Contacts of the helix formed by residues 573 - 578 (chain X) in PDB entry 1T6B
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 ASN 573 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566X LEU* 4.7 2.2 - - - +
571X ALA* 3.5 1.1 - - - +
572X THR* 1.3 92.2 + - + +
574X ILE* 1.3 63.4 + - - +
575X TYR* 3.0 49.5 + - - +
576X THR* 2.7 34.8 + - - +
577X VAL* 3.8 8.4 - - - +
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Residues in contact with ILE 574 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523X LEU* 4.3 12.6 - - + -
552X PHE* 4.0 27.4 - - + -
554X PHE* 3.7 32.3 - - + -
562X ILE* 3.9 18.6 - - + -
566X LEU* 4.2 24.5 - - + +
573X ASN* 1.3 73.7 + - - +
575X TYR* 1.3 78.5 + - + +
576X THR 3.2 0.5 + - - -
577X VAL 3.2 10.2 + - - -
578X LEU* 3.5 21.4 + - + +
581X ILE* 4.6 7.9 - - + -
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Residues in contact with TYR 575 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547X ILE* 3.5 37.1 - - + +
548X THR* 3.6 32.3 - - + -
550X PHE 2.5 23.6 + - - -
551X ASP* 4.0 4.0 + - - -
552X PHE* 3.6 23.6 + + - -
573X ASN* 3.0 28.8 + - - +
574X ILE* 1.3 85.5 - - + +
576X THR* 1.3 60.4 + - - +
577X VAL 3.3 0.3 + - - -
578X LEU* 4.0 16.8 + - + +
594X LYS* 2.9 28.7 + - - -
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Residues in contact with THR 576 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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571X ALA* 4.9 3.3 - - - +
572X THR 5.3 0.2 + - - -
573X ASN* 2.7 35.3 + - + +
575X TYR* 1.3 76.4 - - - +
577X VAL* 1.3 65.9 + - - +
578X LEU 3.8 0.7 - - - -
579X ASP* 4.3 5.9 - - - +
580X LYS* 6.1 0.2 - - - -
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Residues in contact with VAL 577 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566X LEU* 3.6 31.4 - - + -
569X LEU* 4.0 20.4 - - + +
571X ALA* 3.9 20.0 - - + -
573X ASN 3.8 7.6 - - - +
574X ILE 3.2 8.9 + - - +
575X TYR 3.2 0.4 - - - -
576X THR* 1.3 86.9 - - - +
578X LEU* 1.3 58.2 + - - +
579X ASP* 3.2 8.5 - - - -
580X LYS* 3.0 29.9 + - + -
581X ILE* 3.0 20.8 + - + +
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Residues in contact with LEU 578 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523X LEU* 3.5 42.4 + - + +
524X LYS* 3.0 34.9 + - + +
527X LEU* 4.7 2.5 - - + -
540X LEU* 3.7 28.9 - - + -
547X ILE* 3.8 28.0 - - + -
552X PHE* 4.1 13.2 - - + -
574X ILE* 3.5 25.9 + - + +
575X TYR* 4.0 12.5 + - + +
576X THR 3.8 0.8 - - - -
577X VAL* 1.3 76.9 - - - +
579X ASP* 1.3 59.7 + - - +
580X LYS 3.5 0.3 + - - -
581X ILE* 3.8 4.7 + - - -
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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