Contacts of the helix formed by residues 482 - 498 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C LEU* 1.3 74.0 - - - +
483C GLY* 1.3 50.5 + - - +
484C GLY 2.8 3.5 + - - -
485C GLN* 2.8 32.2 + - - +
486C ARG* 2.7 33.3 + - - +
379D GLY* 5.0 1.1 - - - -
5004D ANP 2.4 68.8 + - - -
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Residues in contact with GLY 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C LEU 3.6 1.2 + - - -
482C SER* 1.3 70.7 + - - +
484C GLY* 1.3 56.0 + - - +
486C ARG* 3.3 19.5 - - - +
487C GLN* 2.5 39.6 + - - +
510C ALA* 4.8 5.4 - - - -
424D GLN* 6.3 4.3 - - - +
425D ASN* 6.2 0.7 - - - -
5004D ANP 3.6 6.9 + - - -
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Residues in contact with GLY 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C SER* 2.8 4.8 + - - -
483C GLY* 1.3 77.8 - - - +
485C GLN* 1.3 63.9 + - - +
487C GLN* 3.5 3.3 - - - +
488C ARG* 2.7 33.8 + - - +
510C ALA* 3.4 24.5 + - - +
511C LEU* 4.1 4.4 - - - +
378D SER* 3.8 3.8 - - - -
5004D ANP 3.4 15.4 + - - -
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Residues in contact with GLN 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C PHE* 3.2 52.4 - - + +
481C LEU* 3.4 15.8 - - + +
482C SER* 2.8 42.1 + - - +
484C GLY* 1.3 73.4 - - - +
486C ARG* 1.3 63.8 + - - +
488C ARG* 3.3 24.4 + - - +
489C ILE* 2.9 28.9 + - - +
378D SER* 4.3 2.0 + - - +
379D GLY* 5.0 5.3 - - - -
5004D ANP 3.6 26.2 + - - -
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Residues in contact with ARG 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C ASN* 6.1 0.4 - - - +
426C VAL* 2.5 39.0 + - + +
428C LEU* 3.9 15.5 - - + +
477C ASN* 3.8 22.8 + - - +
478C GLY* 2.8 46.4 + - - +
481C LEU* 3.7 16.8 - - + -
482C SER 2.7 17.2 + - - +
483C GLY* 3.3 15.1 - - - +
485C GLN* 1.3 73.3 - - - +
487C GLN* 1.3 57.5 + - - +
489C ILE* 2.6 33.7 + - - +
490C ALA* 2.8 12.8 + - - +
425D ASN* 3.6 27.9 - - - +
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Residues in contact with GLN 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C VAL* 4.8 2.0 - - + +
424C GLN 4.4 3.8 - - - +
426C VAL* 4.5 17.2 - - + +
483C GLY 2.5 19.3 + - - +
484C GLY* 3.5 3.4 - - - +
486C ARG* 1.3 71.9 - - - +
488C ARG* 1.3 58.0 + - + +
490C ALA* 3.0 9.4 + - - +
491C ILE* 2.8 33.6 + - + +
506C GLU 3.2 1.4 - - - +
507C ALA* 2.5 41.9 + - - +
508C THR 3.2 6.5 + - - -
509C SER* 3.0 21.0 + - - -
510C ALA* 3.1 36.4 + - - +
511C LEU* 4.0 4.7 - - + +
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Residues in contact with ARG 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C ALA* 3.8 17.0 - - - +
458C TYR* 2.9 42.1 + - - +
459C ALA* 3.9 7.4 - - + +
461C ASP* 4.0 4.2 + - - -
462C PHE* 3.0 34.2 - - - +
484C GLY 2.7 26.0 + - - +
485C GLN* 3.4 17.8 - - - +
487C GLN* 1.3 70.7 - - - +
489C ILE* 1.3 52.4 + - - +
491C ILE* 2.9 17.1 + - - +
492C ALA* 2.5 33.4 + - - +
511C LEU* 3.9 20.5 - - + +
515C SER* 5.1 4.9 + - - -
519C ILE* 4.4 8.1 - - + -
378D SER* 2.7 42.9 + - - -
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Residues in contact with ILE 489 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C LEU* 4.6 9.9 - - + -
433C VAL* 4.5 10.1 - - + -
436C ASN* 4.4 18.4 - - + -
437C ILE* 4.0 20.6 - - + -
459C ALA* 5.2 2.7 - - + -
462C PHE* 4.1 17.7 - - + -
463C ILE* 4.4 13.0 - - + -
474C ILE* 4.5 8.5 - - + -
481C LEU* 3.8 28.0 - - + -
485C GLN 2.9 21.2 + - - +
486C ARG* 2.6 17.4 + - - +
488C ARG* 1.3 70.6 - - + +
490C ALA* 1.3 57.8 + - - +
492C ALA* 2.9 9.0 + - + +
493C ARG* 2.8 28.9 + - - +
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Residues in contact with ALA 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421C LEU 4.4 0.9 - - - +
422C VAL* 3.8 9.0 - - + +
426C VAL* 3.0 47.3 - - + -
428C LEU* 4.9 3.3 - - + +
486C ARG 2.8 12.1 + - - +
487C GLN 3.3 9.2 - - - +
489C ILE* 1.3 73.5 - - - +
491C ILE* 1.3 61.3 + - - +
493C ARG* 3.7 16.7 + - - +
494C ALA* 3.1 24.3 + - - +
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Residues in contact with ILE 491 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422C VAL* 3.8 26.2 - - + -
