Contacts of the helix formed by residues 514 - 531 (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 ASN 514 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B ASP* 1.3 81.8 + - + +
515B TYR* 1.3 64.5 + - - +
516B SER* 3.3 20.5 - - - +
517B ASP* 2.8 44.1 + - - +
518B ARG* 3.3 14.2 + - - +
903B SO4 3.4 17.7 - - - +
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Residues in contact with TYR 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B GLU* 4.1 8.5 - - - -
471B SER* 5.8 2.2 - - - -
474B LYS* 4.3 26.3 - - + +
475B MET* 3.6 40.1 - - + +
478B ASP* 4.7 3.7 + - - -
514B ASN* 1.3 67.3 - - - +
516B SER* 1.3 70.5 + - - +
517B ASP 3.1 2.2 - - - -
518B ARG* 2.8 34.8 + - - +
519B ILE* 2.8 48.0 + - + +
522B LEU* 6.2 0.7 - - + -
903B SO4 3.0 29.7 + - - +
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Residues in contact with SER 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B ASN* 3.3 22.2 - - - +
515B TYR* 1.3 82.2 - - - +
517B ASP* 1.3 60.9 + - - +
519B ILE* 3.3 12.9 - - - +
520B GLN* 3.1 34.5 + - - +
523B ARG* 5.1 0.3 + - - -
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Residues in contact with ASP 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B MET* 3.5 27.5 - - + +
512B LEU* 3.9 21.2 - - + +
513B ASP* 4.0 11.3 + - - +
514B ASN* 2.8 27.2 + - - +
515B TYR 3.1 1.0 - - - -
516B SER* 1.3 79.7 + - - +
518B ARG* 1.3 65.3 + - - +
520B GLN* 3.2 4.5 + - - +
521B VAL* 3.0 27.7 + - - +
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Residues in contact with ARG 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B VAL* 3.4 21.8 - - + -
397B PHE* 3.5 12.8 - - + -
398B THR* 5.5 3.6 - - - +
401B GLU* 2.9 39.9 + - - +
512B LEU* 3.8 31.9 + - + -
513B ASP 3.4 15.0 + - - -
514B ASN 3.3 15.7 + - - +
515B TYR* 2.8 41.8 + - + +
517B ASP* 1.3 75.1 - - - +
519B ILE* 1.3 56.7 + - - +
521B VAL* 3.2 1.2 + - - -
522B LEU* 3.0 33.3 + - + +
903B SO4 3.6 13.7 + - - -
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Residues in contact with ILE 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B MET* 4.1 27.4 - - + +
478B ASP* 3.7 26.2 - - + +
479B MET* 4.2 7.4 - - + -
515B TYR* 2.8 50.5 + - + +
516B SER* 3.3 21.8 - - - +
518B ARG* 1.3 70.0 - - - +
520B GLN* 1.3 59.2 + - - +
522B LEU* 4.2 22.9 - - + -
523B ARG* 3.0 43.7 + - - +
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Residues in contact with GLN 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B ASP* 3.1 50.4 + - + +
495B LEU* 5.7 0.7 - - - -
497B THR* 5.6 1.6 - - - -
498B MET* 3.5 27.0 - - + +
516B SER* 3.1 22.6 + - - +
517B ASP* 3.4 11.8 - - - +
518B ARG 3.2 0.2 - - - -
519B ILE* 1.3 78.6 - - - +
521B VAL* 1.3 61.6 + - - +
523B ARG* 3.4 22.9 + - - +
524B ASN* 3.1 38.7 + - - +
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Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B LEU* 4.2 13.7 - - + -
397B PHE* 3.9 19.3 - - + -
495B LEU* 5.5 2.7 - - + -
498B MET* 3.7 19.1 - - + -
512B LEU* 3.7 17.9 - - + -
517B ASP 3.0 14.8 + - - +
518B ARG 3.2 6.2 + - - +
520B GLN* 1.3 75.7 - - - +
522B LEU* 1.3 59.0 + - - +
524B ASN* 3.5 6.0 + - - +
525B MET* 2.9 28.4 + - + +
596B TRP* 3.8 24.7 - - + -
599B LEU* 4.2 14.4 - - + -
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Residues in contact with LEU 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B LEU* 4.0 22.9 - - + -
397B PHE* 3.6 35.0 - - + -
401B GLU* 4.1 28.5 - - + +
405B ALA* 4.1 12.1 - - + -
475B MET* 4.8 4.3 - - - -
479B MET* 3.8 19.5 - - + -
515B TYR* 6.2 0.4 - - + -
518B ARG 3.0 22.6 + - - +
519B ILE* 4.0 17.3 - - + +
521B VAL* 1.3 74.2 - - - +
523B ARG* 1.3 66.0 + - - +
525B MET* 3.2 7.8 + - + +
526B VAL* 3.1 29.6 + - - +
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Residues in contact with ARG 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B ASP* 2.7 45.5 + - - +
479B MET* 3.8 17.1 - - + +
482B ALA* 3.9 20.8 - - + +
483B THR* 6.0 0.2 - - - +
491B LEU* 4.0 28.6 - - + +
494B ASP* 5.1 6.3 + - - +
516B SER 5.1 0.2 + - - -
519B ILE* 3.0 33.0 + - - +
520B GLN* 3.4 38.7 + - - +
522B LEU* 1.3 77.1 - - - +
524B ASN* 1.3 68.0 + - - +
526B VAL* 3.6 2.8 + - - +
527B HIS* 3.2 22.5 + - - +
