Contacts of the strand formed by residues 523 - 529 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445D LEU* 3.6 22.9 - - + -
448D MET* 4.6 4.9 - - + -
449D LEU* 2.7 35.0 - - + -
453D GLN 3.6 12.3 - - - +
454D HIS* 3.5 5.4 + - - +
455D PRO* 3.0 48.5 - - + +
457D ILE* 3.9 13.9 - - + -
490D PRO* 5.2 4.5 - - + -
498D GLN 3.1 13.7 + - - +
499D SER* 3.0 11.1 - - - -
500D GLU 2.8 25.3 + - - -
522D ARG* 1.3 73.3 - - - +
524D SER* 1.3 61.9 + - - +
525D LEU* 4.2 2.2 - - + +
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Residues in contact with SER 524 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455D PRO 3.1 6.3 + - - +
456D ILE* 3.3 27.3 - - - +
457D ILE* 2.8 29.8 + - - +
500D GLU* 3.2 11.9 - - - -
502D TRP* 4.1 4.5 - - - -
517D VAL* 3.9 30.4 - - - +
520D HIS* 5.8 1.8 - - - +
522D ARG* 3.2 7.5 + - - -
523D LEU* 1.3 77.6 - - - +
525D LEU* 1.3 60.8 + - - +
526D ILE* 4.1 2.2 + - - -
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Residues in contact with LEU 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445D LEU* 4.4 14.4 - - + -
457D ILE* 3.3 31.4 - - + +
459D VAL* 3.5 27.6 - - + -
486D TRP* 3.5 33.2 - - + +
487D THR* 5.1 1.7 - - + +
489D ILE* 4.8 3.6 - - + -
490D PRO* 4.0 21.8 - - + -
499D SER* 5.9 0.4 - - - -
500D GLU 2.9 8.3 + - - +
501D CYS* 3.3 17.6 - - + +
502D TRP* 3.0 26.2 + - - +
523D LEU* 4.2 3.7 + - + +
524D SER* 1.3 73.5 - - - +
526D ILE* 1.3 64.5 + - - +
527D GLU* 5.1 1.1 - - - +
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Residues in contact with ILE 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456D ILE* 3.4 30.5 - - + -
457D ILE 2.8 11.6 + - - +
458D LEU* 3.4 9.4 - - + -
459D VAL 2.9 25.8 + - - -
502D TRP* 3.6 11.9 - - + +
504D VAL* 4.2 23.6 - - + -
510D LEU* 4.5 7.4 - - + -
513D VAL* 4.0 26.0 - - + -
514D LEU* 4.3 16.8 - - + -
517D VAL* 4.6 5.6 - - + -
524D SER* 4.9 1.6 - - - +
525D LEU* 1.3 79.5 - - - +
527D GLU* 1.3 63.6 + - - +
528D VAL* 3.3 19.8 + - + +
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Residues in contact with GLU 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495C LEU* 6.0 0.3 - - - +
459D VAL* 3.8 8.3 - - - +
461D ASN* 2.8 31.9 + - + +
484D TRP 4.3 3.6 - - - +
485D ASN* 5.3 0.3 - - - -
486D TRP* 3.1 31.4 + - + +
487D THR* 3.6 20.1 + - + +
502D TRP 2.8 16.3 + - - +
503D ARG* 3.4 29.3 + - + +
504D VAL 2.8 33.3 + - - +
525D LEU* 4.0 2.5 + - + +
526D ILE* 1.3 69.6 - - - +
528D VAL* 1.3 56.3 + - - +
529D MET* 3.7 21.9 + - - +
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Residues in contact with VAL 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D LEU* 3.8 24.0 - - + -
365D PHE* 3.8 35.0 - - + -
458D LEU* 4.4 11.0 - - + -
459D VAL 2.9 12.9 + - - +
460D LEU* 3.6 7.8 - - + -
461D ASN* 2.8 29.0 + - - -
504D VAL* 3.8 4.5 - - + -
510D LEU* 4.7 5.4 - - + -
526D ILE* 3.7 27.1 - - + +
527D GLU* 1.3 70.1 - - - +
529D MET* 1.3 60.4 + - - +
530D LEU* 3.4 16.1 + - + +
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Residues in contact with MET 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D LEU* 3.7 17.5 - - - +
461D ASN* 3.5 33.0 - - - +
463D GLU* 5.8 5.2 - - + +
503D ARG* 4.0 27.1 - - + +
504D VAL 2.9 23.2 + - - +
505D SER* 4.3 14.8 - - - +
527D GLU* 3.7 19.3 - - - +
528D VAL* 1.3 70.0 - - - +
530D LEU* 1.3 68.0 + - - +
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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