Contacts of the strand formed by residues 606 - 613 (chain A) in PDB entry 1OMW
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 ILE 606 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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588A LEU* 5.8 0.2 - - + -
601A LEU* 3.7 28.5 - - + -
602A THR 3.9 3.8 - - - +
603A MET* 3.2 43.9 + - + +
604A GLU 4.6 0.7 - - - -
605A GLU* 1.3 75.2 - - - +
607A GLN* 1.3 63.7 + - - +
608A SER 3.4 13.2 - - - +
609A VAL* 3.9 2.5 - - + -
622A LEU* 3.8 32.5 - - + -
623A LYS 3.6 4.5 - - - +
624A ILE* 4.4 4.0 - - + -
647A LEU* 5.0 6.1 - - + +
651A TYR* 3.9 23.9 - - + -
655A GLN* 3.2 22.7 + - - -
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Residues in contact with GLN 607 (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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605A GLU 3.3 2.5 + - - +
606A ILE* 1.3 73.6 - - - +
608A SER* 1.3 65.1 + - - +
623A LYS* 2.9 23.3 + - + +
624A ILE 4.1 4.2 - - - +
625A ARG* 3.5 39.4 - - + +
627A GLY* 5.3 0.5 + - - -
651A TYR* 4.2 9.5 + - - -
655A GLN* 5.4 0.2 - - - +
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Residues in contact with SER 608 (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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606A ILE* 3.3 5.6 - - - +
607A GLN* 1.3 84.5 - - - +
609A VAL* 1.3 64.6 + - - +
610A GLU* 4.4 12.4 + - - +
621A LEU* 3.7 0.7 + - - +
622A LEU* 3.5 5.2 - - - +
623A LYS* 2.9 52.0 + - - +
651A TYR* 3.9 11.2 - - - -
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Residues in contact with VAL 609 (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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606A ILE* 3.9 2.9 - - + -
608A SER* 1.3 73.1 + - - +
610A GLU* 1.3 71.4 + - - +
620A LEU* 4.5 16.6 - - + -
621A LEU 3.4 6.3 - - - +
622A LEU* 3.2 32.1 - - + -
644A LYS* 4.8 6.7 - - + -
647A LEU* 4.3 25.6 - - + -
648A ARG* 3.2 39.1 + - + -
651A TYR* 3.7 30.8 + - + -
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Residues in contact with GLU 610 (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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608A SER* 4.1 12.2 + - - +
609A VAL* 1.3 82.3 - - - +
611A GLU* 1.3 79.7 + - - +
620A LEU* 3.5 13.0 - - - +
621A LEU* 2.8 47.2 + - + +
623A LYS* 5.5 5.8 - - - +
644A LYS* 5.5 0.4 - - - -
648A ARG* 4.0 16.8 + - - +
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Residues in contact with GLU 611 (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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610A GLU* 1.3 95.0 - - - +
612A THR* 1.3 60.9 + - - +
618A LYS* 6.3 0.9 - - + -
619A CYS 3.1 12.6 - - - +
620A LEU* 4.4 10.1 - - + -
640A LEU* 5.3 8.5 - - + -
644A LYS* 3.9 22.0 + - + +
648A ARG* 3.7 15.9 + - - -
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Residues in contact with THR 612 (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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610A GLU* 4.3 0.6 + - - -
611A GLU* 1.3 76.2 - - - +
613A GLN* 1.3 65.3 + - - +
614A ILE* 3.7 27.4 - - + -
618A LYS* 5.3 0.7 - - - -
619A CYS* 2.8 34.5 + - + +
621A LEU* 4.1 33.7 - - + +
631A VAL* 5.2 0.9 - - + -
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Residues in contact with GLN 613 (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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612A THR* 1.3 75.6 + - - +
614A ILE* 1.3 64.6 + - - +
615A LYS 4.1 1.1 + - - -
616A GLU* 5.3 6.0 - - - +
617A ARG 3.3 16.4 - - - +
618A LYS* 5.5 10.4 - - + +
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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