Contacts of the helix formed by residues 439 - 458 (chain B) in PDB entry 3F7F
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 ASP 439 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B VAL* 4.5 3.7 - - - +
433B ILE 4.0 4.2 - - - +
434B MET* 3.9 5.4 - - + +
435B ALA* 3.0 30.7 + - - +
436B HIS* 3.1 36.4 + - + +
437B ASN 3.5 1.0 - - - -
438B GLU* 1.3 71.8 - - - +
440B GLU* 1.3 56.8 + - - +
441B GLU* 3.1 28.1 - - - +
442B TYR* 2.8 41.2 + - + +
443B LEU* 3.4 3.6 + - - +
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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
----------------------------------------------------------
404B VAL* 5.0 10.8 - - + -
438B GLU* 2.6 27.7 + - + +
439B ASP* 1.3 70.1 - - - +
441B GLU* 1.3 63.3 + - - +
442B TYR 3.0 0.2 + - - -
443B LEU* 3.3 11.5 + - + +
444B ALA* 3.0 25.5 + - - +
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ASP* 3.1 15.0 - - - +
440B GLU* 1.3 77.8 - - - +
442B TYR* 1.3 60.9 + - - +
444B ALA* 3.5 14.3 - - - +
445B ASN* 3.3 19.2 + - - +
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Residues in contact with TYR 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PHE* 4.3 11.7 - + - -
424B GLN* 3.6 19.2 + - - +
427B LEU* 3.2 42.1 - - + +
432B ILE* 4.0 23.5 + - + -
433B ILE* 5.0 1.5 - - - -
434B MET* 3.2 64.9 + - + +
439B ASP* 2.8 29.0 + - - +
441B GLU* 1.3 72.3 - - - +
443B LEU* 1.3 57.6 + - - +
444B ALA 2.9 1.1 - - - -
445B ASN* 2.3 43.1 + - - +
446B LEU* 3.2 7.5 + - + -
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ASP 5.3 0.4 - - - +
404B VAL* 3.6 38.8 - - + +
407B GLY* 4.1 19.1 - - - +
408B PHE* 4.6 7.0 - - + +
411B LEU* 4.3 11.4 - - + -
434B MET* 5.9 0.7 - - + -
439B ASP 3.4 4.8 + - - +
440B GLU* 3.3 13.4 + - + +
442B TYR* 1.3 82.8 - - + +
444B ALA* 1.3 64.8 - - - +
445B ASN 3.1 0.9 + - - -
446B LEU* 3.1 13.4 + - - +
447B GLU* 3.1 44.8 + - + +
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Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440B GLU 3.0 12.4 + - - +
441B GLU* 3.5 15.7 - - - +
442B TYR 2.7 4.4 + - - -
443B LEU* 1.3 82.1 - - - +
445B ASN* 1.3 59.9 + - - +
447B GLU* 3.5 18.0 - - - +
448B THR* 3.7 9.2 + - - -
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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
----------------------------------------------------------
427B LEU* 4.0 17.3 - - + -
432B ILE* 3.8 31.4 - - + +
441B GLU* 3.3 21.8 + - - +
442B TYR* 2.3 29.2 + - - +
444B ALA* 1.3 67.0 - - - +
446B LEU* 1.3 64.3 + - - +
447B GLU 3.1 1.8 - - - -
448B THR* 2.9 18.4 + - - -
449B ILE* 3.0 18.4 + - + +
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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
----------------------------------------------------------
408B PHE* 3.4 39.7 - - + -
411B LEU* 4.4 7.9 - - + -
420B PHE* 3.9 15.3 - - + -
423B ALA* 4.0 14.6 - - + -
424B GLN* 4.3 9.6 - - + +
427B LEU* 3.7 28.6 - - + +
442B TYR* 3.2 9.6 + - + -
443B LEU* 3.1 14.5 + - - +
445B ASN* 1.3 77.3 - - - +
447B GLU* 1.3 64.4 + - - +
449B ILE* 3.2 2.8 + - + +
450B LEU* 2.8 51.8 + - + +
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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
----------------------------------------------------------
391B SER* 5.3 2.6 + - - -
411B LEU* 3.8 23.8 - - + +
414B ARG* 5.3 5.2 + - - -
415B TYR* 4.5 4.2 + - - -
443B LEU* 3.1 37.0 + - + +
444B ALA* 3.5 13.0 - - - +
445B ASN 3.1 0.2 - - - -
446B LEU* 1.3 79.1 - - - +
448B THR* 1.3 59.8 + - - +
450B LEU* 3.7 8.5 - - - +
451B ARG* 3.0 30.9 + - - +
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Residues in contact with THR 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ALA 3.7 10.6 + - - -
445B ASN* 2.9 9.5 + - - -
447B GLU* 1.3 75.4 - - - +
449B ILE* 1.3 66.4 + - + +
451B ARG* 3.4 30.1 + - - +
452B ASP* 2.9 46.8 + - - +
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Residues in contact with ILE 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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423B ALA* 3.4 36.8 - - + +
426B ILE* 4.3 22.2 - - + -
427B LEU* 4.5 16.2 - - + -
432B ILE* 6.2 1.6 - - + -
445B ASN* 3.0 16.2 + - + +
446B LEU* 3.9 6.5 - - - +
448B THR* 1.3 78.2 - - + +
