Contacts of the helix formed by residues 417 - 436 (chain B) in PDB entry 3TQI
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 ALA 417 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B MET* 3.7 24.0 - - + -
416B SER* 1.3 87.5 - - - +
418B GLU* 1.3 63.2 + - - +
419B TYR 3.1 2.9 - - - +
420B ILE* 3.4 25.5 - - + +
421B ASN* 3.0 35.0 + - - +
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B SER* 3.2 15.4 + - - +
417B ALA* 1.3 79.6 - - - +
419B TYR* 1.3 85.5 + - + +
421B ASN* 3.8 6.7 + - - +
422B ILE* 3.2 29.9 + - + +
467B TYR* 3.9 13.2 + - + -
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Residues in contact with TYR 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ILE* 3.9 20.4 - - + +
413B GLY* 5.9 0.2 - - - -
414B GLU* 3.4 35.8 + - + -
416B SER* 3.5 16.2 - - - -
417B ALA 3.1 1.6 - - - +
418B GLU* 1.3 95.6 + - + +
420B ILE* 1.3 64.8 + - - +
421B ASN 3.3 0.2 - - - -
422B ILE* 3.4 6.8 + - + +
423B LEU* 3.0 22.7 + - - +
450B PHE* 3.3 40.8 - + + -
452B PRO* 4.3 16.5 - - + +
467B TYR* 3.7 28.9 + + - -
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Residues in contact with ILE 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B GLY* 3.0 36.6 - - - +
264B LEU* 5.1 2.2 - - + -
291B LYS* 5.8 4.7 - - + -
295B MET* 4.6 10.1 - - + -
407B LEU* 5.0 10.8 - - + +
411B ILE* 3.4 25.1 - - + -
415B VAL* 3.6 19.5 - - + -
417B ALA* 3.3 25.1 + - + +
419B TYR* 1.3 74.8 - - - +
421B ASN* 1.3 68.2 + - - +
423B LEU* 2.9 6.5 + - - +
424B LYS* 2.7 48.5 + - - +
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Residues in contact with ASN 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B ALA* 3.0 23.5 + - - +
418B GLU* 4.0 6.7 - - - +
420B ILE* 1.3 90.1 - - - +
422B ILE* 1.3 61.9 + - + +
424B LYS* 4.1 16.4 + - - +
425B GLN* 3.4 27.7 + - - +
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Residues in contact with ILE 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418B GLU* 3.2 19.9 + - + +
419B TYR* 3.4 8.2 + - + +
420B ILE 3.2 0.6 - - - -
421B ASN* 1.3 76.7 - - + +
423B LEU* 1.3 63.2 + - - +
425B GLN* 3.1 21.5 + - - +
426B ALA* 3.2 10.2 + - - +
450B PHE* 4.1 18.6 - - + -
467B TYR* 4.0 23.3 - - + -
469B ILE* 5.0 3.4 - - + -
503B ILE* 3.9 19.9 - - + +
505B GLU* 3.4 36.6 - - + +
506B VAL* 4.0 13.5 - - + -
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B LEU* 3.8 25.4 - - + -
410B ARG* 3.5 30.5 - - + +
411B ILE* 3.9 13.7 - - + -
419B TYR 3.0 13.2 + - - +
420B ILE* 2.9 7.7 + - - +
422B ILE* 1.3 78.0 - - - +
424B LYS* 1.3 54.4 + - - +
426B ALA* 3.1 5.7 + - - +
427B ASP* 2.8 37.6 + - + +
448B ALA* 3.5 36.6 - - + +
449B VAL 3.9 1.8 - - - -
450B PHE* 3.8 22.6 - - + +
469B ILE* 4.6 5.2 - - + -
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Residues in contact with LYS 424 (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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261B ASP* 5.3 5.5 + - - -
263B GLY* 3.7 27.1 + - - -
265B LEU 3.4 23.1 + - - +
266B ARG* 5.4 1.4 + - - -
267B LEU* 3.8 39.7 + - + +
291B LYS* 5.8 5.3 - - - +
407B LEU* 3.8 17.0 - - + -
420B ILE* 2.7 34.2 + - - +
421B ASN* 4.1 17.3 + - - +
422B ILE 3.3 0.2 - - - -
423B LEU* 1.3 72.0 - - - +
425B GLN* 1.3 57.6 + - + +
427B ASP* 3.8 5.7 - - - +
428B ALA* 2.9 32.3 + - - +
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Residues in contact with GLN 425 (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* 5.6 5.4 - - + -
421B ASN* 3.4 19.4 + - - +
422B ILE* 3.1 6.3 + - - +
424B LYS* 1.3 78.0 - - + +
426B ALA* 1.3 64.7 + - - +
428B ALA* 3.6 5.1 - - - +
429B ILE* 3.1 29.3 + - + +
502B GLU* 4.7 4.9 + - - +
503B ILE* 3.4 43.6 - - + +
505B GLU* 4.9 4.2 - - - +
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Residues in contact with ALA 426 (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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422B ILE 3.2 7.6 + - - +
423B LEU 3.1 7.4 + - - +
425B GLN* 1.3 80.6 - - - +
427B ASP* 1.3 61.4 + - - +
429B ILE* 3.5 3.5 + - - +
430B PHE* 3.2 21.1 + - - +
448B ALA* 4.3 5.6 - - + -
469B ILE* 3.9 35.4 - - + -
499B ILE* 3.9 20.1 - - + +
503B ILE* 3.3 15.1 - - + +
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Residues in contact with ASP 427 (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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266B ARG* 2.8 48.7 + - + +
407B LEU* 5.4 5.5 - - + +
410B ARG* 4.0 5.4 + - - -
