Contacts of the helix formed by residues 491 - 498 (chain C) in PDB entry 1G88
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 GLY 491 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381B LEU* 5.2 2.0 - - - +
450C GLN* 4.9 0.7 + - - -
454C ALA* 4.5 12.9 - - - +
489C GLY 3.2 2.4 + - - -
490C ILE* 1.3 69.4 - - - +
492C VAL* 1.3 62.4 + - - +
493C ASP 3.2 3.6 + - - -
494C ASP* 3.8 12.8 + - - +
495C LEU* 3.1 28.9 + - - +
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Residues in contact with VAL 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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352B GLY 4.2 15.5 - - - +
354B VAL* 4.1 24.0 - - + +
365B GLY* 4.8 6.5 - - - +
381B LEU* 5.8 0.2 - - + -
488C ALA 4.2 4.5 - - - +
489C GLY* 3.1 36.5 + - - +
490C ILE* 2.8 8.6 + - + +
491C GLY* 1.3 75.1 - - - +
493C ASP* 1.3 66.2 + - - +
495C LEU* 3.7 7.9 - - + +
496C ARG* 3.3 18.2 + - - +
540C LEU* 4.0 26.2 - - + -
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Residues in contact with ASP 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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365B GLY 4.8 4.1 - - - +
372B ARG* 3.8 12.8 + - - -
377B GLU* 5.7 7.3 - - - +
380B ARG* 4.8 3.5 + - - -
381B LEU* 6.0 4.7 - - + +
489C GLY 4.7 0.6 + - - -
491C GLY* 3.2 1.2 - - - -
492C VAL* 1.3 75.0 - - - +
494C ASP* 1.3 70.2 + - - +
495C LEU 2.9 5.8 + - - -
496C ARG* 3.0 46.0 + - - +
497C ARG* 3.0 44.7 + - - +
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Residues in contact with ASP 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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412C TYR* 5.6 2.1 + - - -
450C GLN* 3.7 18.7 + - - +
491C GLY* 3.8 12.1 + - - +
493C ASP* 1.3 85.7 + - - +
495C LEU* 1.3 63.1 + - - +
497C ARG* 3.6 24.9 + - - +
498C LEU* 3.6 15.1 - - - +
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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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447C MET* 3.8 14.2 - - - +
450C GLN* 3.4 42.0 - - + +
451C ALA* 4.0 23.6 - - + +
454C ALA* 5.7 1.1 - - + -
490C ILE* 5.0 2.7 - - + +
491C GLY 3.1 23.7 + - - +
492C VAL* 3.7 5.4 - - - +
493C ASP 2.9 1.8 + - - -
494C ASP* 1.3 73.8 - - - +
496C ARG* 1.3 61.5 + - - +
497C ARG 3.0 1.6 - - - -
498C LEU* 2.8 37.5 + - + +
499C CYS* 3.9 2.3 + - - -
536C LEU* 3.6 30.0 - - + +
540C LEU* 4.0 14.4 - - + -
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Residues in contact with ARG 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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354B VAL* 3.9 20.6 - - + -
365B GLY 3.6 13.3 + - - +
366B GLN* 3.4 28.7 + - + +
367B LEU 3.8 7.7 + - - -
368B SER* 2.9 29.9 + - - +
369B ASN 5.6 0.2 - - - +
372B ARG* 3.7 14.9 - - - +
492C VAL 3.3 12.8 + - - +
493C ASP* 3.0 50.6 + - - +
495C LEU* 1.3 78.5 - - - +
497C ARG* 1.3 82.3 + - - +
499C CYS* 3.0 23.1 + - - +
500C ILE* 3.4 22.9 - - - +
526C GLU* 4.7 0.2 + - - -
533C LEU* 4.2 4.8 - - + +
536C LEU* 3.3 11.7 - - + +
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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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377B GLU* 5.7 2.4 + - - -
410C GLN* 5.3 0.2 - - - +
412C TYR* 3.5 35.3 - - + +
493C ASP* 3.0 38.7 + - - +
494C ASP* 3.6 22.4 + - - +
495C LEU 2.9 0.6 + - - -
496C ARG* 1.3 99.2 - - - +
498C LEU* 1.3 60.2 + - - +
499C CYS 3.0 7.1 + - - -
500C ILE* 3.2 27.7 + - + +
502C ARG* 4.1 23.2 - - - +
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Residues in contact with LEU 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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412C TYR* 3.7 42.4 - - + +
422C PRO* 6.2 0.4 - - + -
438C PHE* 3.3 21.7 - - - -
443C CYS* 3.6 13.8 - - - +
446C GLN* 3.8 22.0 - - + -
447C MET* 4.6 11.2 - - + +
450C GLN* 3.2 33.4 - - - +
494C ASP 3.6 8.7 - - - +
495C LEU* 2.8 25.0 + - + +
497C ARG* 1.3 76.9 - - - +
499C CYS* 1.3 58.2 + - - +
500C ILE 3.5 2.4 + - - +
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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