Contacts of the helix formed by residues 439 - 460 (chain B) in PDB entry 1U7V
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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396B ASP* 3.3 9.3 - - - +
413B TYR* 3.6 29.5 - - + +
436B LYS* 3.2 18.9 + - - +
438B PHE* 1.3 78.0 - - - +
440B LEU* 1.3 65.7 + - - +
441B ARG* 3.0 14.0 + - - +
442B GLN* 2.6 44.7 + - + +
443B CYS* 3.0 21.5 + - - +
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Residues in contact with LEU 440 (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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314B ILE* 4.1 6.3 - - + -
393B GLY 4.4 1.1 - - - +
394B GLU* 3.0 47.3 - - + +
395B GLY* 3.6 25.3 + - - +
396B ASP* 3.2 18.9 + - - +
438B PHE* 3.9 7.2 - - + -
439B ASP* 1.3 68.5 - - - +
441B ARG* 1.3 54.0 + - - +
443B CYS* 3.0 5.3 + - + +
444B HIS* 2.8 33.1 + - - +
531B ARG* 3.8 9.2 - - + -
532B ALA* 3.7 34.8 - - + +
535B LEU* 3.7 21.3 - - + -
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Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE* 3.0 43.9 - - + +
396B ASP* 4.7 0.8 + - - -
439B ASP* 3.0 10.8 + - - +
440B LEU* 1.3 78.4 - - - +
442B GLN* 1.3 55.3 + - + +
444B HIS* 3.1 4.9 + - - +
445B ARG* 2.8 67.6 + - - +
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Residues in contact with GLN 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B TYR* 3.0 48.7 + - + +
416B ARG* 4.7 17.7 - - - +
417B GLU* 4.5 8.3 + - - +
439B ASP* 2.6 29.9 + - + +
441B ARG* 1.3 73.5 - - + +
443B CYS* 1.3 62.0 + - - +
445B ARG* 3.6 6.3 - - - +
446B GLN* 3.0 25.6 + - - +
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Residues in contact with CYS 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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438B PHE* 3.4 31.0 - - + -
439B ASP 3.0 5.8 + - - +
440B LEU* 3.1 9.9 - - + +
442B GLN* 1.3 75.0 - - - +
444B HIS* 1.3 66.3 + - - +
446B GLN* 3.0 8.7 + - - +
447B MET* 3.0 55.3 + - - +
498B LEU* 3.3 37.4 - - - +
532B ALA* 4.0 4.9 - - + -
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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
----------------------------------------------------------
314B ILE* 3.4 27.3 + - + +
440B LEU 2.8 15.4 + - - +
441B ARG 3.5 7.2 - - - +
443B CYS* 1.3 71.8 - - - +
445B ARG* 1.3 92.3 + - - +
447B MET* 3.1 26.1 + - - +
448B GLN* 3.1 41.8 + - + +
535B LEU* 3.8 29.8 - - + +
538B GLU* 5.6 7.4 - - - -
539B VAL* 4.6 11.6 - - + +
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Residues in contact with ARG 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B ILE* 4.8 1.4 - - - +
441B ARG* 2.8 60.9 + - - +
442B GLN* 3.6 7.6 - - - +
444B HIS* 1.3 102.1 + - - +
446B GLN* 1.3 64.6 + - - +
447B MET 2.9 1.7 + - - -
448B GLN* 3.1 16.3 + - - +
449B GLN* 2.9 35.3 + - - +
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Residues in contact with GLN 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ARG* 4.4 18.7 + - - -
442B GLN 3.0 15.7 + - - +
443B CYS* 3.4 6.5 - - - +
445B ARG* 1.3 79.1 - - - +
447B MET* 1.3 58.6 + - - +
449B GLN* 2.9 35.9 - - - +
450B GLN* 3.2 30.5 + - - +
498B LEU* 4.0 27.1 - - + +
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Residues in contact with MET 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B CYS* 3.0 43.9 + - - +
444B HIS* 3.3 14.4 - - - +
445B ARG 2.9 0.6 + - - -
446B GLN* 1.3 72.8 - - - +
448B GLN* 1.3 55.4 - - - +
449B GLN 2.9 3.4 - - - -
450B GLN* 2.7 26.7 + - - +
451B ALA* 2.8 12.0 + - - +
495B LEU* 4.7 5.9 - - + +
498B LEU* 3.8 20.2 - - + -
499B CYS* 3.6 6.5 - - - -
532B ALA* 3.1 25.1 - - - +
535B LEU* 4.3 6.1 - - + -
536B LEU* 3.5 40.8 - - + +
539B VAL* 4.1 20.6 - - + +
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Residues in contact with GLN 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B HIS* 3.1 52.3 + - + +
445B ARG* 3.6 18.0 + - - +
447B MET* 1.3 75.1 - - - +
449B GLN* 1.3 56.5 + - - +
451B ALA* 3.8 9.8 - - - +
452B ALA* 2.8 36.4 + - - +
539B VAL* 4.3 11.9 - - + +
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Residues in contact with GLN 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B ARG* 5.4 4.5 + - - -
445B ARG* 2.9 32.9 + - - +
446B GLN* 2.9 43.4 - - - +
448B GLN* 1.3 79.1 - - - +
