Contacts of the helix formed by residues 450 - 461 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A PHE* 3.9 15.5 - - + -
326A GLU* 3.0 47.4 + - - +
328A CYS 5.3 1.7 - - - +
329A ASP* 4.1 13.5 - - - +
449A THR* 1.3 78.6 - - - +
451A LEU* 1.3 60.8 + - - +
452A ILE 3.5 0.7 - - - +
453A PRO* 3.6 15.7 - - + +
454A ALA* 2.9 31.2 + - - +
474A SER* 3.5 0.2 - - - -
476A THR* 3.3 25.8 + - + -
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A CYS 6.0 0.9 - - - +
330A GLN 3.7 19.2 + - - +
331A ILE 3.6 15.5 - - - +
332A HIS 3.7 28.9 - - - +
333A VAL* 3.7 18.8 - - + +
384A TYR* 3.9 25.1 - - + +
450A GLN* 1.3 72.9 - - - +
452A ILE* 1.3 64.6 + - + +
454A ALA* 3.3 4.6 + - + +
455A LEU* 3.1 37.7 + - + +
472A ILE* 4.2 27.4 - - + +
474A SER* 3.5 12.6 + - - +
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Residues in contact with ILE 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A ALA* 4.0 4.0 - - + -
320A LEU* 3.4 35.9 - - + +
322A PHE* 3.7 23.3 - - + -
325A LEU* 3.5 43.1 - - + -
384A TYR* 4.0 17.7 - - + +
387A VAL* 4.0 21.8 - - + -
450A GLN* 4.7 0.2 - - - +
451A LEU* 1.3 76.7 - - + +
453A PRO* 1.3 71.9 - - + +
455A LEU* 3.0 18.3 + - + +
456A ALA* 3.1 11.6 + - - +
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Residues in contact with PRO 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A ILE* 3.8 7.7 - - + +
313A PHE* 4.1 20.4 - - + -
316A ALA* 4.6 4.7 - - + -
322A PHE* 3.4 38.8 - - + -
449A THR* 3.8 17.7 - - + -
450A GLN* 3.5 21.3 - - + +
452A ILE* 1.3 95.0 - - + +
454A ALA* 1.3 56.3 + - - +
456A ALA* 3.4 8.6 + - + +
457A LYS* 3.0 30.6 + - - +
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Residues in contact with ALA 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LEU* 4.8 3.3 - - + +
447A THR* 3.6 29.6 - - + -
449A THR* 3.7 10.0 - - + +
450A GLN 2.9 22.1 + - - +
451A LEU* 3.5 7.0 - - + +
452A ILE 3.1 0.2 - - - -
453A PRO* 1.3 78.6 - - - +
455A LEU* 1.3 56.5 + - - +
457A LYS* 3.5 8.1 - - - +
458A VAL* 3.0 33.9 + - + +
472A ILE* 5.0 8.5 - - + -
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Residues in contact with LEU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 4.6 6.7 - - + -
333A VAL* 5.0 2.7 - - + -
387A VAL* 3.6 29.2 - - + -
391A TYR* 4.0 12.6 - - + -
451A LEU* 3.1 37.0 + - + +
452A ILE* 3.0 11.0 + - + +
454A ALA* 1.3 75.0 - - - +
456A ALA* 1.3 59.2 + - - +
457A LYS 3.1 1.6 - - - -
458A VAL* 3.2 4.0 + - - +
459A LEU* 2.8 37.1 + - + +
469A ILE* 4.0 23.3 - - + -
472A ILE* 3.5 40.4 - - + -
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Residues in contact with ALA 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A ILE* 3.2 29.2 - - + +
315A LEU* 3.4 29.8 - - + -
316A ALA* 4.2 4.0 - - + -
320A LEU* 4.0 4.3 - - + +
452A ILE 3.1 11.7 + - - +
453A PRO 3.7 7.0 - - - +
455A LEU* 1.3 76.6 - - - +
457A LYS* 1.3 58.1 + - - +
459A LEU* 3.7 2.2 - - - +
460A LEU* 2.9 38.2 + - - +
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Residues in contact with LYS 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LEU* 3.6 24.0 - - + +
276A ASP* 3.2 18.7 + - - +
280A ILE* 3.8 22.0 - - + -
282A PHE* 3.8 17.0 - - + -
283A HIS* 4.2 6.5 + - - -
312A ILE* 3.8 37.7 - - + +
449A THR* 3.4 28.4 + - - +
453A PRO* 3.0 18.3 + - - +
454A ALA* 3.5 7.0 - - - +
456A ALA* 1.3 75.0 - - - +
458A VAL* 1.3 64.1 + - - +
460A LEU* 3.4 0.8 + - - -
461A TYR* 3.0 33.9 + - + +
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 4.6 8.7 - - + -
391A TYR* 3.5 23.8 - - + +
445A LEU* 3.8 29.4 - - + -
454A ALA 3.0 22.3 + - - +
455A LEU* 3.2 7.2 + - - +
457A LYS* 1.3 75.6 - - - +
459A LEU* 1.3 57.8 + - - +
461A TYR 3.6 0.2 + - - -
462A GLY 3.4 2.6 + - - -
463A LEU* 2.7 55.1 + - + +
464A GLY* 3.4 19.1 - - - +
467A PHE* 5.0 2.7 - - + -
472A ILE* 4.3 7.4 - - + -
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Residues in contact with LEU 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A LEU* 4.8 7.4 - - + -
320A LEU* 5.1 7.9 - - + -
390A MET 5.2 0.4 - - - +
391A TYR* 3.8 40.8 - - + +
394A TYR* 4.4 1.1 - - + +
395A LYS* 3.5 36.8 - - + +
398A VAL* 3.5 32.1 - - + +
401A LEU* 4.4 21.8 - - + -
410A TRP* 4.5 1.7 - - - -
455A LEU* 2.8 22.9 + - + +
456A ALA* 3.7 7.2 - - - +
458A VAL* 1.3 78.5 - - - +
460A LEU* 1.3 58.9 + - - +
462A GLY* 2.9 17.8 + - - -
464A GLY* 4.2 4.9 - - - +
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Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A MET* 3.8 17.8 - - + +
311A MET* 3.5 19.5 - - + +
312A ILE* 3.4 40.8 - - + +
315A LEU* 3.6 21.1 - - + -
398A VAL* 4.3 7.4 - - + -
402A ILE* 4.8 9.0 - - + -
410A TRP* 3.0 51.8 + - + +
414A ARG* 3.1 14.6 + - - -
456A ALA 2.9 19.0 + - - +
457A LYS 4.0 1.3 - - - +
459A LEU* 1.3 76.2 - - - +
461A TYR* 1.3 58.7 + - - +
462A GLY 3.3 1.1 - - - -
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Residues in contact with TYR 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ILE* 3.6 49.4 - - + -
281A ILE 3.1 25.6 + - - -
282A PHE* 3.6 17.1 - - + +
285A LEU* 4.7 0.5 - - - +
308A MET* 3.3 30.4 - - + +
312A ILE* 4.6 2.2 - - + -
414A ARG* 3.4 14.0 + - - +
417A LEU* 3.4 32.0 - - + +
425A LEU* 3.4 36.7 - - + +
429A LEU* 5.5 0.9 - - - +
457A LYS* 3.0 31.8 + - + +
458A VAL 3.6 0.2 + - - -
459A LEU 3.1 0.4 - - - -
460A LEU* 1.3 77.1 - - - +
462A GLY* 1.3 63.0 + - - +
463A LEU* 3.4 12.0 + - + +
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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