Contacts of the helix formed by residues 450 - 461 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322B PHE* 4.0 15.9 - - - -
325B LEU 4.6 2.3 - - - +
326B GLU* 3.2 33.2 + - - +
329B ASP* 3.4 37.8 + - + +
448B THR 3.7 0.6 + - - -
449B THR* 1.3 76.4 - - - +
451B LEU* 1.3 58.0 + - - +
452B ILE* 3.2 2.6 - - - +
453B PRO* 2.9 18.8 - - + +
454B ALA* 2.8 32.9 + - - +
476B THR* 3.5 16.8 + - + +
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Residues in contact with LEU 451 (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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329B ASP* 5.7 2.5 - - - +
330B GLN* 3.3 39.8 - - + +
331B ILE 4.6 1.1 - - - +
332B HIS* 3.0 40.6 - - - +
333B VAL* 3.8 18.2 - - + +
384B TYR* 4.4 13.5 - - + +
450B GLN* 1.3 72.6 - - - +
452B ILE* 1.3 64.3 + - + +
454B ALA* 3.5 4.8 - - + +
455B LEU* 3.2 35.1 + - + +
472B ILE* 4.7 19.1 - - + +
474B SER* 3.3 18.6 + - - -
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Residues in contact with ILE 452 (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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316B ALA* 4.1 2.8 - - + +
320B LEU* 3.3 41.6 - - + +
322B PHE* 3.5 25.8 - - + -
325B LEU* 3.5 44.6 - - + +
384B TYR* 3.5 25.6 - - + +
387B VAL* 5.1 6.3 - - + -
450B GLN* 4.5 2.4 - - - +
451B LEU* 1.3 75.7 - - + +
453B PRO* 1.3 74.4 - - + +
454B ALA 3.4 0.2 + - - -
455B LEU* 3.4 15.8 + - + +
456B ALA* 3.4 8.7 + - - +
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Residues in contact with PRO 453 (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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312B ILE* 3.8 6.4 - - + +
313B PHE* 3.8 23.6 - - + -
316B ALA* 4.7 4.0 - - + -
322B PHE* 3.5 30.5 - - + -
449B THR* 3.9 15.5 - - + -
450B GLN* 2.9 33.2 - - + +
452B ILE* 1.3 88.6 - - + +
454B ALA* 1.3 60.2 + - - +
456B ALA* 3.2 8.7 + - + +
457B LYS* 3.0 27.9 + - + +
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Residues in contact with ALA 454 (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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275B LEU* 4.9 2.9 - - + +
445B LEU* 6.5 0.2 - - + -
447B THR* 3.9 28.0 - - + -
449B THR* 3.6 12.0 - - - +
450B GLN 2.8 19.7 + - - +
451B LEU* 3.5 9.2 - - + +
453B PRO* 1.3 79.2 - - - +
455B LEU* 1.3 55.7 + - - +
457B LYS* 3.4 7.8 + - - +
458B VAL* 3.0 34.8 + - + +
472B ILE* 5.3 8.1 - - + -
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Residues in contact with LEU 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU* 4.6 7.0 - - + -
333B VAL* 4.9 7.4 - - + -
384B TYR* 6.3 0.9 - - + -
387B VAL* 3.9 27.6 - - + -
391B TYR* 3.7 31.1 - - + -
451B LEU* 3.2 31.2 + - + +
452B ILE* 3.8 10.1 - - + +
453B PRO 3.2 0.4 - - - -
454B ALA* 1.3 77.4 - - + +
456B ALA* 1.3 64.4 + - - +
457B LYS 3.2 0.4 - - - -
458B VAL* 3.4 3.8 + - - +
459B LEU* 3.0 32.9 + - + +
469B ILE* 3.9 17.0 - - + -
472B ILE* 3.8 25.1 - - + -
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Residues in contact with ALA 456 (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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312B ILE* 3.3 30.7 - - + +
315B LEU* 3.6 26.7 - - + -
316B ALA* 4.3 1.6 - - + -
