Contacts of the helix formed by residues 482 - 498 (chain B) in PDB entry 3B60
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 482 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A GLY* 5.0 1.6 - - - -
5001A ANP 2.5 65.7 + - - -
481B LEU* 1.3 74.0 - - - +
483B GLY* 1.3 52.0 + - - +
484B GLY 2.9 5.0 + - - -
485B GLN* 2.8 32.7 + - - +
486B ARG* 2.7 32.7 + - - +
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Residues in contact with GLY 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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424A GLN* 6.2 5.0 - - - +
425A ASN* 6.2 1.1 - - - -
5001A ANP 3.7 6.3 + - - -
481B LEU 3.6 1.2 + - - -
482B SER* 1.3 69.8 + - - +
484B GLY* 1.3 57.0 + - - +
486B ARG* 3.3 20.2 - - - +
487B GLN* 2.5 40.3 + - - +
510B ALA* 4.8 5.6 - - - -
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Residues in contact with GLY 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A SER* 3.8 9.2 - - - -
5001A ANP 3.7 5.2 + - - -
482B SER* 2.9 8.9 + - - -
483B GLY* 1.3 77.2 - - - +
485B GLN* 1.3 63.4 + - - +
487B GLN* 3.1 3.7 + - - +
488B ARG* 2.7 34.0 + - - +
510B ALA* 3.4 26.0 + - - +
511B LEU* 4.1 4.0 - - - -
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Residues in contact with GLN 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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378A SER* 4.2 2.2 + - - +
379A GLY* 5.0 5.5 - - - -
5001A ANP 3.6 27.7 + - - -
462B PHE* 3.2 53.7 - - + +
481B LEU* 3.4 15.0 - - + +
482B SER* 2.8 43.6 + - - +
484B GLY* 1.3 73.6 - - - +
486B ARG* 1.3 64.5 + - - +
488B ARG* 3.3 24.2 + - - +
489B ILE* 2.9 28.7 + - - +
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Residues in contact with ARG 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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425A ASN* 3.6 29.4 - - - +
425B ASN* 6.1 0.4 - - - +
426B VAL* 2.5 39.0 + - + +
428B LEU* 3.9 15.4 - - + +
477B ASN* 3.8 22.7 + - - +
478B GLY* 2.8 48.4 + - - +
481B LEU* 3.7 15.9 - - + -
482B SER 2.7 18.4 + - - +
483B GLY* 3.1 16.2 + - - +
485B GLN* 1.3 71.8 - - - +
487B GLN* 1.3 56.5 + - - +
489B ILE* 2.6 34.1 + - - +
490B ALA* 2.8 12.4 + - - +
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Residues in contact with GLN 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B VAL* 4.8 1.3 - - + +
424B GLN 4.4 4.2 - - - +
426B VAL* 4.5 17.2 - - + +
483B GLY 2.5 19.1 + - - +
484B GLY 3.5 3.1 - - - +
486B ARG* 1.3 72.0 - - - +
488B ARG* 1.3 57.7 + - + +
490B ALA* 3.0 10.1 + - - +
491B ILE* 2.8 33.6 + - + +
506B GLU 3.2 1.4 - - - +
507B ALA* 2.5 39.6 + - - +
508B THR 3.2 7.1 + - - -
509B SER* 3.0 21.3 + - - -
510B ALA* 3.1 36.8 + - - +
511B LEU* 4.0 4.7 - - + +
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Residues in contact with ARG 488 (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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378A SER* 2.7 43.6 + - - -
457B ALA* 3.8 16.1 - - - +
458B TYR* 2.9 43.0 + - - +
459B ALA* 4.2 6.5 - - + -
461B ASP* 4.0 4.2 + - - -
462B PHE* 3.0 33.4 - - - +
484B GLY 2.7 26.1 + - - +
485B GLN* 3.4 17.2 - - - +
487B GLN* 1.3 71.1 - - - +
489B ILE* 1.3 52.3 + - - +
491B ILE* 2.9 16.7 + - - +
492B ALA* 2.5 33.3 + - - +
511B LEU* 3.9 19.4 - - + +
515B SER* 5.1 4.9 + - - -
519B ILE* 4.4 8.7 - - + -
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Residues in contact with ILE 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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428B LEU* 4.6 10.3 - - + -
433B VAL* 4.5 10.5 - - + -
436B ASN* 4.4 18.8 - - + +
437B ILE* 4.0 20.2 - - + -
459B ALA* 5.2 3.4 - - + -
462B PHE* 4.1 17.9 - - + -
463B ILE* 4.4 12.6 - - + -
474B ILE* 4.5 8.7 - - + -
481B LEU* 3.9 27.6 - - + -
485B GLN 2.9 20.7 + - - +
486B ARG* 2.6 17.4 + - - +
488B ARG* 1.3 68.6 - - - +
490B ALA* 1.3 58.0 + - - +
492B ALA* 2.9 10.2 + - + +
493B ARG* 2.8 29.3 + - - +
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Residues in contact with ALA 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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421B LEU 4.4 1.0 - - - +
422B VAL* 3.7 9.4 - - + +
426B VAL* 3.0 47.3 - - + -
428B LEU* 4.9 2.9 - - + +
486B ARG 2.8 13.0 + - - +
487B GLN 3.3 9.4 - - - +
489B ILE* 1.3 74.0 - - - +
491B ILE* 1.3 61.3 + - - +
493B ARG* 3.7 16.7 - - - +
494B ALA* 3.1 24.6 + - - +
