Contacts of the helix formed by residues 480 - 500 (chain B) in PDB entry 4U7C
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 THR 480 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443B ALA* 3.8 3.6 - - - -
479B SER* 1.3 80.2 - - - +
481B ALA* 1.3 65.5 + - - +
482B GLU* 2.9 28.4 + - - +
483B GLU* 2.5 38.2 + - - +
484B ILE* 3.2 24.1 + - - +
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Residues in contact with ALA 481 (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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436B GLN* 5.3 1.1 - - + +
439B CYS* 4.2 6.1 - - + +
440B SER* 3.8 35.9 - - - +
443B ALA* 3.4 15.3 - - + +
480B THR* 1.3 74.4 - - - +
482B GLU* 1.3 66.3 + - - +
484B ILE* 4.7 1.8 - - - -
485B PHE* 2.9 33.1 + - - +
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Residues in contact with GLU 482 (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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480B THR* 2.9 26.4 + - - +
481B ALA* 1.3 88.8 + - - +
483B GLU* 1.3 58.5 + - + +
485B PHE* 3.8 4.6 - - - +
486B ALA* 2.9 27.7 + - - +
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Residues in contact with GLU 483 (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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477B VAL 5.4 0.6 - - - +
478B VAL* 3.4 27.1 - - + -
479B SER* 2.4 35.5 + - - -
480B THR* 2.5 35.2 + - - +
482B GLU* 1.3 76.1 - - + +
484B ILE* 1.3 62.4 + - - +
486B ALA* 2.8 23.4 + - - +
487B ILE* 3.0 17.9 + - - +
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Residues in contact with ILE 484 (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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439B CYS* 3.7 28.3 - - + +
442B LEU* 4.3 10.8 - - + -
443B ALA* 4.1 15.7 - - - +
446B LEU* 3.9 28.7 - - + -
456B VAL* 4.3 17.4 - - + +
478B VAL* 3.7 18.4 - - + -
479B SER 4.0 5.4 - - - +
480B THR 3.2 17.4 + - - +
481B ALA 4.2 0.4 - - - +
483B GLU* 1.3 75.4 - - - +
485B PHE* 1.3 56.9 + - - +
487B ILE* 3.3 2.6 + - - +
488B ALA* 2.9 27.7 + - - +
511B VAL* 3.9 19.1 - - + -
513B ILE* 4.7 4.5 - - + -
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Residues in contact with PHE 485 (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 TYR* 3.4 29.8 - + + -
435B CYS* 3.9 17.9 - - + -
436B GLN* 3.5 47.3 - - + -
439B CYS* 3.6 10.9 - - + -
481B ALA 2.9 22.3 + - - +
482B GLU* 4.0 4.0 - - - +
484B ILE* 1.3 74.4 - - - +
486B ALA* 1.3 66.8 + - - +
488B ALA* 4.4 0.2 - - - -
489B LYS* 2.9 60.6 + - + +
605B PEG 3.8 26.0 - - - -
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Residues in contact with ALA 486 (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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482B GLU 2.9 16.8 + - - +
483B GLU* 2.8 17.8 + - - +
485B PHE* 1.3 79.1 - - - +
487B ILE* 1.3 62.8 + - + +
489B LYS* 3.7 18.8 - - - +
490B GLU* 3.8 9.4 + - - +
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Residues in contact with ILE 487 (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 ARG 5.6 0.7 - - - +
456B VAL* 3.7 30.3 - - + -
472B SER* 3.6 31.6 - - - +
474B VAL* 3.9 32.8 - - + -
478B VAL* 4.5 13.7 - - + -
483B GLU 3.0 13.8 + - - +
484B ILE 3.7 3.6 - - - +
486B ALA* 1.3 75.1 - - + +
488B ALA* 1.3 65.6 + - - +
489B LYS 3.1 2.0 - - - -
490B GLU* 3.0 24.4 + - + +
491B LEU* 3.0 19.0 + - + +
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Residues in contact with ALA 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B CYS* 3.5 24.6 - - - -
439B CYS* 3.9 11.0 - - - -
456B VAL* 4.4 7.6 - - + +
458B ILE* 3.7 23.7 - - + +
484B ILE 2.9 20.5 + - - +
485B PHE 4.2 0.2 - - - +
487B ILE* 1.3 73.1 - - - +
489B LYS* 1.3 56.6 + - - +
491B LEU* 3.2 6.7 + - - +
492B LEU* 2.9 32.7 + - - +
511B VAL* 4.6 1.8 - - + -
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Residues in contact with LYS 489 (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 TYR* 3.6 21.7 - - + -
435B CYS* 4.4 1.5 - - - -
485B PHE* 2.9 49.2 + - + +
486B ALA* 3.7 12.6 - - - +
488B ALA* 1.3 77.7 - - - +
490B GLU* 1.3 60.5 + - + +
492B LEU* 3.8 2.0 - - - +
493B LYS* 2.9 28.0 + - + +
605B PEG 3.6 32.3 + - - +
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Residues in contact with GLU 490 (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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472B SER* 5.6 2.2 - - - +
486B ALA 3.8 7.6 + - - +
487B ILE* 3.0 26.3 + - + +
