Contacts of the helix formed by residues 456 - 462 (chain D) 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 ARG 456 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454C LEU 4.6 4.9 - - - +
455C ASP* 3.4 27.6 + - - +
456C ARG* 3.4 29.3 - - - +
458C ASN* 3.8 36.0 + - - +
459C PHE* 3.5 25.5 - - - -
510C GLU* 5.5 1.8 - - - -
452D LEU* 4.9 9.0 - - + -
453D PRO* 3.6 6.1 + - + +
455D ASP* 1.3 98.3 - - + +
457D LEU* 1.3 62.8 + - - +
458D ASN 3.1 2.7 - - - -
459D PHE* 3.0 37.5 + - + +
460D GLU* 3.1 15.2 + - - +
456E ARG* 3.7 11.6 - - - +
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Residues in contact with LEU 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D ASN 4.4 8.3 - - - +
450D VAL* 3.8 31.4 - - + -
452D LEU* 5.2 1.3 - - - +
453D PRO 3.5 6.1 + - - +
454D LEU* 3.6 32.5 - - + +
455D ASP 3.1 1.0 - - - -
456D ARG* 1.3 78.8 - - - +
458D ASN* 1.3 55.1 + - - +
460D GLU* 3.2 4.2 + - + +
461D LEU* 2.8 65.8 + - + +
493D ASN* 3.3 24.7 - - + +
496D ASN* 6.1 0.2 - - + -
497D LEU* 4.3 16.8 - - + -
452E LEU* 4.7 9.2 - - + -
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Residues in contact with ASN 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D LEU 3.6 8.0 - - - +
455D ASP 3.9 1.7 - - - +
456D ARG 3.1 0.6 - - - -
457D LEU* 1.3 78.0 - - - +
459D PHE* 1.3 64.6 + - + +
460D GLU 3.1 0.7 + - - -
461D LEU* 4.5 6.6 - - - +
462D GLY* 3.5 15.6 + - - -
500D TYR* 5.7 1.4 + - - -
510D GLU* 3.5 40.2 + - + +
452E LEU* 3.5 25.8 - - - +
456E ARG* 3.4 39.6 + - - +
459E PHE* 5.6 1.4 - - - +
460E GLU* 4.6 9.1 + - - +
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Residues in contact with PHE 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458C ASN* 5.8 1.1 - - - +
459C PHE* 6.2 4.9 - + - -
510C GLU* 4.6 20.1 - - - +
515C ASN* 5.2 9.0 + - - +
455D ASP 4.0 11.4 - - - -
456D ARG* 3.0 26.7 + - + +
458D ASN* 1.3 75.8 - - - +
460D GLU* 1.3 58.2 + - - +
462D GLY* 4.4 3.4 + - - -
463D VAL* 4.6 7.1 - - - +
510D GLU* 3.7 25.0 - - - +
513D HIS* 5.6 13.5 - + - -
456E ARG* 3.7 30.7 - - - -
459E PHE* 6.3 3.8 - + - -
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Residues in contact with GLU 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458C ASN* 4.1 17.9 + - - +
500C TYR* 4.3 13.1 + - - -
508C ASN* 3.8 26.6 + - + +
448D LEU* 3.2 18.9 - - + +
449D ASN* 2.7 51.9 + - - +
452D LEU* 4.4 10.2 - - - +
456D ARG 3.1 12.6 + - - +
457D LEU* 3.9 6.1 - - + +
459D PHE* 1.3 80.3 - - - +
461D LEU* 1.3 58.9 + - + +
462D GLY 3.0 5.4 - - - -
463D VAL* 3.0 25.7 - - - +
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Residues in contact with LEU 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D LEU* 3.9 13.7 - - + -
449D ASN 6.0 0.4 - - - +
450D VAL* 5.1 0.2 - - + -
457D LEU* 2.8 55.4 + - + +
458D ASN* 4.5 5.8 - - - +
460D GLU* 1.3 72.4 - - - +
462D GLY* 1.3 57.4 + - - +
463D VAL 3.0 9.7 + - - -
464D ALA 3.5 9.1 + - - -
472D PHE* 4.4 13.5 - - + -
497D LEU* 3.9 22.9 - - + -
500D TYR* 4.0 19.1 - - + +
509D LEU* 3.4 21.2 - - + +
521D PHE* 3.8 31.9 - - + -
452E LEU* 5.7 3.6 - - + -
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Residues in contact with GLY 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D ASN 3.5 8.8 + - - -
459D PHE 5.1 2.2 - - - -
460D GLU* 3.0 2.6 - - - +
461D LEU* 1.3 77.2 - - - +
463D VAL* 1.3 60.5 + - - +
464D ALA 3.5 0.7 - - - -
465D ILE* 3.0 32.7 - - - +
509D LEU* 4.4 6.3 - - - -
510D GLU 3.7 23.9 - - - +
511D LYS* 4.5 8.3 - - - +
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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