Contacts of the helix formed by residues 450 - 461 (chain C) in PDB entry 3GEB
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 GLN 450 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322C PHE* 3.8 23.5 - - - -
325C LEU 4.0 2.8 - - - +
326C GLU* 3.3 21.1 + - - +
329C ASP* 3.3 34.6 - - + +
449C THR* 1.3 77.9 - - + +
451C LEU* 1.3 66.8 + - - +
452C ILE* 4.6 0.6 - - - +
453C PRO* 3.2 16.1 - - + +
454C ALA* 2.8 23.8 + - - +
476C THR* 3.4 17.0 - - + +
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Residues in contact with LEU 451 (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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329C ASP* 5.1 2.2 - - - +
330C GLN* 3.6 32.3 + - + +
331C ILE 4.2 12.6 - - - +
332C HIS* 3.4 11.9 - - - +
333C VAL* 3.3 35.2 - - + +
384C TYR* 4.1 11.4 - - + +
450C GLN* 1.3 72.9 - - - +
452C ILE* 1.3 58.9 + - - +
454C ALA* 3.3 3.9 - - + +
455C LEU* 2.9 49.1 + - + +
472C ILE* 4.2 30.1 - - + +
474C SER* 3.5 14.6 + - - +
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Residues in contact with ILE 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C ALA* 4.1 2.2 - - + -
320C LEU* 3.5 35.0 - - + +
322C PHE* 3.4 26.2 - - + -
325C LEU* 3.8 42.0 - - + +
329C ASP* 6.3 0.8 - - - +
384C TYR* 4.0 20.0 - - + +
387C VAL* 4.1 27.4 - - + -
450C GLN* 4.6 0.6 - - - +
451C LEU* 1.3 75.5 - - - +
453C PRO* 1.3 71.3 - - + +
455C LEU* 3.4 10.0 + - + +
456C ALA* 3.2 15.1 + - - +
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Residues in contact with PRO 453 (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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312C ILE* 3.8 5.9 - - + +
313C PHE* 4.7 17.0 - - + -
316C ALA* 4.5 4.9 - - + -
322C PHE* 3.2 34.8 - - + -
449C THR* 3.7 16.4 - - + -
450C GLN* 3.2 23.3 - - + +
452C ILE* 1.3 94.8 - - + +
454C ALA* 1.3 51.0 + - - +
456C ALA* 2.8 12.9 + - + +
457C LYS* 2.7 35.9 + - - +
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Residues in contact with ALA 454 (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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275C LEU* 5.2 4.0 - - + -
447C THR* 3.8 28.0 - - + -
449C THR* 3.7 9.7 - - - +
450C GLN 2.8 20.0 + - - +
451C LEU* 3.3 7.2 - - - +
453C PRO* 1.3 76.1 - - - +
455C LEU* 1.3 53.3 + - + +
457C LYS* 3.0 10.7 + - - +
458C VAL* 2.6 41.4 + - + +
472C ILE* 5.0 8.1 - - + -
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Residues in contact with LEU 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C LEU* 4.8 6.3 - - + -
333C VAL* 5.8 3.1 - - + -
384C TYR* 6.4 0.4 - - + -
387C VAL* 3.8 27.6 - - + -
391C TYR* 4.2 16.2 - - + -
451C LEU* 2.9 36.4 + - + +
452C ILE* 3.7 10.3 - - + +
454C ALA* 1.3 76.1 - - - +
456C ALA* 1.3 63.9 + - - +
458C VAL* 3.8 4.3 - - - +
459C LEU* 3.0 32.9 + - + +
469C ILE* 4.5 16.2 - - + -
472C ILE* 3.4 41.3 - - + -
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Residues in contact with ALA 456 (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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312C ILE* 3.5 32.1 - - + +
315C LEU* 4.2 12.1 - - + -
316C ALA* 4.1 12.8 - - + +
