Contacts of the strand formed by residues 667 - 674 (chain B) in PDB entry 5MJ6
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 LYS 667 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659B VAL* 4.2 17.0 - - + +
660B THR 3.1 12.8 - - - +
661B GLU* 4.2 14.1 - - + +
665B TYR 3.4 3.6 + - - -
666B SER* 1.3 79.0 - - - +
668B TYR* 1.3 61.7 + - - +
669B GLN* 2.8 34.2 + - - -
689B TRP* 5.9 2.2 - - + -
722B VAL 5.3 8.5 - - - +
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Residues in contact with TYR 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658B TYR* 4.0 18.3 + + - -
659B VAL* 3.4 2.3 - - - +
660B THR* 2.7 48.6 + - + +
666B SER* 4.1 4.0 + - - +
667B LYS* 1.3 75.9 - - - +
669B GLN* 1.3 72.9 + - - +
670B SER* 3.5 31.5 + - - -
682B ASN 6.1 0.2 - - - -
683B LEU* 5.6 4.5 - - + -
684B THR* 4.9 26.9 - - + +
685B GLU* 5.1 12.1 - - + +
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Residues in contact with GLN 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658B TYR 3.2 13.0 - - - +
659B VAL* 4.0 7.0 - - + +
667B LYS* 2.8 33.8 + - - +
668B TYR* 1.3 90.1 - - - +
670B SER* 1.3 65.0 + - - +
694B ILE* 3.5 30.6 - - + +
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Residues in contact with SER 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B SER* 3.3 6.2 - - - -
658B TYR* 3.0 55.2 + - - +
668B TYR* 3.5 24.0 + - - -
669B GLN* 1.3 78.6 - - - +
671B VAL* 1.3 80.3 + - - +
694B ILE* 4.8 1.4 - - - +
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Residues in contact with VAL 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562B TYR* 3.7 36.8 - - + -
656B LEU 3.2 14.4 - - - +
657B SER* 4.5 3.1 - - - -
658B TYR* 4.4 4.6 + - - -
670B SER* 1.3 94.3 + - - +
672B SER* 1.3 71.7 + - - +
1128B BR 4.0 20.4 - - + -
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Residues in contact with SER 672 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630B ILE* 4.7 2.9 - - - +
656B LEU* 2.9 36.1 + - - +
658B TYR* 4.5 2.9 - - - -
671B VAL* 1.3 81.5 - - - +
673B LEU* 1.3 63.0 + - - +
681B ILE* 3.1 38.1 - - - +
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Residues in contact with LEU 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562B TYR* 3.8 28.0 + - + +
601B LEU* 5.4 7.0 - - + -
606B MET* 4.4 20.6 - - + -
653B HIS* 4.0 12.1 - - + +
654B ILE 3.3 32.5 - - - +
655B PRO* 3.8 7.9 - - + -
671B VAL* 4.8 0.8 - - - +
672B SER* 1.3 74.6 - - - +
674B LEU* 1.3 62.3 + - - +
675B ASP* 3.9 20.0 + - + +
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Residues in contact with LEU 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619B VAL* 5.2 3.6 - - + -
630B ILE* 4.3 18.6 - - + +
631B GLN 4.5 4.7 - - - +
632B GLN* 4.0 32.1 - - + +
652B TRP 3.3 6.9 - - - +
654B ILE* 2.8 45.6 + - + +
656B LEU* 3.4 24.0 - - + -
672B SER 3.8 0.6 + - - -
673B LEU* 1.3 71.0 - - - +
675B ASP* 1.3 59.9 + - - +
676B LYS* 3.3 26.0 - - + +
678B SER 3.7 25.8 - - - +
679B GLY* 3.9 8.3 - - - +
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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