Contacts of the strand formed by residues 618 - 624 (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 LYS 618 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A HIS* 6.0 1.6 - - - -
611A GLU* 6.3 0.9 - - + -
612A THR 4.5 1.3 - - - -
613A GLN* 5.2 10.5 - - + +
617A ARG* 1.3 76.3 + - - +
619A CYS* 1.3 61.6 - - - +
633A GLN* 4.1 6.9 - - - +
634A CYS 5.1 0.9 + - - +
637A ASP* 4.9 22.3 + - - +
640A LEU* 3.4 38.7 - - + +
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Residues in contact with CYS 619 (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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576A TRP* 5.0 1.8 - - + -
611A GLU* 3.1 10.2 - - - +
612A THR* 2.8 37.2 + - + +
614A ILE* 4.0 22.4 - - + -
617A ARG* 3.2 17.5 - - - -
618A LYS* 1.3 79.3 - - - +
620A LEU* 1.3 67.1 + - - +
631A VAL* 5.6 0.4 - - + -
632A LEU 3.4 14.4 - - - +
633A GLN* 2.8 34.8 - - + -
640A LEU* 4.3 3.3 - - - +
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Residues in contact with LEU 620 (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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565A MET* 4.2 12.6 - - + -
609A VAL* 4.5 8.7 - - + -
610A GLU 3.6 13.7 - - - +
611A GLU* 4.4 8.5 - - + -
612A THR* 5.2 0.7 - - - -
619A CYS* 1.3 77.6 - - - +
621A LEU* 1.3 59.7 + - - +
622A LEU* 3.9 2.3 + - + +
631A VAL* 3.4 12.0 - - - +
632A LEU* 3.0 40.9 + - + +
640A LEU* 4.4 20.6 - - + +
643A TRP* 4.1 15.0 - - + -
644A LYS* 3.7 46.4 - - + +
647A LEU* 4.4 13.2 - - + -
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Residues in contact with LEU 621 (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* 3.7 1.3 + - - +
609A VAL* 3.4 6.8 - - - +
610A GLU* 2.8 50.1 + - + +
612A THR* 4.1 27.1 - - + +
619A CYS 3.8 1.8 + - - -
620A LEU* 1.3 73.2 - - - +
622A LEU* 1.3 63.1 + - - +
623A LYS* 4.1 32.1 - - + +
629A GLN* 3.9 32.3 - - + +
631A VAL* 4.2 15.7 - - + -
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Residues in contact with LEU 622 (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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588A LEU* 4.8 2.7 - - + -
601A LEU* 4.1 18.2 - - + -
606A ILE* 3.8 18.2 - - + -
608A SER 3.6 4.9 - - - +
609A VAL* 3.2 42.0 - - + -
620A LEU* 5.2 2.2 - - + +
621A LEU* 1.3 74.6 - - - +
623A LYS* 1.3 65.8 + - - +
624A ILE* 3.6 5.6 + - + +
629A GLN* 3.8 1.0 - - - -
630A PHE* 2.9 68.3 + - + +
632A LEU* 4.3 11.0 - - + -
647A LEU* 4.2 18.8 - - + -
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Residues in contact with LYS 623 (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* 3.6 3.5 - - - +
607A GLN* 2.9 36.4 + - + +
608A SER* 2.9 37.7 + - - +
610A GLU* 5.5 6.6 - - + +
621A LEU* 3.9 23.7 - - + +
622A LEU* 1.3 73.7 - - - +
624A ILE* 1.3 57.0 + - - +
628A LYS 4.2 2.7 - - - -
629A GLN* 4.0 30.7 - - + +
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Residues in contact with ILE 624 (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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601A LEU* 3.2 33.4 - - + -
605A GLU* 3.2 34.5 - - + +
606A ILE* 4.4 7.9 - - + -
607A GLN* 4.1 10.0 - - - +
622A LEU* 3.9 3.6 - - + +
623A LYS* 1.3 78.0 - - - +
625A ARG* 1.3 71.4 + - + +
626A GLY 4.2 5.2 - - - +
627A GLY* 3.1 15.5 + - - -
628A LYS* 2.9 36.7 + - + +
629A GLN 5.1 0.2 - - - -
630A PHE* 3.8 27.4 - - + +
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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