Contacts of the strand formed by residues 523 - 529 (chain B) in PDB entry 1OVM
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 LEU 523 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445B LEU* 4.2 6.7 - - + -
448B MET* 4.1 17.0 - - + -
449B LEU* 3.7 21.8 - - + -
453B GLN 3.5 16.4 - - - +
454B HIS* 3.5 5.8 + - - +
455B PRO* 3.7 32.8 - - + -
457B ILE* 3.9 21.3 - - + -
490B PRO* 5.3 2.9 - - + -
498B GLN 3.1 12.5 + - - +
499B SER* 3.0 15.6 - - - -
500B GLU* 2.9 23.4 + - - +
522B ARG* 1.3 73.4 - - - +
524B SER* 1.3 77.4 + - - +
525B LEU* 4.0 7.4 - - + +
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Residues in contact with SER 524 (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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455B PRO 3.0 6.3 + - - +
456B ILE* 3.4 26.2 - - - +
457B ILE* 2.8 27.4 + - - +
500B GLU* 3.2 11.9 - - - -
502B TRP* 4.4 5.2 - - - -
517B VAL* 3.8 31.6 - - - +
520B HIS* 5.8 1.4 - - - -
522B ARG* 3.2 6.1 + - - -
523B LEU* 1.3 81.0 - - - +
525B LEU* 1.3 61.2 + - - +
526B ILE* 4.9 1.6 - - - -
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Residues in contact with LEU 525 (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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445B LEU* 4.5 13.9 - - + -
457B ILE* 3.4 35.2 - - + +
459B VAL* 3.6 20.4 - - + -
486B TRP* 3.5 36.1 - - + +
487B THR* 4.9 1.5 - - + +
489B ILE* 4.9 1.6 - - + -
490B PRO* 4.0 17.9 - - + -
500B GLU 2.9 8.9 + - - -
501B CYS* 3.1 17.4 - - + +
502B TRP* 2.9 25.1 + - - +
523B LEU* 4.0 9.6 - - + +
524B SER* 1.3 72.3 - - - +
526B ILE* 1.3 64.3 + - - +
527B GLU 5.1 1.6 - - - +
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Residues in contact with ILE 526 (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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456B ILE* 3.4 30.7 - - + -
457B ILE 2.8 11.7 + - - +
458B LEU* 3.4 9.0 - - + -
459B VAL 2.9 26.3 + - - -
502B TRP* 3.4 13.7 - - + +
504B VAL* 4.2 20.6 - - + -
510B LEU* 4.4 8.5 - - + -
513B VAL* 3.5 29.2 - - + -
514B LEU* 4.0 14.6 - - + -
517B VAL* 4.6 3.6 - - + -
524B SER* 4.9 1.3 - - - +
525B LEU* 1.3 79.8 - - - +
527B GLU* 1.3 61.5 + - - +
528B VAL* 3.4 19.2 + - + +
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Residues in contact with GLU 527 (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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459B VAL* 3.8 7.6 - - + +
461B ASN* 2.8 32.7 + - + -
484B TRP 4.4 2.9 - - - +
485B ASN* 4.9 2.6 + - - -
486B TRP* 3.0 31.9 + - + +
487B THR* 3.8 15.0 + - + +
502B TRP 2.6 15.9 + - - +
503B ARG* 3.2 36.6 + - + +
504B VAL 2.8 30.5 + - - +
525B LEU* 4.0 2.5 + - + +
526B ILE* 1.3 70.3 - - - +
528B VAL* 1.3 58.8 + - - +
529B MET* 3.7 12.7 + - - +
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Residues in contact with VAL 528 (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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360B LEU* 3.7 24.5 - - + -
365B PHE* 3.8 35.7 - - + -
458B LEU* 4.4 8.7 - - + -
459B VAL 2.8 15.0 + - - +
460B LEU* 3.7 9.9 - - + -
461B ASN* 2.8 27.1 + - - -
504B VAL* 3.7 3.8 - - + -
510B LEU* 5.0 4.9 - - + -
526B ILE* 3.8 25.1 - - + +
527B GLU* 1.3 72.1 - - - +
529B MET* 1.3 63.1 + - - +
530B LEU* 3.4 15.0 + - + +
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Residues in contact with MET 529 (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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360B LEU* 3.7 18.4 - - - +
461B ASN* 3.5 34.1 - - - +
463B GLU* 5.9 4.9 - - + +
503B ARG* 4.0 24.0 - - + -
504B VAL 3.0 18.6 + - - +
505B SER* 4.1 15.7 - - - -
527B GLU* 3.8 18.8 - - - +
528B VAL* 1.3 69.4 - - - +
530B LEU* 1.3 68.9 + - - +
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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