457C ALA* 4.2 16.6 - - + +
487C GLN* 2.8 15.6 + - + +
488C ARG* 3.0 18.2 - - - +
490C ALA* 1.3 76.6 - - - +
492C ALA* 1.3 70.6 + - - +
494C ALA* 3.3 1.2 + - - +
495C LEU* 2.7 36.7 + - + +
504C LEU* 4.7 6.7 - - + -
507C ALA* 3.4 34.1 - - + +
511C LEU* 5.0 1.3 - - + -
519C ILE* 4.4 30.7 - - + -
523C LEU* 5.5 2.9 - - + -
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Residues in contact with ALA 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C ILE* 3.9 25.4 - - + -
453C ALA* 4.1 15.7 - - - +
454C ALA* 4.4 6.3 - - - -
457C ALA* 4.0 13.5 - - + -
459C ALA* 6.0 1.1 - - + -
488C ARG 2.5 17.2 + - - +
489C ILE* 2.9 16.8 - - + +
491C ILE* 1.3 69.1 - - - +
493C ARG* 1.3 56.6 + - - +
495C LEU* 2.5 30.4 + - - +
496C LEU 2.9 9.3 + - - -
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Residues in contact with ARG 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421C LEU 4.8 6.8 + - - -
422C VAL* 6.1 0.8 - - - +
423C SER* 5.5 0.8 + - - -
426C VAL* 4.0 14.0 - - - +
427C HIS 2.8 26.1 + - - -
428C LEU* 3.1 23.5 - - - +
429C PHE* 5.4 3.6 - - - +
436C ASN* 3.6 22.7 + - - +
437C ILE* 3.4 17.9 - - - +
439C TYR 5.6 0.4 - - - -
440C ALA* 3.4 17.3 - - + +
489C ILE 2.8 16.3 + - - +
490C ALA* 3.7 10.8 + - - +
492C ALA* 1.3 74.6 - - - +
494C ALA* 1.3 63.1 + - - +
495C LEU 3.1 0.2 + - - -
496C LEU* 3.2 10.2 + - - +
497C ARG* 3.0 49.8 + - - +
216D GLU* 3.9 26.6 + - - +
219D ILE* 5.8 2.2 - - - +
220D PHE* 5.3 7.4 - - - -
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Residues in contact with ALA 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C ALA* 3.1 25.0 - - + +
421C LEU 3.4 31.4 - - - +
422C VAL* 3.4 14.6 - - + -
490C ALA 3.1 16.7 + - - +
491C ILE 3.7 1.3 - - - +
492C ALA 2.9 1.2 + - - -
493C ARG* 1.3 78.5 - - - +
495C LEU* 1.3 61.3 + - - +
497C ARG* 4.0 13.7 - - - +
498C ASP* 4.1 6.6 + - - -
502C LEU* 4.6 6.7 - - + +
504C LEU* 5.3 0.2 - - + -
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Residues in contact with LEU 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452C GLU* 5.7 1.6 - - - +
453C ALA* 4.5 9.9 - - + +
456C MET* 3.0 39.0 - - + +
457C ALA* 4.5 4.9 - - + -
491C ILE* 2.7 23.9 + - + +
492C ALA* 2.5 14.8 + - - +
494C ALA* 1.3 71.6 - - - +
496C LEU* 1.3 64.4 + - - +
498C ASP* 3.2 16.6 + - - +
502C LEU* 4.2 24.7 - - + -
504C LEU* 6.2 1.8 - - + -
519C ILE* 6.3 0.4 - - + -
522C ALA* 5.8 1.8 - - + -
523C LEU* 4.5 18.4 - - + +
526C LEU* 4.2 31.1 - - + +
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Residues in contact with LEU 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437C ILE* 3.8 23.1 - - + +
438C ALA* 4.6 2.9 - - - -
440C ALA 5.0 1.8 - - - +
445C TYR* 3.2 39.0 + - + -
449C GLN* 3.3 28.9 - - + +
450C ILE* 3.5 30.5 - - + -
452C GLU* 5.9 2.2 - - - +
453C ALA* 3.6 21.2 - - + +
492C ALA 2.9 5.9 + - - +
493C ARG 3.7 7.0 - - - +
495C LEU* 1.3 73.0 - - - +
497C ARG* 1.3 68.5 + - - +
498C ASP* 2.8 10.7 + - - +
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Residues in contact with ARG 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419C VAL 5.5 2.2 - - - +
420C ALA* 4.8 11.0 - - + +
421C LEU 4.2 5.7 + - - +
440C ALA* 3.0 45.3 - - + +
441C ARG* 4.3 9.6 - - + -
445C TYR* 3.8 15.7 + - - -
493C ARG* 3.0 43.6 + - - +
494C ALA* 4.0 15.8 - - - +
496C LEU* 1.3 78.9 - - - +
498C ASP* 1.3 70.8 + - - +
499C SER* 5.1 1.8 - - - +
216D GLU* 4.7 1.2 + - - +
219D ILE* 3.9 26.2 + - - +
220D PHE* 2.8 57.0 + - - +
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Residues in contact with ASP 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494C ALA 4.1 2.9 + - - -
495C LEU 3.2 13.8 + - - +
496C LEU 2.8 11.4 + - - +
497C ARG* 1.3 83.2 - - - +
499C SER* 1.3 60.3 + - - +
500C PRO* 4.5 1.7 - - - +
526C LEU* 4.7 13.6 - - - +
530C ARG* 2.8 41.8 + - - -
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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
------------------------------------------------------------
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