320C LEU* 4.2 6.9 - - + +
452C ILE 3.2 12.0 + - - +
453C PRO 2.8 13.1 + - - +
455C LEU* 1.3 75.3 - - - +
457C LYS* 1.3 61.8 + - - +
459C LEU* 3.1 4.3 + - - +
460C LEU* 2.9 30.2 + - - +
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Residues in contact with LYS 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C LEU* 3.5 25.4 - - + -
276C ASP* 3.2 19.4 + - - -
280C ILE* 3.7 24.9 - - + -
282C PHE* 3.9 15.5 - - - -
283C HIS* 4.0 7.1 + - - -
312C ILE* 3.9 35.8 - - + +
449C THR* 3.3 32.1 + - - +
453C PRO* 2.7 9.6 + - - +
454C ALA* 3.2 8.7 - - - +
456C ALA* 1.3 77.7 - - - +
458C VAL* 1.3 63.6 + - - +
460C LEU* 3.3 0.6 + - - -
461C TYR* 3.0 33.7 + - + +
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Residues in contact with VAL 458 (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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275C LEU* 4.4 10.5 - - + -
391C TYR* 3.7 21.8 - - + +
445C LEU* 4.0 27.4 - - + -
454C ALA* 2.6 24.8 + - - +
455C LEU* 3.8 7.0 - - - +
457C LYS* 1.3 74.1 - - - +
459C LEU* 1.3 58.3 + - - +
461C TYR 3.7 0.2 + - - -
462C GLY 3.5 1.4 + - - -
463C LEU* 2.8 55.5 + - + +
464C GLY* 3.5 18.6 - - - +
467C PHE* 4.8 3.4 - - + -
472C ILE* 4.6 9.0 - - + -
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Residues in contact with LEU 459 (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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315C LEU* 4.5 21.8 - - + -
320C LEU* 5.6 7.2 - - + -
390C MET 5.7 1.1 - - - +
391C TYR* 3.9 39.3 - - + +
394C TYR* 4.0 8.5 - - + +
395C LYS* 3.9 26.9 - - - +
398C VAL* 3.3 27.9 - - + +
401C LEU* 5.7 8.7 - - + -
410C TRP* 4.5 1.2 - - - -
455C LEU* 3.0 25.4 + - + +
456C ALA* 3.1 4.0 + - - +
458C VAL* 1.3 72.8 - - - +
460C LEU* 1.3 61.7 + - - +
461C TYR 3.1 1.8 - - - -
462C GLY* 3.0 17.5 + - - -
464C GLY* 4.2 7.9 - - - +
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Residues in contact with LEU 460 (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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308C MET* 3.6 17.6 - - + +
311C MET* 3.6 12.8 - - + +
312C ILE* 3.4 47.8 - - + +
315C LEU* 3.5 22.7 - - + -
398C VAL* 4.0 11.9 - - + -
402C ILE* 4.2 13.5 - - + -
410C TRP* 3.1 36.5 + - + +
414C ARG* 3.0 22.2 + - - -
456C ALA 2.9 14.1 + - - +
457C LYS 4.0 2.7 - - - +
459C LEU* 1.3 75.3 - - - +
461C TYR* 1.3 58.8 + - + +
462C GLY 3.3 0.7 - - - -
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Residues in contact with TYR 461 (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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280C ILE* 3.5 55.4 - - + -
281C ILE 3.0 20.6 + - - -
282C PHE* 3.4 18.1 - + - -
285C LEU* 4.6 1.0 - - - +
308C MET* 3.7 28.3 - - + +
312C ILE* 4.6 1.3 - - + -
414C ARG* 3.4 17.7 + - - +
417C LEU* 3.4 31.8 - - + +
425C LEU* 3.6 24.5 - - + +
429C LEU* 5.5 1.2 - - - +
457C LYS* 3.0 32.5 + - + +
458C VAL 4.3 2.5 - - - +
459C LEU 3.1 0.4 - - - -
460C LEU* 1.3 81.3 - - + +
462C GLY* 1.3 61.8 + - - +
463C LEU* 3.4 12.2 + - + +
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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