Contacts of the strand formed by residues 458 - 465 (chain D) in PDB entry 5HIE
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 THR 458 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455D GLY 5.2 1.6 + - - -
456D GLN 4.3 4.2 + - - -
457D ILE* 1.4 77.7 + - - +
459D VAL* 1.3 68.3 + - - +
460D GLY* 4.0 0.4 + - - -
474D GLY* 3.2 4.5 - - - -
475D LYS* 2.8 54.2 + - + +
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Residues in contact with VAL 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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457D ILE* 4.5 9.9 - - + -
458D THR* 1.3 82.3 - - - +
460D GLY* 1.3 65.1 + - - +
472D TYR* 3.7 33.7 - - + -
473D LYS 4.2 1.6 - - - +
474D GLY* 4.4 0.7 - - - -
482D VAL* 4.2 23.3 - - + -
484D MET* 3.7 14.8 - - + -
522D LYS 4.2 6.3 - - - +
523D PRO* 3.9 27.8 - - + -
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Residues in contact with GLY 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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458D THR 4.0 1.0 + - - -
459D VAL* 1.3 79.3 - - - +
461D GLN* 1.3 64.7 + - - +
472D TYR* 4.0 9.4 - - - -
473D LYS* 2.7 19.9 + - - -
474D GLY* 4.3 0.6 - - - -
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Residues in contact with GLN 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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460D GLY* 1.3 76.2 - - - +
462D ARG* 1.3 66.7 + - - +
463D ILE* 3.5 7.0 + - + +
472D TYR* 3.2 5.3 - - - -
473D LYS* 2.9 30.3 + - + +
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Residues in contact with ARG 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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461D GLN* 1.3 75.0 - - - +
463D ILE* 1.3 63.6 + - - +
464D GLY* 4.0 15.0 - - - +
465D SER* 5.6 1.1 - - - -
470D THR* 4.7 12.5 - - - +
471D VAL 3.4 12.8 - - - +
472D TYR* 3.5 37.6 + - + -
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Residues in contact with ILE 463 (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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461D GLN* 3.8 12.3 - - + +
462D ARG* 1.3 77.8 - - - +
464D GLY* 1.3 56.1 + - - +
471D VAL* 2.7 17.6 + - + +
472D TYR 4.0 3.4 - - - -
473D LYS* 3.8 21.3 - - + +
531D TRP* 3.7 35.2 - - + -
801D P06 4.0 31.2 - - + +
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Residues in contact with GLY 464 (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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462D ARG* 3.7 9.4 - - - +
463D ILE* 1.3 81.1 - - - +
465D SER* 1.3 59.6 + - - -
470D THR* 3.4 4.6 - - - -
471D VAL* 2.8 29.7 + - - +
801D P06 3.5 11.6 - - - +
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Residues in contact with SER 465 (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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462D ARG* 5.6 1.9 - - - -
464D GLY* 1.3 72.6 - - - -
466D GLY* 1.3 63.9 + - - +
469D GLY 3.5 13.0 - - - -
470D THR* 3.3 23.2 - - - +
801D P06 3.6 10.4 - - - +
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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