Contacts of the strand formed by residues 523 - 529 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445A LEU* 4.2 8.1 - - + -
448A MET* 4.1 18.8 - - + -
449A LEU* 3.6 20.6 - - + -
453A GLN 3.6 21.1 - - - +
454A HIS* 3.6 6.0 + - - +
455A PRO* 3.7 30.3 - - + +
457A ILE* 4.2 17.0 - - + -
490A PRO* 5.1 3.6 - - + -
498A GLN 3.1 8.0 + - - +
499A SER* 2.9 36.8 - - - -
500A GLU 2.9 8.0 + - - -
522A ARG* 1.3 71.9 - - - +
524A SER* 1.3 77.1 + - - +
525A LEU* 4.0 8.7 - - + +
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Residues in contact with SER 524 (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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455A PRO 3.0 7.0 + - - +
456A ILE* 3.3 26.8 - - - +
457A ILE* 2.8 29.3 + - - +
500A GLU* 3.1 12.3 - - - -
502A TRP* 4.1 4.5 - - - -
517A VAL* 3.6 32.6 - - - +
520A HIS* 5.9 0.9 - - - -
522A ARG 3.3 5.3 + - - -
523A LEU* 1.3 78.6 - - - +
525A LEU* 1.3 60.0 + - - +
526A ILE* 4.1 1.6 - - - -
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Residues in contact with LEU 525 (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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445A LEU* 4.4 15.0 - - + -
457A ILE* 3.4 27.1 - - + +
459A VAL* 3.5 28.7 - - + -
486A TRP* 3.5 34.5 - - + +
487A THR* 5.0 1.4 - - + +
489A ILE* 4.9 1.1 - - + -
490A PRO* 4.0 20.0 - - + -
500A GLU 2.9 8.9 + - - -
501A CYS* 3.1 18.7 - - + +
502A TRP* 3.0 24.6 + - - +
523A LEU* 4.0 9.1 - - + +
524A SER* 1.3 73.2 - - - +
526A ILE* 1.3 65.7 + - - +
527A GLU 5.1 1.1 - - - +
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Residues in contact with ILE 526 (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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456A ILE* 3.4 30.5 - - + -
457A ILE 2.8 11.6 + - - +
458A LEU* 3.4 8.4 - - + -
459A VAL 2.9 26.6 + - - -
502A TRP* 3.5 14.8 - - + +
504A VAL* 4.3 20.2 - - + -
510A LEU* 5.1 5.2 - - + -
513A VAL* 3.2 31.6 - - + -
514A LEU* 4.1 14.1 - - + -
517A VAL* 4.5 5.4 - - + -
524A SER 4.9 0.9 - - - -
525A LEU* 1.3 80.8 - - - +
527A GLU* 1.3 61.7 + - - +
528A VAL* 3.4 19.4 + - + +
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Residues in contact with GLU 527 (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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459A VAL* 3.8 8.1 - - + +
461A ASN* 2.8 33.6 + - + +
484A TRP 4.3 3.8 - - - +
485A ASN* 4.9 0.5 + - - -
486A TRP* 3.1 32.5 + - + +
487A THR* 3.7 19.1 + - + +
502A TRP 2.8 15.2 + - - +
503A ARG* 3.3 31.1 + - + +
504A VAL* 2.7 34.3 + - - +
525A LEU* 4.0 2.1 + - + +
526A ILE* 1.3 69.6 - - - +
528A VAL* 1.3 57.2 + - - +
529A MET* 3.6 21.8 + - - +
495B LEU* 6.1 0.2 - - - +
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Residues in contact with VAL 528 (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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360A LEU* 3.8 24.0 - - + -
365A PHE* 3.8 35.2 - - + -
458A LEU* 4.3 11.7 - - + -
459A VAL 2.8 16.1 + - - +
460A LEU* 3.6 7.2 - - + -
461A ASN* 2.7 30.0 + - - -
504A VAL* 3.8 6.7 - - + -
510A LEU* 5.2 2.5 - - + -
526A ILE* 3.8 24.2 - - + +
527A GLU* 1.3 72.7 - - - +
529A MET* 1.3 60.6 + - - +
530A LEU* 3.4 16.1 + - + +
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Residues in contact with MET 529 (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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360A LEU* 3.8 17.5 - - - +
461A ASN* 3.5 25.8 - - - +
463A GLU* 5.9 4.5 - - + +
503A ARG* 3.9 31.0 - - + +
504A VAL 2.9 21.2 + - - +
505A SER* 4.4 14.2 - - - +
527A GLU* 3.7 28.5 - - - +
528A VAL* 1.3 70.2 - - - +
530A LEU* 1.3 67.8 + - - +
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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