Contacts of the helix formed by residues 551 - 555 (chain I) in PDB entry 6PSU
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 551 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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444I ASP* 3.5 22.7 + - - -
446I ASP* 3.0 34.5 + - + +
447I HIS* 3.5 15.0 - + - -
550I VAL* 1.3 80.4 - - - +
552I PRO* 1.3 70.7 - - + +
553I THR* 3.0 49.3 + - + -
554I HIS* 2.6 52.9 + - + +
749J LYS* 5.9 1.3 - - - -
773J PHE* 4.0 5.9 - - - -
777J HIS* 4.6 0.2 - - - -
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Residues in contact with PRO 552 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551I HIS* 1.3 103.9 - - + +
553I THR* 1.3 58.1 + - - -
554I HIS 3.1 2.5 + - - -
555I TYR* 3.8 14.8 + - - +
611I GLU* 4.9 7.1 - - - +
637I ARG* 5.3 2.3 + - - -
640I GLY* 4.7 25.8 - - - +
749J LYS* 4.3 15.0 - - - +
773J PHE* 4.1 13.5 - - + -
777J HIS* 4.1 19.5 - - + +
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Residues in contact with THR 553 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447I HIS* 3.4 26.7 - - + +
448I LEU* 2.7 35.5 + - - +
551I HIS* 3.0 27.3 + - + -
552I PRO* 1.3 75.8 - - - +
554I HIS* 1.3 62.4 + - - +
555I TYR 3.2 1.6 - - - -
557I ARG* 2.9 35.2 + - - +
608I ALA* 3.8 14.4 - - + +
611I GLU* 5.3 2.0 - - - -
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Residues in contact with HIS 554 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446I ASP 3.8 15.0 - - - -
448I LEU* 3.7 24.3 - - + +
451I ARG* 4.3 8.1 + - - -
549I ASP 4.0 10.4 + - - -
550I VAL* 4.0 13.2 - - + -
551I HIS* 2.6 58.3 + - + +
553I THR* 1.3 72.0 + - - +
555I TYR* 1.3 63.7 + - - +
556I GLY 3.0 2.1 + - - -
557I ARG 3.9 1.6 - - - -
558I VAL* 2.9 46.3 + - + +
559I CYS 5.5 1.8 - - - -
560I PRO* 5.5 0.4 - - + -
573I ASN* 3.7 28.2 + - - -
773J PHE* 4.0 10.4 - - + -
780J ARG* 5.8 0.4 - - - -
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Residues in contact with TYR 555 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552I PRO 3.8 12.5 + - - +
553I THR 3.2 2.8 - - - -
554I HIS* 1.3 74.2 - - - +
556I GLY* 1.3 62.0 + - - +
557I ARG* 2.9 25.9 + - - +
589I THR* 3.9 5.2 - - - +
591I TYR* 3.9 3.8 + + - -
618I GLN* 3.1 10.6 + - - -
637I ARG* 3.2 49.1 - - - +
654I ASP* 3.4 13.1 + - - -
659I GLN* 4.9 9.6 - - + -
660I VAL* 3.7 19.9 - - + +
769J VAL* 3.0 33.5 - - + +
770J LEU* 3.5 20.9 - - + -
773J PHE* 3.7 36.9 - + + -
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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