450B GLN* 1.3 58.3 + - - +
452B ALA* 3.9 3.6 - - - +
453B THR* 3.3 27.8 + - + +
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Residues in contact with GLN 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B GLN* 3.2 33.5 + - - +
447B MET* 2.7 15.8 + - - +
449B GLN* 1.3 74.1 - - - +
451B ALA* 1.3 63.2 + - - +
452B ALA 3.2 1.8 - - - -
453B THR* 3.0 24.2 + - - +
454B ALA* 3.2 13.2 + - - +
490B ILE* 3.6 41.5 - - + +
495B LEU* 5.2 12.4 - - + +
498B LEU* 4.7 12.3 - - + +
543B MET* 4.0 2.5 - - + +
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Residues in contact with ALA 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B MET 2.8 8.1 + - - +
448B GLN* 3.8 7.0 - - - +
450B GLN* 1.3 77.3 - - - +
452B ALA* 1.3 60.3 + - - +
454B ALA* 3.5 2.4 + - - +
455B GLN* 2.9 34.0 + - - +
539B VAL* 3.7 29.6 - - + -
542B THR* 4.6 8.7 - - - +
543B MET* 3.3 26.7 - - + +
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Residues in contact with ALA 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B GLN 2.8 17.4 + - - +
449B GLN* 3.9 6.7 - - - +
451B ALA* 1.3 74.5 - - - +
453B THR* 1.3 67.8 + - + +
454B ALA 3.1 0.7 + - - -
455B GLN* 3.1 26.7 + - - +
456B ALA* 3.2 11.7 + - - +
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Residues in contact with THR 453 (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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449B GLN* 3.3 15.2 + - + +
450B GLN* 3.0 24.6 + - - +
452B ALA* 1.3 77.0 - - + +
454B ALA* 1.3 50.4 + - - +
456B ALA* 3.2 8.9 - - - +
457B ALA* 2.7 36.9 + - - +
490B ILE* 5.2 6.2 - - - +
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Residues in contact with ALA 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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450B GLN 3.2 14.7 + - - +
451B ALA 3.7 0.9 - - - +
452B ALA 3.1 0.4 - - - -
453B THR* 1.3 77.7 + - - +
455B GLN* 1.3 54.9 - - + +
456B ALA 2.8 4.5 - - - -
457B ALA* 4.2 5.4 - - - +
458B ALA* 2.7 38.6 + - - +
490B ILE* 5.0 11.7 - - + +
543B MET* 3.6 24.5 - - + -
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Residues in contact with GLN 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 ALA* 2.9 24.7 - - - +
452B ALA* 3.1 19.0 + - - +
454B ALA* 1.3 74.9 - - - +
456B ALA* 1.3 59.1 + - - +
458B ALA* 3.7 6.0 - - - +
459B ALA* 3.4 21.1 + - - +
542B THR* 2.8 27.7 + - - +
543B MET* 4.7 3.4 - - - -
544B PRO* 3.7 24.2 - - + +
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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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452B ALA 3.2 11.0 + - - +
453B THR* 3.2 12.6 - - - +
454B ALA 2.8 0.8 - - - -
455B GLN* 1.3 75.5 - - - +
457B ALA* 1.3 51.3 + - - +
458B ALA 2.8 6.7 + - - -
459B ALA* 2.9 5.7 + - - +
460B ALA* 2.6 38.4 + - + +
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Residues in contact with ALA 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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453B THR* 2.7 21.6 + - - +
454B ALA* 4.1 5.4 - - - +
456B ALA* 1.3 72.5 - - - +
458B ALA* 1.3 54.9 + - - +
460B ALA* 3.9 11.5 - - - +
461B GLN* 3.1 29.9 + - - +
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Residues in contact with ALA 458 (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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454B ALA* 2.7 18.8 + - + +
455B GLN* 3.7 7.4 - - - +
456B ALA 2.8 1.2 + - - -
457B ALA* 1.3 78.5 - - - +
459B ALA* 1.3 58.8 + - - +
460B ALA 3.3 1.3 - - - -
461B GLN* 3.0 34.0 + - - +
544B PRO 5.7 3.8 - - - +
546B ALA* 4.6 17.0 - - + +
547B ASP* 5.9 2.0 - - + -
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Residues in contact with ALA 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455B GLN 3.4 13.1 + - - +
456B ALA* 2.9 5.2 + - - +
458B ALA* 1.3 74.8 - - - +
460B ALA* 1.3 64.4 + - - +
461B GLN 3.1 6.6 + - - -
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Residues in contact with ALA 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ALA 2.6 18.5 + - - +
457B ALA* 3.9 11.9 - - - -
458B ALA 3.3 0.2 - - - -
459B ALA* 1.3 78.0 - - - +
461B GLN* 1.3 55.8 + - - +
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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