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Residues in contact with ASN 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B LEU* 3.3 45.5 + - - +
494B ASP* 5.1 0.8 - - - +
495B LEU* 3.6 42.9 - - + +
520B GLN* 3.1 28.8 + - - +
521B VAL 3.8 4.3 - - - +
523B ARG* 1.3 84.8 - - - +
525B MET* 1.3 56.9 + - - +
527B HIS* 3.5 5.7 + - - +
528B CYS* 2.8 34.7 + - - -
592B LEU* 4.1 10.2 - - - +
596B TRP* 4.5 3.8 - - + -
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Residues in contact with MET 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B THR* 4.1 11.0 - - + +
387B LEU* 3.8 22.9 - - + +
388B LEU* 3.6 47.3 - - + -
393B LEU* 4.0 17.5 - - + -
397B PHE* 4.1 12.3 - - + -
405B ALA* 5.5 0.9 - - - -
521B VAL* 2.9 22.2 + - + +
522B LEU* 3.4 14.6 - - + +
523B ARG 3.2 0.2 - - - -
524B ASN* 1.3 75.7 - - - +
526B VAL* 1.3 55.4 + - + +
528B CYS* 3.1 6.7 + - - +
529B ALA* 2.8 34.4 + - - +
596B TRP* 3.8 28.2 - - + -
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Residues in contact with VAL 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B VAL* 4.3 6.2 - - + +
384B THR* 4.4 11.7 - - + +
405B ALA* 4.2 15.9 - - + +
408B ALA* 4.8 2.0 - - + -
409B ALA* 4.6 21.1 - - + +
412B HIS* 5.1 4.7 - - + -
479B MET* 3.8 32.8 - - + +
480B VAL* 5.9 0.2 - - - -
483B THR* 4.0 21.1 - - + -
522B LEU 3.1 15.7 + - - +
523B ARG 4.1 3.6 - - - +
525B MET* 1.3 75.5 - - + +
527B HIS* 1.3 53.4 + - - +
529B ALA* 3.1 8.6 + - - +
530B ASP* 2.7 33.9 + - + +
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Residues in contact with HIS 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ALA 3.9 15.5 + - - +
483B THR* 4.6 10.5 - - - +
484B ASP 5.6 0.2 - - - -
485B MET* 3.8 22.0 - - - -
488B HIS* 3.0 31.4 + - + +
491B LEU* 4.0 23.8 - - + -
523B ARG 3.2 18.8 + - - +
524B ASN* 3.5 4.9 - - - +
526B VAL* 1.3 76.9 - - - +
528B CYS* 1.3 56.1 + - - +
530B ASP* 3.1 11.8 + - - +
531B LEU* 3.0 50.0 + - + +
592B LEU* 3.6 29.6 - - + -
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Residues in contact with CYS 528 (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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387B LEU* 4.4 4.0 - - + -
495B LEU* 5.2 1.6 - - - -
524B ASN 2.8 24.1 + - - +
525B MET* 3.4 9.4 - - - +
527B HIS* 1.3 72.3 - - - +
529B ALA* 1.3 58.0 + - - +
531B LEU 3.0 4.7 + - - -
532B SER* 2.9 27.9 + - - -
592B LEU* 3.8 33.2 - - - -
593B TRP* 3.5 27.7 + - + +
596B TRP* 4.0 33.7 - - + -
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Residues in contact with ALA 529 (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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380B VAL* 3.5 27.6 - - + +
383B SER* 4.1 5.6 - - - -
384B THR* 3.4 34.8 - - - +
387B LEU* 4.3 5.3 - - + +
525B MET 2.8 14.8 + - - +
526B VAL 3.3 8.7 - - - +
528B CYS* 1.3 72.8 - - - +
530B ASP* 1.3 57.9 + - - +
532B SER* 3.0 27.4 + - - -
533B ASN* 5.4 0.5 + - - -
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Residues in contact with ASP 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B TYR* 4.3 6.8 + - - -
376B HIS* 3.1 15.6 + - - -
380B VAL* 4.0 6.7 - - + +
412B HIS* 2.9 12.0 + - - -
483B THR* 3.8 25.2 - - + +
485B MET* 6.0 1.2 - - - +
526B VAL 2.7 17.5 + - - +
527B HIS* 3.1 17.0 + - - +
529B ALA* 1.3 73.4 - - - +
531B LEU* 1.3 69.6 + - + +
532B SER 3.4 1.3 + - - -
533B ASN* 5.0 3.1 + - - -
900B ZN 2.3 35.3 - - - -
901B MG 4.1 3.5 - - - -
902B PNX 5.0 3.1 - - - +
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Residues in contact with LEU 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B MET* 4.1 16.8 - - + -
527B HIS* 3.0 44.8 + - + +
528B CYS 3.0 5.6 + - - +
530B ASP* 1.3 87.3 - - + +
532B SER* 1.3 60.4 + - - +
533B ASN 3.3 2.5 - - - +
534B PRO* 3.5 13.5 - - - +
584B PHE* 4.1 19.5 - - + -
588B ILE* 3.7 26.9 - - + -
589B VAL* 3.5 15.9 - - + +
592B LEU* 3.8 16.4 - - + -
593B TRP* 3.3 11.1 + - - -
902B PNX 4.4 13.7 - - + -
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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
------------------------------------------------------------
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