 2.9 64.7 + - + +
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Residues in contact with ASN 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B TYR 6.1 0.4 - - - +
265B ALA* 4.0 27.9 + - - +
270B ILE* 3.9 4.8 - - + +
273B LEU* 3.4 23.4 - - + +
441B GLN* 3.0 43.6 + - - +
442B LEU* 3.8 9.2 - - + +
443B GLN 3.3 0.2 - - - -
444B TYR* 1.3 78.6 - - - +
446B LEU* 1.3 56.4 + - - +
448B LEU* 3.5 19.2 + - - +
449B ALA 3.0 21.1 + - - -
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 4.1 17.5 - - + -
277B VAL* 3.6 31.6 - - + -
338B LEU* 4.8 6.3 - - + -
339B SER 5.4 0.4 - - - +
419B LEU* 5.1 4.7 - - + +
422B ALA* 4.2 19.5 - - + +
423B LEU* 3.7 15.6 - - + +
426B ILE* 3.5 37.0 - - + -
442B LEU* 2.9 33.5 + - + +
443B GLN 3.2 4.9 + - - +
445B ASN* 1.3 73.7 - - - +
447B GLU* 1.3 60.9 + - - +
449B ALA* 3.3 5.1 + - + +
450B PHE* 2.9 28.1 + - - +
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Residues in contact with GLU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B LEU* 3.6 23.8 - - + +
443B GLN* 2.8 46.1 + - - +
444B TYR* 3.4 28.1 - - + +
446B LEU* 1.3 75.1 - - - +
448B LEU* 1.3 57.2 + - + +
450B PHE* 3.2 2.4 + - - +
451B HIS* 2.8 55.9 + - + +
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Residues in contact with LEU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ALA* 5.5 5.4 - - + +
270B ILE* 3.9 27.7 - - + +
444B TYR* 2.9 56.4 + - + +
445B ASN* 3.5 15.9 - - - +
447B GLU* 1.3 77.7 - - + +
449B ALA* 1.3 56.1 + - - +
451B HIS* 4.1 9.0 - - + +
452B HIS* 2.9 33.1 + - - +
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Residues in contact with ALA 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B ILE* 3.8 9.8 - - + +
273B LEU* 4.0 18.4 - - + -
274B VAL* 3.4 33.6 - - + +
419B LEU* 4.1 12.7 - - + +
445B ASN 3.0 14.2 + - - +
446B LEU* 3.5 10.1 - - + +
447B GLU 3.3 0.2 - - - -
448B LEU* 1.3 72.7 - - - +
450B PHE* 1.3 66.5 + - - +
452B HIS* 4.0 0.2 - - - +
453B HIS* 3.1 20.4 + - - +
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Residues in contact with PHE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B PHE* 5.2 1.8 - + - -
416B GLU* 3.9 23.8 - - + -
419B LEU* 3.5 26.6 - - + +
420B TYR* 4.2 19.1 - + + -
423B LEU* 3.6 26.9 - - + -
446B LEU 2.9 13.7 + - - +
447B GLU 3.2 7.6 + - - +
449B ALA* 1.3 75.8 - - - +
451B HIS* 1.3 60.9 + + - +
453B HIS* 3.3 3.5 + - - +
454B LEU* 2.9 59.3 + - + +
462B ILE* 4.7 10.5 - - + -
463B LEU* 3.7 29.6 - - + -
466B LEU* 4.3 13.9 - - + -
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Residues in contact with HIS 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B GLU* 2.8 47.9 + - + +
448B LEU* 4.1 10.6 + - + +
450B PHE* 1.3 76.2 - - + +
452B HIS* 1.3 56.9 + - - +
454B LEU* 3.2 6.1 + - + +
455B SER* 2.8 33.8 + - - -
460B GLN* 4.7 8.6 + - + +
463B LEU* 3.6 41.5 - - + +
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Residues in contact with HIS 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B LEU* 3.7 30.8 - - + +
270B ILE* 4.2 15.3 - - + -
271B GLU* 4.8 13.1 + - - +
274B VAL* 4.6 11.7 - - + -
448B LEU 2.9 19.7 + - - +
449B ALA 4.0 2.5 - - - +
451B HIS* 1.3 76.2 - - - +
453B HIS* 1.3 58.4 + - - +
455B SER* 3.0 10.5 + - - -
456B LYS* 3.0 57.4 + - + +
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Residues in contact with HIS 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B VAL* 3.7 21.5 - - + +
413B SER* 4.9 3.4 + - - -
415B ASP* 3.6 36.1 + - + +
416B GLU* 4.6 15.0 - - + -
419B LEU* 3.8 20.9 - - + -
449B ALA 3.1 18.1 + - - +
450B PHE 3.7 3.6 - - - +
452B HIS* 1.3 78.7 - - - +
454B LEU* 1.3 62.5 + - + +
456B LYS* 3.4 21.1 + - + +
457B THR* 2.8 41.3 + - + +
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Residues in contact with LEU 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B GLU* 3.4 36.1 - - + +
450B PHE* 2.9 44.4 + - + +
451B HIS* 3.6 4.7 - - - +
453B HIS* 1.3 76.4 - - + +
455B SER* 1.3 56.9 + - - +
457B THR* 3.0 4.6 + - - +
458B HIS 3.0 8.7 + - - -
459B ARG* 2.7 52.1 + - + +
460B GLN* 4.1 6.1 - - + +
462B ILE* 3.8 12.8 - - + -
463B LEU* 3.6 36.3 - - + -
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Residues in contact with SER 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451B HIS 2.8 16.0 + - - -
452B HIS* 3.0 21.5 + - - -
454B LEU* 1.3 67.8 - - - +
456B LYS* 1.3 63.7 + - - +
457B THR 3.1 2.7 + - - -
458B HIS* 3.4 12.5 + - - +
459B ARG 4.8 0.9 - - - +
460B GLN* 3.3 30.1 - - - +
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Residues in contact with LYS 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B GLU* 3.2 36.4 + - - -
274B VAL* 5.0 2.4 - - - +
452B HIS* 3.0 43.9 + - + +
453B HIS* 3.4 28.7 + - + +
455B SER* 1.3 78.0 + - - +
457B THR* 1.3 64.2 + - + +
458B HIS 4.0 0.2 + - - -
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Residues in contact with THR 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B GLU* 4.5 3.4 + - - -
453B HIS* 2.8 38.1 + - + +
454B LEU* 3.0 12.0 + - - -
456B LYS* 1.3 86.8 - - + +
458B HIS* 1.3 69.8 + - - +
459B ARG* 3.4 22.5 - - - +
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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
------------------------------------------------------------
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