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Residues in contact with ILE 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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422B VAL* 3.8 25.6 - - + -
457B ALA* 4.2 16.4 - - + +
487B GLN* 2.8 16.4 + - + +
488B ARG* 3.0 17.0 - - - +
490B ALA* 1.3 75.6 - - - +
492B ALA* 1.3 71.6 + - - +
494B ALA* 3.3 1.2 + - - +
495B LEU* 2.7 36.6 + - + +
504B LEU* 4.7 6.7 - - + -
507B ALA* 3.4 34.3 - - + +
511B LEU* 5.0 1.3 - - + -
519B ILE* 4.4 29.8 - - + -
523B LEU* 5.5 4.0 - - + -
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Residues in contact with ALA 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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437B ILE* 3.9 25.4 - - + -
453B ALA* 4.1 15.5 - - - +
454B ALA* 4.4 6.3 - - + -
457B ALA* 4.0 13.2 - - + -
459B ALA* 6.0 1.3 - - + -
488B ARG 2.5 16.4 + - - +
489B ILE* 2.9 16.8 + - + +
491B ILE* 1.3 70.1 - - - +
493B ARG* 1.3 58.3 + - - +
495B LEU* 2.5 29.7 + - - +
496B LEU 2.9 9.4 + - - -
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Residues in contact with ARG 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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216A GLU* 3.9 28.4 + - - +
219A ILE* 5.6 2.8 - - - +
220A PHE* 5.3 7.3 - - - -
421B LEU 4.8 6.8 + - - -
422B VAL* 6.1 0.6 - - - +
423B SER* 5.5 1.0 + - - -
426B VAL* 4.0 12.9 - - - +
427B HIS 2.8 26.1 + - - -
428B LEU* 3.1 24.8 - - - +
429B PHE* 5.7 2.6 - - - -
436B ASN* 3.6 24.0 + - - +
437B ILE* 3.4 16.9 - - - +
439B TYR 5.6 0.4 - - - -
440B ALA* 3.4 17.3 - - + +
489B ILE 2.8 15.8 + - - +
490B ALA* 3.7 9.5 + - - +
492B ALA* 1.3 74.7 - - - +
494B ALA* 1.3 63.8 + - - +
495B LEU 3.1 0.3 + - - -
496B LEU* 3.2 10.4 + - - +
497B ARG* 3.0 49.5 + - - +
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Residues in contact with ALA 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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420B ALA* 3.1 24.4 - - + +
421B LEU* 3.4 31.6 - - - +
422B VAL* 3.4 15.3 - - + -
490B ALA 3.1 16.3 + - - +
491B ILE 3.7 1.3 - - - +
492B ALA 2.9 1.4 + - - -
493B ARG* 1.3 78.9 - - - +
495B LEU* 1.3 61.0 + - - +
497B ARG* 4.0 13.0 - - - +
498B ASP* 4.1 6.2 + - - -
502B LEU* 4.6 5.7 - - + +
504B LEU* 5.3 0.2 - - + -
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Residues in contact with LEU 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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452B GLU* 5.7 1.3 - - - +
453B ALA* 4.5 10.1 - - + +
456B MET* 3.0 38.6 - - + +
457B ALA* 4.5 4.9 - - + -
491B ILE* 2.7 23.1 + - + +
492B ALA* 2.5 15.4 + - - +
494B ALA* 1.3 70.8 - - + +
496B LEU* 1.3 64.6 + - - +
498B ASP* 3.2 17.7 + - - +
502B LEU* 4.2 24.2 - - + -
504B LEU* 6.2 1.3 - - + -
519B ILE* 6.3 0.7 - - + -
522B ALA* 5.8 1.8 - - + -
523B LEU* 4.5 19.5 - - + +
526B LEU* 4.2 32.6 - - + +
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Residues in contact with LEU 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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437B ILE* 3.8 23.8 - - + +
438B ALA* 4.6 2.9 - - - -
440B ALA 5.0 2.2 - - - +
445B TYR* 3.2 38.1 + - + -
449B GLN* 3.3 28.0 - - + +
450B ILE* 3.5 30.1 - - + -
452B GLU* 5.9 1.8 - - - +
453B ALA* 3.6 20.7 - - + +
492B ALA 2.9 6.3 + - - +
493B ARG 3.7 6.5 - - - +
495B LEU* 1.3 72.8 - - - +
497B ARG* 1.3 69.1 + - - +
498B ASP* 2.8 10.7 + - - +
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Residues in contact with ARG 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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216A GLU* 4.7 1.4 + - - +
219A ILE* 3.8 28.3 + - - +
220A PHE* 2.7 55.4 + - - +
419B VAL 5.5 1.8 - - - +
420B ALA* 4.8 11.4 - - + +
421B LEU 4.2 5.1 + - - +
440B ALA* 3.0 44.6 - - + +
441B ARG* 4.3 8.5 - - + -
445B TYR* 3.8 16.4 + - - -
493B ARG* 3.0 44.9 + - - +
494B ALA* 4.0 15.6 - - - +
496B LEU* 1.3 79.6 - - - +
498B ASP* 1.3 69.2 + - - +
499B SER* 5.1 2.0 - - - +
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Residues in contact with ASP 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 ALA 4.1 2.5 + - - -
495B LEU 3.2 13.8 + - - +
496B LEU 2.8 11.1 + - - +
497B ARG* 1.3 83.7 - - - +
499B SER* 1.3 59.9 + - - +
500B PRO* 4.5 1.6 - - - +
526B LEU* 4.7 13.5 - - - +
530B ARG* 2.8 42.3 + - - -
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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