Contacts of the helix formed by residues 549 - 560 (chain A) in PDB entry 6T8O
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 549 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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542A MET* 3.4 9.7 - - - +
547A VAL* 3.2 20.9 - - - +
548A ARG* 1.3 81.6 - - - +
550A LEU* 1.3 63.6 + - - +
551A ALA* 3.8 14.7 - - - +
552A GLY* 2.6 31.6 + - - +
553A PHE 3.5 0.5 + - - -
555A ARG* 5.3 0.3 + - - -
621A ALA* 3.7 26.0 - - + -
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Residues in contact with LEU 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A ARG* 5.2 0.4 - - - +
542A MET* 4.6 3.6 - - - -
549A ASN* 1.3 75.0 - - - +
551A ALA* 1.3 60.8 + - - +
553A PHE* 2.8 27.9 + - + +
554A ASN* 2.9 30.4 + - - +
587A LEU* 4.1 26.0 - - + +
589A THR* 3.3 30.3 - - + +
620A ARG 5.0 2.5 - - - +
621A ALA* 3.3 20.0 + - - +
622A ALA 3.7 15.9 - - - +
623A GLY* 3.7 19.5 - - - +
625A HIS* 5.2 4.5 - - + -
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Residues in contact with ALA 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ASN* 3.4 14.1 + - - +
550A LEU* 1.3 78.4 - - - +
552A GLY* 1.3 57.2 + - - +
554A ASN* 3.7 10.4 - - - +
555A ARG* 2.9 38.4 + - - +
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Residues in contact with GLY 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A VAL* 3.5 13.0 - - - -
548A ARG 5.4 1.1 - - - -
549A ASN* 2.6 23.3 + - - -
551A ALA* 1.3 74.3 - - - +
553A PHE* 1.3 55.8 + - - +
555A ARG* 3.2 22.5 + - - +
556A LYS* 2.9 29.1 + - - +
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Residues in contact with PHE 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A LEU* 3.6 33.0 - - + -
542A MET* 4.5 14.6 - - + -
545A MET* 4.2 13.5 - - + -
547A VAL* 3.3 28.4 - - + +
549A ASN 4.0 3.6 - - - +
550A LEU* 2.8 17.4 + - + +
552A GLY* 1.3 73.9 - - - +
554A ASN* 1.3 62.9 + - - +
556A LYS* 3.2 12.6 + - + +
557A VAL* 2.9 33.1 + - + +
584A LEU* 3.9 20.9 - - + -
585A SER 4.3 11.2 - - - -
587A LEU* 3.6 39.5 - - + -
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Residues in contact with ASN 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491A GLU* 6.1 2.8 - - - +
550A LEU* 2.9 40.3 + - - +
551A ALA* 3.8 10.7 - - - +
552A GLY 3.3 0.2 - - - -
553A PHE* 1.3 76.2 - - - +
555A ARG* 1.3 59.3 + - - +
557A VAL* 3.2 19.6 + - + +
558A LYS* 2.9 35.4 + - - +
586A THR* 4.8 10.3 - - - +
587A LEU 4.3 14.6 + - - +
589A THR* 5.2 1.4 + - - -
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Residues in contact with ARG 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A ASN* 5.3 0.8 + - - -
551A ALA* 2.9 19.9 + - - +
552A GLY* 3.2 26.8 + - - +
554A ASN* 1.3 76.6 - - - +
556A LYS* 1.3 57.8 + - + +
558A LYS* 3.2 17.5 + - + +
559A ASP* 2.9 39.8 + - - +
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Residues in contact with LYS 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A MET* 3.9 30.4 + - + +
547A VAL* 4.0 23.6 - - + -
552A GLY 2.9 18.7 + - - +
553A PHE* 3.2 19.9 + - + +
555A ARG* 1.3 74.8 - - + +
557A VAL* 1.3 58.8 + - - +
559A ASP* 3.1 25.4 + - - +
560A ALA* 2.9 25.6 + - - +
567A LEU* 3.9 16.8 - - + +
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Residues in contact with VAL 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A PHE* 2.9 28.6 + - + +
554A ASN* 3.2 20.2 + - - +
556A LYS* 1.3 77.0 - - - +
558A LYS* 1.3 58.8 + - + +
560A ALA* 3.0 30.3 + - + +
562A GLU* 3.5 11.6 + - + +
584A LEU* 5.0 3.6 - - + +
585A SER 3.8 22.7 - - - +
586A THR* 3.7 32.5 - - + +
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Residues in contact with LYS 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A LYS* 4.6 21.4 - - - +
554A ASN* 2.9 22.3 + - - +
555A ARG* 3.2 20.2 + - + +
557A VAL* 1.3 77.4 - - + +
559A ASP* 1.3 61.5 + - - +
562A GLU* 3.8 20.8 - - + +
563A ALA* 3.3 28.6 + - - +
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Residues in contact with ASP 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A ARG* 2.9 27.4 + - - +
556A LYS* 3.1 38.4 + - + +
558A LYS* 1.3 73.8 - - - +
560A ALA* 1.3 63.5 + - - +
563A ALA* 4.7 4.4 - - - +
565A THR* 3.4 18.9 - - - +
567A LEU* 5.0 7.8 - - + +
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Residues in contact with ALA 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A LYS 2.9 12.4 + - - +
557A VAL* 3.0 17.8 + - + +
558A LYS 3.4 0.3 - - - +
559A ASP* 1.3 79.6 - - - +
561A GLU* 1.3 57.3 + - + +
562A GLU 2.8 17.9 + - - -
563A ALA* 2.9 14.6 + - - -
564A GLY 3.6 3.3 + - - -
565A THR 3.3 14.2 + - - +
567A LEU* 3.8 23.8 - - + +
584A LEU 4.7 11.9 - - - +
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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