Contacts of the helix formed by residues 487 - 503 (chain C) in PDB entry 3D8F
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 PRO 487 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462C GLU* 3.5 12.6 - - + +
463C ARG* 3.8 20.6 - - - +
484C CYS* 4.9 0.2 - - - -
486C ALA* 1.3 91.1 - - + +
488C ALA* 1.3 60.7 + - - +
489C LYS* 3.2 25.8 - - + +
490C ASN* 2.9 54.6 + - - +
491C ILE* 4.2 2.3 + - - +
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Residues in contact with ALA 488 (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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455C VAL* 3.6 15.4 - - + +
462C GLU 2.6 19.7 + - - +
463C ARG* 3.9 4.5 - - - +
464C ASP 3.3 34.8 - - - +
465C PHE* 4.0 9.5 - - + -
484C CYS* 4.0 11.7 - - - -
486C ALA 3.6 2.6 + - - -
487C PRO* 1.3 71.4 - - - +
489C LYS* 1.3 55.8 + - - +
491C ILE* 2.9 24.5 + - - +
492C ALA 3.3 8.3 + - - -
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Residues in contact with LYS 489 (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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455C VAL* 3.6 21.2 - - + +
462C GLU* 4.3 12.5 + - + +
487C PRO* 4.0 27.4 - - + +
488C ALA* 1.3 75.0 - - - +
490C ASN* 1.3 68.0 + - - +
491C ILE 3.1 0.2 - - - -
492C ALA* 4.0 4.7 - - + -
493C THR* 2.7 36.2 + - - +
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Residues in contact with ASN 490 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C PHE* 4.1 19.5 - - + -
486C ALA* 4.2 8.3 - - + +
487C PRO* 2.9 43.1 + - - +
489C LYS* 1.3 85.2 + - - +
491C ILE* 1.3 57.9 + - + +
493C THR* 3.9 3.8 - - - -
494C SER* 2.9 28.6 + - - -
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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
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370C PHE* 3.6 59.0 - - + -
372C VAL* 4.6 0.9 - - + -
424C LEU* 4.4 21.1 - - + -
426C LEU* 4.5 2.7 - - + -
465C PHE* 4.1 27.8 - - + -
484C CYS* 3.7 31.9 - - + -
487C PRO 4.6 2.5 - - - +
488C ALA* 2.9 12.4 + - - +
490C ASN* 1.3 74.3 - - - +
492C ALA* 1.3 55.4 + - - +
494C SER* 2.9 4.5 + - - -
495C LEU* 2.8 40.1 + - + +
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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
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453C TRP* 4.1 26.5 - - + +
454C GLY* 5.5 0.7 - - - -
455C VAL* 4.1 23.3 - - + -
465C PHE* 4.3 6.7 - - + -
488C ALA 3.3 2.4 + - - -
489C LYS* 3.9 8.3 - - + +
491C ILE* 1.3 77.0 - - - +
493C THR* 1.3 55.4 + - - +
495C LEU* 2.6 28.1 + - - +
496C HIS* 2.8 21.3 + - + +
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Residues in contact with THR 493 (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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489C LYS* 2.7 25.2 + - - +
490C ASN* 3.9 4.0 - - - -
492C ALA* 1.3 78.5 - - - +
494C SER* 1.3 63.4 + - - +
496C HIS* 3.2 13.3 + - + +
497C GLU* 3.1 38.0 + - + +
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Residues in contact with SER 494 (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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368C LYS* 3.3 38.8 + - - +
370C PHE* 4.2 5.4 - - - -
426C LEU* 4.0 10.8 - - - +
490C ASN 2.9 20.2 + - - -
491C ILE* 2.9 11.7 + - - -
493C THR* 1.3 76.9 - - - +
495C LEU* 1.3 58.3 + - - +
497C GLU* 3.6 12.6 + - - +
498C ILE* 3.1 30.2 + - - +
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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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426C LEU* 3.7 31.6 - - + -
431C LEU* 4.7 10.5 - - + -
447C ILE* 3.8 28.0 - - + -
450C ILE* 5.0 4.0 - - + -
