Contacts of the strand formed by residues 499 - 504 (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 SER 499 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D LEU* 4.5 1.6 - - - -
490D PRO* 3.3 22.2 - - - +
491D GLN* 4.9 1.2 + - - -
497D PRO* 2.7 38.3 + - - +
498D GLN* 1.3 75.1 - - - +
500D GLU* 1.3 72.5 + - - +
501D CYS* 4.3 2.7 - - - -
522D ARG* 4.3 7.2 + - - +
523D LEU* 3.0 26.2 - - - +
525D LEU 5.9 0.4 - - - -
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Residues in contact with GLU 500 (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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499D SER* 1.3 74.8 - - - +
501D CYS* 1.3 63.5 + - - +
502D TRP* 3.1 45.6 - - + -
517D VAL* 5.6 0.4 - - + -
522D ARG* 3.3 47.1 + - + +
523D LEU 2.8 11.7 + - - +
524D SER* 3.2 6.3 - - - -
525D LEU 2.9 23.4 + - - -
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Residues in contact with CYS 501 (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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487D THR* 3.3 40.6 - - - +
490D PRO* 3.6 29.8 - - - -
491D GLN* 4.1 7.2 - - - +
499D SER* 4.9 2.7 - - - -
500D GLU* 1.3 80.3 + - - +
502D TRP* 1.3 74.5 + - - +
525D LEU* 3.3 17.0 - - - +
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Residues in contact with TRP 502 (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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487D THR* 3.5 10.1 - - - +
500D GLU* 3.1 68.2 - - + -
501D CYS* 1.3 79.5 + - - +
503D ARG* 1.3 62.9 + - - +
504D VAL* 4.0 3.6 - - + -
513D VAL* 3.4 44.0 - - + +
516D LYS* 4.5 21.4 - - + +
517D VAL* 3.7 28.3 - - + -
524D SER* 4.1 2.9 - - - -
525D LEU 3.0 11.2 + - - +
526D ILE* 3.6 7.7 - - + -
527D GLU 2.8 26.5 + - - -
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Residues in contact with ARG 503 (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* 5.1 6.7 - - - +
485D ASN* 3.4 27.3 - - - +
487D THR* 4.1 11.1 + - + +
488D HIS* 5.6 1.8 - - - -
502D TRP* 1.3 75.8 - - - +
504D VAL* 1.3 62.3 + - - +
505D SER* 4.2 1.8 + - - -
509D GLN* 4.4 10.0 + - - +
527D GLU* 3.4 33.8 + - - +
529D MET* 4.0 31.2 - - + +
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Residues in contact with VAL 504 (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* 3.3 22.3 - - + +
502D TRP* 4.0 2.7 - - + -
503D ARG* 1.3 77.5 - - - +
505D SER* 1.3 64.1 + - - +
506D GLU 3.4 4.3 - - - +
509D GLN* 3.8 16.8 - - + -
510D LEU* 3.4 33.4 - - + +
513D VAL* 3.9 21.1 - - + -
526D ILE* 4.2 18.8 - - + -
527D GLU 2.8 13.5 + - - +
528D VAL* 4.8 2.5 - - + -
529D MET* 2.9 31.2 + - - +
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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