Contacts of the helix formed by residues 439 - 452 (chain B) in PDB entry 3TVX
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 SER 439 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421B ASN* 4.2 3.7 - - - +
437B ASP 3.9 2.4 + - - -
438B GLU* 1.3 76.7 + - - +
440B VAL* 1.3 64.5 + - - +
441B LEU 3.4 2.0 - - - -
442B GLU* 3.5 18.6 - - - -
443B ASN* 2.7 36.7 + - - -
481B LEU* 4.2 11.2 + - - +
484B ASP* 2.5 34.0 + - - +
487B LYS* 4.5 12.0 - - - -
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Residues in contact with VAL 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ASN* 3.3 16.6 + - + +
424B LEU* 4.1 15.5 - - + -
425B ILE* 4.4 9.6 - - + -
431B LEU* 3.5 42.2 - - + +
432B ALA* 3.6 15.0 - - + +
435B TYR* 3.7 8.7 - - + -
437B ASP* 3.8 33.7 - - - +
438B GLU 3.9 2.5 - - - +
439B SER* 1.3 77.3 - - - +
441B LEU* 1.3 64.1 + - - +
443B ASN* 3.6 2.9 - - - +
444B HIS* 3.0 20.8 + - - +
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B ASP 5.3 0.9 - - - +
416B HIS* 3.6 19.1 - - - +
417B PRO* 3.5 28.9 - - + -
419B VAL 3.4 21.8 - - - +
420B SER* 4.1 1.3 - - - -
421B ASN* 2.8 38.9 + - - +
424B LEU* 3.5 22.2 - - + -
431B LEU* 5.3 5.8 - - + -
439B SER 3.4 0.2 - - - -
440B VAL* 1.3 72.7 - - - +
442B GLU* 1.3 60.3 + - - +
444B HIS* 2.9 9.4 + - + +
445B HIS* 2.7 56.3 + - + +
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Residues in contact with GLU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ASN* 3.1 27.1 + - - -
439B SER* 3.5 15.1 - - - +
441B LEU* 1.3 77.2 - - - +
443B ASN* 1.3 61.7 + - - +
445B HIS* 3.4 15.8 + - + +
446B LEU* 3.1 27.5 + - - +
480B VAL* 3.7 26.4 - - - +
481B LEU* 4.2 14.8 - - + -
483B THR* 3.7 14.3 - - - +
484B ASP* 3.4 30.9 - - + +
485B MET 4.8 0.5 + - - -
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Residues in contact with ASN 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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435B TYR* 3.5 36.4 + - + +
438B GLU 3.1 17.0 + - - -
439B SER* 2.7 35.7 + - - +
440B VAL 3.6 2.5 - - - +
442B GLU* 1.3 75.0 - - - +
444B HIS* 1.3 62.5 + - - +
446B LEU* 3.4 8.9 + - - +
447B ALA* 3.0 23.2 + - - +
481B LEU* 4.0 17.3 - - - +
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Residues in contact with HIS 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B VAL 4.3 1.8 - - - -
415B ASP* 2.7 50.5 + - + +
431B LEU* 3.4 45.1 - - + +
435B TYR* 3.9 10.1 + - + -
440B VAL 3.0 12.9 + - - +
441B LEU* 2.9 15.0 + - + +
443B ASN* 1.3 76.3 - - - +
445B HIS* 1.3 65.9 + + - +
447B ALA* 3.2 3.2 + - - +
448B VAL* 3.0 44.2 + - + +
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Residues in contact with HIS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ILE* 3.6 14.6 - - - +
412B HIS 3.0 26.0 - - - +
413B ASP* 3.2 30.1 + - - -
414B VAL* 2.8 35.5 + - - +
415B ASP 4.5 0.9 - - - -
416B HIS* 3.8 25.4 - + + -
441B LEU* 2.7 50.1 + - + +
442B GLU* 3.5 16.7 + - + +
443B ASN 3.3 0.2 - - - -
444B HIS* 1.3 72.6 - + - +
446B LEU* 1.3 61.7 + - - +
449B GLY* 3.0 21.5 + - - -
480B VAL* 4.3 4.3 - - + -
