Contacts of the strand formed by residues 608 - 614 (chain N) in PDB entry 2AS5
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 608 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606N GLU* 2.8 16.5 + - - +
607N SER* 1.3 73.9 - - - +
609N VAL* 1.3 65.6 + - - +
625N GLU* 2.6 37.9 + - + +
628N VAL* 4.5 7.6 - - + -
660N VAL* 3.3 4.5 - - - +
661N ILE* 2.8 54.1 + - + +
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Residues in contact with VAL 609 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598N LEU* 4.4 4.3 - - + -
608N LYS* 1.3 74.3 - - - +
610N VAL* 1.3 76.9 + - - +
611N PHE* 3.9 27.1 - - + -
625N GLU* 3.6 16.3 - - - +
626N ALA* 3.6 12.5 + - + +
628N VAL* 3.5 28.6 - - + +
638N LEU* 3.7 14.1 - - + -
640N VAL* 3.6 19.3 - - + -
658N PHE* 4.4 9.4 - - + -
659N TYR 3.3 14.6 - - - +
660N VAL* 4.0 11.7 - - + -
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Residues in contact with VAL 610 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608N LYS* 5.1 0.4 - - + -
609N VAL* 1.3 84.2 - - - +
611N PHE* 1.3 79.0 - - - +
612N THR* 3.7 13.7 - - + -
623N GLU* 4.2 14.8 - - + -
624N MET 3.4 10.5 - - - +
625N GLU* 4.3 15.3 - - + +
626N ALA 4.6 0.4 - - - +
658N PHE* 3.1 22.5 - - - +
659N TYR* 3.1 32.1 + - + +
661N ILE* 3.7 28.0 - - + -
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Residues in contact with PHE 611 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596N MET* 4.1 17.0 - - + -
609N VAL* 3.9 9.0 - - + -
610N VAL* 1.3 81.3 - - - +
612N THR* 1.3 72.9 + - - +
622N TRP* 4.3 12.3 - - + -
624N MET* 2.8 26.5 + - + +
626N ALA* 3.6 31.2 - - + -
640N VAL* 5.1 2.5 - - + -
642N ILE* 4.9 8.1 - - + -
643N PRO* 3.8 18.6 - - + -
656N VAL* 3.4 21.3 - - + -
657N ASN 3.3 3.6 - - - -
658N PHE* 3.8 26.2 - + + -
673N PHE* 3.7 30.7 - + - -
675N TYR* 4.0 13.2 - - - -
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Residues in contact with THR 612 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610N VAL* 3.7 15.9 - - + -
611N PHE* 1.3 87.3 - - - +
613N GLU* 1.3 63.6 + - - +
620N GLN* 4.0 19.1 - - - +
622N TRP* 3.2 20.8 - - - +
623N GLU* 4.2 6.7 - - - +
656N VAL* 3.5 7.3 - - - +
657N ASN* 2.7 46.9 + - - +
659N TYR* 4.1 19.1 - - + -
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Residues in contact with GLU 613 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612N THR* 1.3 76.8 - - - +
614N LYS* 1.3 71.4 + - - +
620N GLN* 3.5 6.4 - - - +
621N ILE* 3.0 38.8 + - + +
622N TRP* 3.2 24.0 + - + +
645N TYR* 2.8 40.9 + - - -
646N ARG* 3.3 15.1 + - - -
654N VAL* 4.4 11.1 - - - +
655N LYS 3.9 21.3 - - - +
656N VAL* 4.5 2.7 - - + +
657N ASN* 5.2 2.5 - - - +
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Residues in contact with LYS 614 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613N GLU* 1.3 83.6 - - - +
615N THR* 1.3 76.4 + - - +
616N THR* 5.8 1.2 - - - +
618N GLY* 4.0 18.5 - - - +
619N GLN 3.4 17.7 - - - +
620N GLN* 3.9 7.6 - - + -
621N ILE* 4.1 7.2 - - - -
655N LYS 5.4 1.3 + - - +
657N ASN* 4.3 22.4 - - - +
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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