450B LEU* 1.3 56.5 + - - +
452B ASP* 2.8 12.9 + - + +
453B VAL* 2.6 43.9 + - + +
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Residues in contact with LEU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU* 3.7 38.4 - - + -
415B TYR* 3.6 28.8 - - + -
419B ILE* 4.1 11.3 - - + +
420B PHE* 3.6 32.3 - - + -
423B ALA* 3.5 22.9 - - + -
446B LEU* 2.8 43.6 + - + +
447B GLU* 3.7 2.7 - - - +
449B ILE* 1.3 71.2 - - - +
451B ARG* 1.3 65.0 + - - +
453B VAL* 3.8 0.7 - - - +
454B LYS* 2.8 26.9 + - - +
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Residues in contact with ARG 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B GLU* 5.2 16.4 - - - +
414B ARG* 5.9 2.2 - - - +
415B TYR* 3.8 17.0 + - - +
447B GLU 3.0 18.7 + - - +
448B THR* 3.5 33.8 + - - +
450B LEU* 1.3 77.1 - - - +
452B ASP* 1.3 76.1 + - - +
454B LYS* 3.5 3.6 + - - +
455B THR* 2.9 36.1 + - - +
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Residues in contact with ASP 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B THR* 2.9 32.7 + - - +
449B ILE* 2.8 20.6 + - + +
451B ARG* 1.3 87.3 + - - +
453B VAL* 1.3 55.0 + - + +
455B THR* 3.1 10.2 + - - +
456B ALA* 2.7 36.7 + - - +
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Residues in contact with VAL 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ILE* 3.8 17.9 - - + -
422B ARG* 3.7 16.4 - - + +
423B ALA* 4.2 5.2 - - - -
426B ILE* 4.1 19.7 - - + -
449B ILE* 2.6 42.0 + - + +
450B LEU* 3.8 2.9 - - - +
452B ASP* 1.3 70.8 - - + +
454B LYS* 1.3 53.6 + - - +
456B ALA* 3.0 6.9 + - - +
457B PHE* 2.7 68.1 + - + -
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Residues in contact with LYS 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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6B ARG* 5.0 1.2 - - - +
8B ASP* 3.1 28.8 + - - -
385B SER* 4.8 0.4 + - - -
387B VAL* 6.6 0.2 - - - -
388B ASP* 3.0 36.2 + - - +
415B TYR* 4.1 19.3 - - + -
419B ILE* 3.8 27.7 - - + +
450B LEU 2.8 17.7 + - - +
451B ARG* 3.5 5.2 - - - +
453B VAL* 1.3 77.9 - - - +
455B THR* 1.3 55.2 + - - +
457B PHE* 3.0 1.7 + - - +
458B ASN* 2.7 59.9 + - - +
480B ASN* 5.7 0.2 - - - +
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Residues in contact with THR 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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359B THR* 3.1 43.1 - - + +
384B LYS* 5.6 7.4 - - - -
451B ARG* 2.9 21.8 + - - +
452B ASP* 3.1 13.9 + - - +
454B LYS* 1.3 78.6 - - - +
456B ALA* 1.3 65.9 + - - +
458B ASN* 3.4 8.2 + - - +
459B GLU 3.4 12.0 + - - -
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Residues in contact with ALA 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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359B THR* 4.5 11.4 - - + -
422B ARG* 6.1 2.2 - - - +
452B ASP 2.7 17.2 + - - +
453B VAL* 3.4 11.4 - - - +
455B THR* 1.3 68.3 - - - +
457B PHE* 1.3 71.7 + - + +
458B ASN 2.9 1.3 - - - -
459B GLU* 2.8 23.3 + - - +
476B PHE* 4.3 5.5 - - - +
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Residues in contact with PHE 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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418B GLN* 3.4 34.1 - - + -
419B ILE* 3.5 27.8 - - + -
422B ARG* 3.9 35.4 - - + -
453B VAL* 2.7 40.5 + - + +
454B LYS* 3.4 5.6 - - - +
456B ALA* 1.3 75.8 - - + +
458B ASN* 1.3 65.2 + - - +
459B GLU 3.5 0.3 + - - -
475B CYS* 3.2 11.4 - - - +
477B GLN* 3.1 65.9 + - + +
480B ASN* 3.7 9.3 - - - +
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Residues in contact with ASN 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ARG* 3.1 33.0 + - - +
8B ASP* 3.6 16.7 - - - +
359B THR 5.0 2.8 - - - +
361B SER* 6.1 0.5 - - - -
454B LYS* 2.7 56.6 + - - +
455B THR* 3.7 9.2 - - - +
456B ALA 2.9 0.4 + - - -
457B PHE* 1.3 79.6 - - - +
459B GLU* 1.3 67.4 + - - +
460B ALA* 3.1 4.2 + - - +
473B VAL* 6.1 0.2 - - - +
475B CYS* 3.9 16.2 - - - -
480B ASN* 4.3 10.5 + - - +
481B HIS 4.9 1.4 - - - +
482B SER* 3.7 5.0 + - - -
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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
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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