423B LEU* 2.8 24.9 + - + +
424B LYS* 3.8 6.1 - - - +
426B ALA* 1.3 69.9 - - - +
428B ALA* 1.3 67.0 + - - +
430B PHE* 3.0 15.4 + - - +
431B ILE* 3.1 18.1 + - - +
447B PHE* 3.8 4.0 - - - +
448B ALA* 3.2 34.9 + - + +
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Residues in contact with ALA 428 (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* 4.1 27.4 - - + -
424B LYS 2.9 19.9 + - - +
425B GLN* 3.6 6.7 - - - +
427B ASP* 1.3 77.6 + - - +
429B ILE* 1.3 63.8 + - + +
431B ILE* 3.3 11.6 + - - +
432B GLU* 3.0 26.4 + - - +
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Residues in contact with ILE 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B GLN* 3.1 17.6 + - + +
426B ALA 3.7 4.7 - - - +
428B ALA* 1.3 80.3 - - + +
430B PHE* 1.3 65.0 + - - +
432B GLU* 3.4 4.4 + - - +
433B GLU* 3.3 24.7 + - + +
495B VAL* 4.5 4.9 - - + +
498B ARG* 3.7 59.4 + - + +
499B ILE* 4.1 21.8 - - + -
502B GLU* 3.5 25.8 - - + +
503B ILE* 4.5 10.1 - - + -
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Residues in contact with PHE 430 (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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426B ALA 3.2 10.7 + - - +
427B ASP* 3.0 11.5 + - - +
429B ILE* 1.3 80.6 - - - +
431B ILE* 1.3 54.1 + - + +
433B GLU* 2.7 24.6 - - - +
434B LEU* 3.2 27.4 - - + +
446B ALA* 4.0 7.2 - - + -
447B PHE* 3.8 24.9 - - - -
471B LEU* 3.5 40.4 - - + -
472B ARG 3.7 19.3 - - - -
473B ALA* 4.3 19.1 - - + -
487B LEU* 5.0 4.0 - - + -
491B PHE* 4.6 10.3 - + - -
492B LEU* 5.2 3.4 - - + -
495B VAL* 3.9 24.7 - - + -
511B TYR* 5.0 3.8 - + - -
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Residues in contact with ILE 431 (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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266B ARG* 4.1 26.9 - - - +
427B ASP* 3.1 31.5 + - - +
428B ALA* 3.6 12.3 - - - +
430B PHE* 1.3 79.7 - - + +
432B GLU* 1.3 61.7 + - - +
433B GLU 2.4 18.7 - - - +
434B LEU* 3.7 13.8 - - + +
435B LYS* 3.2 28.6 + - + +
440B TYR* 4.6 20.0 - - + -
446B ALA* 4.5 8.7 - - + +
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Residues in contact with GLU 432 (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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428B ALA* 3.0 17.7 + - - +
429B ILE* 3.4 8.4 + - - +
431B ILE* 1.3 77.1 - - - +
433B GLU* 1.3 59.9 + - - +
435B LYS* 3.2 7.9 - - - +
436B LYS* 2.9 53.7 + - + +
498B ARG* 2.7 29.4 + - - +
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Residues in contact with GLU 433 (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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429B ILE* 3.3 13.8 + - + +
430B PHE 2.7 10.5 - - - +
431B ILE 2.4 29.6 - - - +
432B GLU* 1.3 75.9 - - - +
434B LEU* 1.3 60.5 + - - +
436B LYS* 3.2 34.0 + - - +
437B SER* 4.9 3.8 + - - -
491B PHE* 3.7 17.1 - - + -
494B LYS* 3.1 35.2 + - + -
495B VAL* 3.9 20.0 - - + -
498B ARG* 3.2 28.8 + - - +
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Residues in contact with LEU 434 (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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430B PHE* 3.2 35.2 - - + +
431B ILE* 3.7 13.2 - - + +
433B GLU* 1.3 74.5 - - - +
435B LYS* 1.3 58.3 + - - +
436B LYS 3.3 0.2 - - - -
437B SER 3.7 7.6 - - - +
438B ASP* 2.8 24.6 + - - -
439B TYR* 2.8 36.2 + - + +
440B TYR* 3.1 26.6 + - + +
443B VAL* 5.3 4.0 - - + -
446B ALA* 4.1 21.1 - - + -
487B LEU* 4.2 12.1 - - + -
491B PHE* 3.5 32.2 - - + -
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Residues in contact with LYS 435 (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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395B ASP* 5.8 7.3 + - - +
431B ILE* 3.2 24.5 + - + +
432B GLU* 3.2 13.7 - - - +
433B GLU 3.1 2.2 + - - -
434B LEU* 1.3 79.8 - - - +
436B LYS* 1.3 62.8 + - - +
438B ASP* 3.3 16.5 + - - +
440B TYR* 3.7 48.2 - - + -
441B HIS* 5.9 0.9 - - - -
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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
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432B GLU* 2.9 43.6 + - + +
433B GLU* 3.2 37.4 + - - +
434B LEU 3.3 0.2 - - - -
435B LYS* 1.3 77.0 - - + +
437B SER* 1.3 60.9 + - - +
438B ASP* 3.6 3.6 + - - +
494B LYS* 5.0 8.9 - - - +
498B ARG* 4.8 4.0 - - - +
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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