489B LYS* 1.3 80.0 - - + +
491B LEU* 1.3 67.4 + - + +
493B LYS* 3.4 8.8 - - + +
494B THR* 2.8 32.6 + - - -
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Residues in contact with LEU 491 (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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456B VAL* 3.7 23.3 - - + +
458B ILE* 3.9 21.3 - - + -
470B ARG* 3.8 23.9 - - + +
471B ALA 3.6 13.0 - - - +
472B SER* 3.2 26.2 - - - +
487B ILE* 3.0 26.6 + - + +
488B ALA* 3.2 12.5 + - - +
490B GLU* 1.3 79.1 - - + +
492B LEU* 1.3 62.1 + - - +
494B THR* 3.2 11.2 + - - +
495B GLU* 3.0 24.6 + - - +
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Residues in contact with LEU 492 (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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431B GLN* 3.7 29.4 - - + +
432B TYR* 4.0 15.9 - - + +
435B CYS* 4.2 4.3 - - + -
458B ILE* 3.8 10.2 - - + +
460B LEU* 4.2 24.2 - - + -
488B ALA 2.9 17.5 + - - +
489B LYS* 3.8 4.5 - - - +
491B LEU* 1.3 72.8 - - - +
493B LYS* 1.3 67.5 + - - +
495B GLU* 2.9 2.6 + - + +
496B ILE* 2.9 44.3 + - + +
504B LEU* 4.1 15.0 - - + -
506B LEU* 5.3 1.1 - - + -
509B MET* 3.6 25.8 - - + -
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Residues in contact with LYS 493 (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 TYR* 3.1 30.7 + - + +
489B LYS* 2.9 21.6 + - + +
490B GLU* 3.4 12.1 - - + +
492B LEU* 1.3 76.8 - - - +
494B THR* 1.3 63.1 + - - +
496B ILE* 3.2 2.2 + - - +
497B ASP* 2.9 59.4 + - - +
605B PEG 4.2 11.4 - - - +
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Residues in contact with THR 494 (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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490B GLU* 2.8 19.7 + - - +
491B LEU* 3.2 13.3 - - - +
493B LYS* 1.3 76.9 - - - +
495B GLU* 1.3 67.0 + - - +
497B ASP* 3.9 4.7 - - - +
498B ALA* 2.9 31.7 + - + +
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Residues in contact with GLU 495 (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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458B ILE* 4.6 0.7 - - + -
460B LEU* 3.7 29.4 - - + -
468B LYS* 4.0 14.3 + - - +
470B ARG* 3.0 50.0 + - + +
491B LEU 3.0 13.8 + - - +
492B LEU 2.9 8.2 + - - +
494B THR* 1.3 86.6 - - - +
496B ILE* 1.3 65.2 + - - +
498B ALA* 3.2 11.0 + - - +
499B ASP* 3.0 29.2 + - - +
504B LEU* 4.2 14.2 - - + +
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Residues in contact with ILE 496 (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* 3.7 26.5 - - + +
431B GLN* 3.2 26.7 - - + +
432B TYR* 4.1 19.1 - - + +
492B LEU* 2.9 27.2 + - + +
493B LYS* 3.7 5.4 - - - +
495B GLU* 1.3 76.2 - - - +
497B ASP* 1.3 69.9 + - - +
499B ASP* 3.3 5.2 + - - +
500B PHE* 3.2 24.6 + - + +
502B HIS 4.2 7.2 - - - +
503B PRO* 6.2 0.9 - - + -
504B LEU* 3.7 23.1 - - + +
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Residues in contact with ASP 497 (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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493B LYS* 2.9 55.4 + - - +
494B THR* 4.1 3.9 - - - +
496B ILE* 1.3 80.7 - - - +
498B ALA* 1.3 65.7 + - - +
500B PHE* 2.8 32.6 + - + +
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Residues in contact with ALA 498 (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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494B THR* 2.9 23.3 + - + +
495B GLU* 3.2 18.4 - - - +
497B ASP* 1.3 76.5 - - - +
499B ASP* 1.3 61.6 + - - +
500B PHE 4.9 0.9 - - - +
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Residues in contact with ASP 499 (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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468B LYS* 4.9 10.6 + - - -
495B GLU* 3.0 18.0 + - - +
496B ILE 3.3 2.0 + - - +
497B ASP 3.0 0.4 - - - -
498B ALA* 1.3 81.4 - - - +
500B PHE* 1.3 68.6 + - - +
501B PRO* 3.5 0.3 - - - +
502B HIS* 3.0 42.7 + - + +
503B PRO 5.2 2.7 - - - +
504B LEU* 4.0 24.1 - - + +
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Residues in contact with PHE 500 (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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496B ILE* 3.2 14.7 + - + +
497B ASP* 2.8 28.3 + - + +
498B ALA 4.9 0.9 - - - +
499B ASP* 1.3 78.9 - - - +
501B PRO* 1.3 86.2 - - + +
502B HIS 3.3 3.1 - - - +
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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