320B LEU* 4.0 9.1 - - + +
452B ILE 3.4 5.5 + - - +
453B PRO 3.2 9.2 + - - +
455B LEU* 1.3 78.7 - - - +
457B LYS* 1.3 58.0 + - - +
459B LEU* 3.6 3.7 + - - +
460B LEU* 2.9 37.3 + - - +
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Residues in contact with LYS 457 (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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275B LEU* 3.6 25.7 - - + +
276B ASP* 3.2 25.9 + - - +
280B ILE* 4.8 3.3 - - + +
282B PHE* 3.4 22.8 - - + +
283B HIS* 3.9 6.7 + - - -
312B ILE* 3.3 36.1 - - + -
449B THR* 3.7 25.7 + - + +
453B PRO* 3.0 19.8 + - + +
454B ALA* 3.4 8.3 - - - +
456B ALA* 1.3 75.8 - - - +
458B VAL* 1.3 54.7 + - - +
460B LEU* 3.2 0.4 + - - -
461B TYR* 2.8 52.7 + - + +
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Residues in contact with VAL 458 (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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275B LEU* 5.1 4.7 - - + -
280B ILE* 5.3 0.6 - - - +
391B TYR* 3.2 30.3 - - + +
445B LEU* 4.2 25.4 - - + -
454B ALA* 3.0 20.3 + - + +
455B LEU* 3.6 9.2 - - - +
457B LYS* 1.3 78.1 - - + +
459B LEU* 1.3 59.2 + - - +
461B TYR 3.5 0.2 + - - -
462B GLY 3.4 1.0 + - - -
463B LEU* 2.8 64.0 + - + +
464B GLY 3.3 1.0 + - - +
467B PHE* 4.6 2.0 - - + -
472B ILE* 4.4 12.6 - - + -
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Residues in contact with LEU 459 (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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315B LEU* 4.8 14.6 - - + -
320B LEU* 5.0 7.4 - - + -
390B MET 5.4 0.7 - - - +
391B TYR* 3.5 43.1 - - + +
394B TYR* 4.6 5.2 - - + +
395B LYS* 3.7 32.7 - - + +
398B VAL* 3.3 27.4 - - + +
401B LEU* 5.1 11.9 - - + -
410B TRP* 4.0 2.3 - - - -
455B LEU* 3.0 25.1 + - + +
456B ALA* 3.9 8.1 - - - +
458B VAL* 1.3 77.1 - - - +
460B LEU* 1.3 63.0 + - + +
462B GLY* 3.4 10.7 + - - -
464B GLY* 4.4 4.7 - - - +
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Residues in contact with LEU 460 (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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308B MET* 3.2 33.2 - - + +
311B MET* 3.7 10.3 - - + +
312B ILE* 3.4 29.8 - - + +
315B LEU* 3.6 25.1 - - + -
398B VAL* 4.2 9.6 - - + -
402B ILE* 5.2 2.7 - - + -
410B TRP* 3.1 38.7 + - + +
414B ARG* 2.9 22.7 + - - -
456B ALA 2.9 26.5 + - - +
457B LYS* 3.9 3.6 - - - +
459B LEU* 1.3 75.6 - - - +
461B TYR* 1.3 59.3 + - + +
462B GLY 3.4 1.6 - - - -
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Residues in contact with TYR 461 (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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280B ILE* 3.5 50.9 - - + -
281B ILE 3.1 21.2 + - - -
282B PHE* 3.5 18.6 - - + +
285B LEU* 4.8 1.7 - - - +
308B MET* 3.8 27.3 - - + +
312B ILE* 4.5 10.1 - - + -
414B ARG* 3.7 11.2 + - - +
417B LEU* 3.7 26.7 - - + +
425B LEU* 3.5 35.8 - - + +
429B LEU* 4.8 1.4 - - - +
457B LYS* 2.8 29.7 + - + +
458B VAL 4.3 1.3 - - - +
459B LEU 3.2 0.2 - - - -
460B LEU* 1.3 83.4 - - + +
462B GLY* 1.3 54.6 + - - +
463B LEU* 3.1 18.3 + - + +
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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