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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
----------------------------------------------------------
411B ILE* 4.5 2.9 - - + -
442B GLU 3.1 18.8 + - - +
443B ASN* 3.6 10.5 - - - +
444B HIS 3.3 0.2 - - - -
445B HIS* 1.3 75.6 - - - +
447B ALA* 1.3 66.2 + - - +
449B GLY* 3.8 0.2 - - - -
450B PHE* 3.1 50.4 + - + -
476B VAL* 3.7 5.6 - - + +
477B ILE* 3.5 49.8 - - + +
480B VAL* 3.6 27.1 - - + -
481B LEU* 3.8 20.9 - - + -
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Residues in contact with ALA 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B TYR* 3.7 17.9 - - - +
443B ASN 3.0 17.0 + - - +
444B HIS* 3.2 6.0 + - - +
446B LEU* 1.3 76.3 - - - +
448B VAL* 1.3 60.8 + - + +
450B PHE* 3.6 3.9 + - - +
451B LYS* 2.8 30.9 + - - +
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Residues in contact with VAL 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B HIS* 4.6 9.6 - - + -
414B VAL* 4.1 22.9 - - + -
415B ASP* 4.4 9.0 - - + +
444B HIS* 3.0 46.4 + - + +
447B ALA* 1.3 75.5 - - + +
449B GLY* 1.3 67.7 + - - +
451B LYS* 2.9 7.4 + - + -
452B LEU* 2.8 51.9 + - + +
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Residues in contact with GLY 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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357B TYR* 2.8 37.0 + - - -
361B LEU* 4.7 3.6 - - - -
407B PHE* 4.1 2.0 - - - -
411B ILE* 4.0 16.4 - - - -
414B VAL* 3.8 9.3 - - - +
445B HIS 3.0 19.0 + - - -
446B LEU 3.8 0.7 - - - -
448B VAL* 1.3 77.9 - - - +
450B PHE* 1.3 59.4 + - - +
452B LEU* 3.8 1.3 + - - -
453B LEU* 4.1 2.6 - - - +
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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
----------------------------------------------------------
407B PHE* 4.3 11.7 - + - -
411B ILE* 4.4 4.0 - - + -
446B LEU* 3.1 43.7 + - + +
447B ALA* 4.0 3.4 - - - +
449B GLY* 1.3 73.8 - - - +
451B LYS* 1.3 65.9 + - - +
452B LEU 3.3 0.4 - - - -
453B LEU* 3.2 40.7 + - + +
454B GLN* 3.8 9.9 + - - +
461B PHE* 5.1 1.3 - + - -
472B LEU* 4.5 7.6 - - + -
473B ARG* 3.5 54.3 - - + +
476B VAL* 3.7 39.3 - - + -
477B ILE* 4.5 4.3 - - + -
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Residues in contact with LYS 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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430A GLU* 3.1 52.6 + - + +
433A LEU* 5.5 6.7 - - - +
447B ALA 2.8 23.3 + - - +
448B VAL* 2.9 9.6 + - - +
450B PHE* 1.3 73.2 - - - +
452B LEU* 1.3 61.9 + - + +
454B GLN* 3.0 57.8 + - - +
455B GLU* 4.1 2.8 + - - +
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Residues in contact with LEU 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B TYR* 3.8 15.3 - - + -
360B THR* 3.9 16.4 - - + +
361B LEU* 3.9 40.8 - - + +
364B HIS* 3.7 42.0 - - + +
448B VAL* 2.8 28.3 + - + +
449B GLY 4.0 0.7 - - - +
450B PHE 3.3 0.2 - - - -
451B LYS* 1.3 74.8 - - + +
453B LEU* 1.3 56.8 + - - +
454B GLN 2.9 11.1 + - - -
455B GLU* 3.1 30.3 + - + +
458B CYS* 3.3 14.7 - - - +
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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