453C TRP* 3.7 32.1 - - + -
465C PHE* 3.6 32.3 - - + -
491C ILE* 2.8 15.1 + - + +
492C ALA 2.6 14.1 + - - +
494C SER* 1.3 71.4 - - - +
496C HIS* 1.3 63.0 + - - +
497C GLU 3.3 0.2 - - - -
498C ILE* 3.6 3.6 + - + +
499C CYS* 3.2 28.6 + - - -
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Residues in contact with HIS 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453C TRP* 3.3 32.3 + + - -
492C ALA* 2.8 32.1 + - + +
493C THR* 3.2 12.8 + - + +
495C LEU* 1.3 75.1 - - - +
497C GLU* 1.3 64.6 + - + +
499C CYS* 3.3 4.5 + - - +
500C SER* 3.1 28.9 + - - +
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Residues in contact with GLU 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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368C LYS* 3.6 27.8 + - - +
493C THR* 3.1 36.8 + - + +
494C SER* 3.6 11.5 + - - +
495C LEU 3.3 0.2 - - - -
496C HIS* 1.3 75.9 - - - +
498C ILE* 1.3 65.8 + - + +
500C SER* 3.3 5.4 + - - -
501C LYS* 3.1 25.7 + - - +
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Residues in contact with ILE 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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366C GLY 5.6 6.3 - - - +
368C LYS* 4.3 19.5 - - - +
426C LEU* 5.2 17.0 - - + +
427C GLU* 6.4 0.4 - - - -
429C GLU* 4.4 12.3 - - + +
447C ILE* 3.9 30.3 - - + -
494C SER 3.1 19.2 + - - +
495C LEU* 3.9 8.1 - - - +
496C HIS 3.3 0.4 - - - -
497C GLU* 1.3 77.0 - - + +
499C CYS* 1.3 60.6 + - - +
501C LYS* 3.6 10.3 + - + +
502C ILE* 3.1 39.0 + - + +
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Residues in contact with CYS 499 (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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447C ILE* 4.0 23.3 - - - -
453C TRP* 3.7 21.3 - - + -
495C LEU 3.2 17.5 + - - +
496C HIS* 3.8 4.3 - - - +
497C GLU 3.3 0.2 - - - -
498C ILE* 1.3 76.8 - - - +
500C SER* 1.3 52.5 + - - +
502C ILE* 2.9 12.9 + - - +
503C MET* 2.6 50.6 + - + +
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Residues in contact with SER 500 (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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496C HIS* 3.1 19.2 + - - +
497C GLU* 3.3 6.0 + - - -
499C CYS* 1.3 74.6 - - - +
501C LYS* 1.3 63.9 + - - +
503C MET* 3.2 27.9 + - - +
504C ALA* 3.3 13.7 + - - +
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Residues in contact with LYS 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C GLU 3.1 17.0 + - - +
498C ILE* 3.7 11.2 - - + +
500C SER* 1.3 77.6 - - - +
502C ILE* 1.3 59.8 + - + +
504C ALA* 3.0 18.0 + - + +
505C GLU* 2.8 47.0 + - + +
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Residues in contact with ILE 502 (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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429C GLU* 3.7 38.1 - - + -
447C ILE* 5.2 7.6 - - + -
448C ILE* 5.7 7.9 - - + +
498C ILE* 3.1 24.9 + - + +
499C CYS* 2.9 14.9 + - - +
501C LYS* 1.3 79.7 - - + +
503C MET* 1.3 58.4 + - + +
504C ALA 3.2 2.9 + - - -
505C GLU* 3.5 14.4 + - - +
506C LEU* 2.9 32.4 - - + +
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Residues in contact with MET 503 (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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499C CYS* 2.6 34.1 + - + +
500C SER* 3.2 20.6 + - - +
502C ILE* 1.3 73.2 - - + +
504C ALA* 1.3 57.2 + - - +
505C GLU 3.6 0.4 - - - -
506C LEU* 3.8 18.0 - - + +
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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
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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