Contacts of the helix formed by residues 497 - 503 (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 LEU 497 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C VAL* 5.0 7.0 - - + -
457C LEU* 4.3 13.0 - - + -
461C LEU* 3.9 34.8 - - + -
472C PHE* 5.3 6.7 - - + -
493C ASN 3.2 20.4 - - - +
494C LEU* 3.2 12.0 + - + +
495C ASP 2.9 1.2 - - - -
496C ASN* 1.3 86.4 - - + +
498C ARG* 1.3 63.4 + - - +
499C ASP* 3.5 3.6 - - - -
500C TYR* 3.3 42.6 + - + -
501C LEU* 3.1 26.7 + - + +
521C PHE* 6.3 0.7 - - + -
452D LEU* 4.2 14.8 - - + -
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Residues in contact with ARG 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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494C LEU 5.0 0.7 - - - -
495C ASP* 2.8 49.4 + - - +
496C ASN 3.8 1.0 - - - -
497C LEU* 1.3 71.6 - - - +
499C ASP* 1.3 66.2 + - - +
501C LEU* 2.9 17.9 + - - +
502C ASP* 2.7 25.0 + - - +
536C THR* 2.9 35.9 + - - +
537C LEU* 5.7 0.4 - - - +
540C ARG* 3.2 26.7 - - - +
451D ASN* 5.0 1.7 - - - +
473D GLU 5.1 0.7 - - - +
474D ASP* 3.1 44.4 + - + +
476D LYS* 5.3 1.8 - - + +
486D PRO* 4.4 0.2 - - - +
529D ASN* 3.2 25.1 + - - +
531D TYR* 3.2 23.6 + - - -
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Residues in contact with ASP 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C ARG* 1.3 80.2 + - - +
500C TYR* 1.3 73.3 + - - +
502C ASP* 3.5 9.8 + - - -
503C GLY* 2.8 30.8 + - - -
505C VAL* 3.6 15.0 - - + +
507C VAL* 3.1 30.3 - - - +
433D THR* 5.5 0.2 - - - -
447D ALA* 5.5 2.3 - - - +
448D LEU 5.1 2.2 - - - +
449D ASN* 3.7 22.9 - - - +
473D GLU* 3.4 37.9 - - + +
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Residues in contact with TYR 500 (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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420C ARG* 3.2 18.2 + - - -
421C TYR* 3.9 1.0 + - - -
458C ASN* 5.8 1.2 + - - -
461C LEU* 4.0 20.1 - - + +
497C LEU* 3.4 42.0 - - + +
498C ARG 3.1 0.8 - - - -
499C ASP* 1.3 116.0 - - - +
501C LEU* 1.3 60.0 + - + +
507C VAL* 3.8 24.5 - - + -
508C ASN 3.5 21.4 + - - -
509C LEU* 4.7 3.4 - - + -
521C PHE* 3.3 53.2 - + + +
449D ASN* 4.6 13.6 - - + +
452D LEU* 5.5 4.9 - - + +
460D GLU* 4.3 15.8 + - - -
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Residues in contact with LEU 501 (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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418C LYS* 4.4 5.6 + - - -
420C ARG* 3.3 13.5 + - - +
421C TYR* 3.8 47.1 - - + -
472C PHE* 4.9 8.7 - - + -
494C LEU* 3.3 33.4 - - + +
495C ASP* 5.4 0.2 - - - -
497C LEU* 3.1 15.7 + - + +
498C ARG* 2.9 8.8 + - - +
500C TYR* 1.3 79.3 - - + +
502C ASP* 1.3 64.4 + - - +
521C PHE* 6.2 0.7 - - + -
526C VAL* 5.1 3.1 - - + -
537C LEU* 3.8 22.0 - - + -
540C ARG* 3.9 31.4 - - + +
541C PHE* 5.5 3.4 - - + -
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Residues in contact with ASP 502 (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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417C PRO* 3.4 8.1 - - - +
418C LYS* 3.1 45.8 + - + +
420C ARG* 3.2 14.6 + - - -
498C ARG 2.7 22.8 + - - +
499C ASP* 3.2 6.9 + - - +
501C LEU* 1.3 75.3 - - - +
503C GLY* 1.3 60.3 + - - +
504C SER* 3.4 4.9 - - - +
540C ARG* 2.8 37.1 + - - -
433D THR* 4.0 27.8 + - + +
474D ASP* 4.2 2.4 - - - +
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Residues in contact with GLY 503 (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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417C PRO* 4.9 1.1 - - - -
420C ARG* 3.2 21.5 - - - +
499C ASP 2.8 18.5 + - - -
500C TYR 4.8 0.2 - - - -
502C ASP* 1.3 74.1 - - - +
504C SER* 1.3 59.3 + - - +
505C VAL 3.2 8.5 - - - -
507C VAL* 6.2 0.2 - - - -
520C ILE* 3.1 29.0 - - - +
521C PHE* 4.7 1.8 - - - -
567D ARG* 3.7 15.4 + - - -
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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