Contacts of the strand formed by residues 497 - 503 (chain D) in PDB entry 5U03
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 497 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405D ALA* 6.3 0.9 - - + -
406D VAL* 4.2 19.7 - - + -
409D PHE* 3.8 39.0 - - + -
492D LEU* 3.4 44.6 - - + +
493D GLU* 5.3 0.7 - - - +
495D GLN* 3.1 2.8 - - - +
496D GLY* 1.3 76.0 - - - +
498D LYS* 1.3 61.2 + - - +
499D PHE* 3.9 18.5 + - + -
512D VAL* 3.5 25.6 - - + -
513D GLU 4.4 0.2 - - - -
514D LEU* 3.7 26.5 - - + +
520D PHE* 5.1 9.2 - - + -
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Residues in contact with LYS 498 (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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492D LEU 5.3 0.2 - - - +
493D GLU* 2.9 34.0 + - - +
494D GLU* 4.5 2.8 - - - +
495D GLN 2.9 21.8 + - - +
496D GLY* 4.2 5.2 - - - +
497D LEU* 1.3 74.9 - - - +
499D PHE* 1.4 62.8 + - - +
500D VAL* 3.7 7.1 + - + +
512D VAL* 3.2 5.0 - - - +
513D GLU 2.8 40.1 + - - +
515D GLU* 3.5 31.6 - - + +
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Residues in contact with PHE 499 (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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402D MET* 4.6 2.5 - - + -
406D VAL* 4.4 9.0 - - + -
458D GLN* 3.2 19.7 + - - +
459D THR* 5.7 0.9 - - - +
484D VAL* 3.9 29.8 - - + -
489D LYS* 4.0 15.3 - - + -
492D LEU* 3.7 41.1 - - + -
493D GLU* 3.9 19.6 + - - +
497D LEU* 4.1 18.8 - - + -
498D LYS* 1.4 73.7 - - - +
500D VAL* 1.3 60.9 + - - +
509D MET* 3.6 38.1 - - + -
511D ILE 3.5 4.3 - - - +
512D VAL* 4.0 21.3 - - + -
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Residues in contact with VAL 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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457D PHE* 3.6 18.3 - - + -
458D GLN* 2.7 36.1 + - - +
459D THR* 4.4 16.2 - - + -
461D ASN 5.1 1.3 - - - +
462D SER* 3.4 31.2 - - - +
498D LYS* 4.1 13.2 - - + +
499D PHE* 1.3 75.5 - - - +
501D GLY* 1.3 58.3 + - - +
511D ILE* 2.8 22.7 + - + +
513D GLU* 3.8 29.6 - - + +
515D GLU* 5.8 0.9 - - - +
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Residues in contact with GLY 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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455D THR* 4.0 6.5 - - - -
456D LEU 3.5 7.0 - - - -
457D PHE* 4.8 0.4 - - - -
458D GLN* 3.4 7.3 + - - -
500D VAL* 1.3 78.7 - - - +
502D GLN* 1.4 61.1 + - - -
509D MET* 3.5 6.1 - - - +
510D GLU 2.8 23.3 + - - -
511D ILE* 3.1 31.7 + - - +
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Residues in contact with GLN 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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455D THR* 3.2 9.0 - - - +
456D LEU* 2.7 50.4 + - + +
457D PHE 5.3 2.0 + - - -
458D GLN* 3.3 32.8 + - + +
501D GLY* 1.4 75.6 - - - +
503D ASP* 1.3 68.9 + - - +
504D VAL 5.3 0.8 + - - -
506D GLY* 3.6 27.2 - - - +
508D ARG 3.2 5.8 - - - +
509D MET* 3.6 18.2 - - + +
510D GLU* 4.2 2.9 - - - +
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Residues in contact with ASP 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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449D ARG* 3.8 21.8 - - - +
454D ARG 4.2 7.4 - - - -
455D THR* 4.8 0.9 - - - +
456D LEU* 4.3 1.3 - - - +
502D GLN* 1.3 85.7 + - - +
504D VAL* 1.3 58.7 + - - +
505D GLU* 2.9 17.7 + - - +
506D GLY* 2.5 44.9 + - - -
507D GLU* 2.8 9.3 + - - +
508D ARG* 2.8 57.9 + - + +
510D GLU* 4.4 5.2 - - + +
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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