Contacts of the helix formed by residues 464 - 466 (chain D) in PDB entry 1T5A
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 HIS 464 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D GLY* 4.0 11.1 - - - -
70D ASN* 3.1 50.9 + - + -
71D VAL* 4.0 17.3 - - + -
106D ARG* 6.3 0.7 - - + -
107D PRO* 3.1 32.6 + - + +
109D ALA 4.5 2.5 - - - -
358D CYS* 3.4 15.5 - - - -
460D ALA 4.0 4.5 - - - -
461D ARG* 3.1 25.4 - - - +
462D GLN 3.1 1.6 + - - -
463D ALA* 1.3 71.2 - - - +
465D LEU* 1.3 58.2 + - - +
466D TYR 3.0 17.2 + - - +
469D ILE 5.0 4.7 + - - -
470D PHE* 6.3 1.3 - + - -
471D PRO* 3.5 29.7 - - + +
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Residues in contact with LEU 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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48D ILE* 5.0 3.4 - - + -
71D VAL* 5.6 1.8 - - + -
239D MET* 3.7 36.1 - - + -
266D LYS* 4.3 21.1 - - + -
268D ILE* 3.9 29.6 - - + -
288D ASP* 6.2 0.4 - - + -
323D PRO* 2.9 39.5 - - + +
325D ILE* 4.3 19.5 - - + -
357D ASP* 3.2 15.0 - - - +
358D CYS* 4.0 9.2 - - - -
462D GLN* 3.3 16.4 + - - +
463D ALA 3.1 0.4 - - - -
464D HIS* 1.3 77.3 - - - +
466D TYR* 1.3 61.9 + - + +
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Residues in contact with TYR 466 (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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44D ASN 4.2 3.5 - - - +
288D ASP* 4.7 2.6 + - - +
321D GLY 4.0 16.2 + - - -
322D LYS* 5.1 1.0 - - - +
323D PRO* 3.2 37.8 - - + +
357D ASP* 4.0 6.5 - - - -
439D HIS* 3.4 61.3 + + + -
442D ALA* 4.3 9.0 - - + -
443D ARG* 5.7 0.9 - - + -
445D ARG* 6.2 0.7 - - - -
462D GLN 4.4 4.9 - - - -
463D ALA 3.1 9.1 + - - +
464D HIS 3.0 9.2 - - - +
465D LEU* 1.3 88.7 - - + +
467D ARG* 1.3 65.3 + - - +
468D GLY 3.3 2.1 + - - -
469D ILE* 3.3 37.4 + - + +
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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