Contacts of the helix formed by residues 489 - 496 (chain C) in PDB entry 4E2I
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 489 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450C VAL 4.0 7.0 - - - +
451C ASN* 4.4 14.8 + - - +
452C LEU 4.9 2.5 - - - +
453C PRO* 5.5 6.3 - - + -
454C LEU* 4.5 13.1 - - + +
476C LYS* 3.5 1.7 - - - +
478C THR* 6.2 0.4 - - - +
488C GLY* 1.3 89.8 + - - -
490C GLY* 1.3 57.2 + - - +
491C ILE 3.5 1.1 - - - -
492C ASN* 3.9 23.8 + - - +
493C ASN* 2.7 53.1 + - - +
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Residues in contact with GLY 490 (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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450C VAL* 3.7 23.7 + - - +
451C ASN* 4.3 4.2 + - - +
475C VAL* 3.7 9.2 - - - -
476C LYS 2.7 23.6 + - - +
489C GLN* 1.3 80.2 - - - +
491C ILE* 1.3 61.2 + - - -
493C ASN* 3.3 2.4 + - - +
494C LEU* 3.1 23.0 + - - +
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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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475C VAL* 3.6 28.0 - - + +
476C LYS 3.0 5.8 + - - -
477C GLY* 3.4 31.4 - - - +
478C THR 5.3 0.2 - - - +
490C GLY* 1.3 71.2 - - - -
492C ASN* 1.3 66.0 + - - +
494C LEU* 3.3 18.1 + - + +
495C ASP* 3.4 11.4 + - - +
528C MET* 3.6 22.4 - - + -
531C TYR* 4.4 3.6 - - + -
532C SER 3.8 16.8 - - - +
533C VAL* 4.7 0.4 - - + -
534C PRO* 3.5 34.5 - - + -
537C LEU* 3.8 7.3 - - + +
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Residues in contact with ASN 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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476C LYS 4.9 1.6 + - - -
477C GLY* 5.1 0.6 - - - -
478C THR* 4.4 20.6 - - - +
488C GLY 3.4 24.9 + - - -
489C GLN* 3.4 24.0 + - - +
490C GLY 3.2 0.4 - - - -
491C ILE* 1.3 79.8 - - - +
493C ASN* 1.3 60.0 + - - +
495C ASP* 3.0 17.8 + - - +
496C ASN* 2.7 27.8 + - - +
476D LYS* 3.9 8.3 + - - +
486D PRO* 5.8 3.1 - - - +
487D SER 5.7 0.3 - - - +
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Residues in contact with ASN 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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450C VAL* 3.7 28.1 + - + -
452C LEU 3.9 6.1 + - - -
454C LEU* 3.2 42.3 - - - +
457C LEU* 3.3 25.8 - - + +
489C GLN* 2.7 40.1 + - - +
490C GLY 3.7 3.1 - - - +
492C ASN* 1.3 72.6 - - - +
494C LEU* 1.3 62.1 + - - +
496C ASN* 3.0 17.7 + - - +
497C LEU* 3.2 22.8 - - + +
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Residues in contact with LEU 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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450C VAL* 4.6 7.0 - - + -
472C PHE* 4.2 26.2 - - + -
475C VAL* 4.0 16.4 - - + -
490C GLY 3.1 15.7 + - - +
491C ILE* 3.4 17.0 - - + +
492C ASN 3.1 0.2 - - - -
493C ASN* 1.3 76.6 - - - +
495C ASP* 1.3 62.0 + - - +
497C LEU* 3.2 16.8 + - + +
501C LEU* 3.3 28.7 - - + +
526C VAL* 3.8 35.9 - - + -
528C MET* 4.9 2.0 - - + -
537C LEU* 3.6 28.3 - - + -
541C PHE* 4.9 2.7 - - + -
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Residues in contact with ASP 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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491C ILE 3.4 6.8 + - - +
492C ASN* 3.0 11.3 + - - +
494C LEU* 1.3 74.6 - - - +
496C ASN* 1.3 58.2 + - - +
497C LEU 2.9 9.2 + - - -
498C ARG* 2.8 47.3 + - - +
534C PRO* 4.5 5.4 - - + +
536C THR* 2.9 26.0 + - - -
537C LEU* 4.2 11.3 + - + +
451D ASN* 4.5 0.9 + - - -
476D LYS* 3.3 28.8 - - - +
486D PRO* 3.4 16.3 - - + +
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Residues in contact with ASN 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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454C LEU* 3.8 25.2 - - + +
492C ASN* 2.7 36.5 + - - +
493C ASN* 3.0 13.8 + - - +
495C ASP* 1.3 75.7 - - - +
497C LEU* 1.3 69.4 + - + +
498C ARG 3.8 1.3 - - - -
449D ASN* 3.4 8.8 + - - -
451D ASN* 3.4 39.3 + - + +
452D LEU* 3.9 2.2 - - + +
476D LYS* 3.0 28.8 + - - +
488D GLY* 4.7 5.0 - - - -
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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