Contacts of the strand formed by residues 509 - 514 (chain D) in PDB entry 2UZX
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 LYS 509 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D ASN* 3.9 21.1 - - + +
46D PHE 3.5 9.4 - - - +
47D THR* 3.8 18.2 - - + +
52D ILE* 4.8 1.1 - - - -
481D LEU* 3.8 19.2 - - - +
482D ASP* 3.9 29.9 - - - +
504D VAL 4.3 0.2 - - - -
505D ILE* 3.2 7.3 - - - +
506D THR* 2.7 43.9 + - - +
507D GLY 3.2 1.4 - - - -
508D LYS* 1.3 80.0 - - - +
510D ILE* 1.3 61.6 + - - +
511D THR* 3.2 28.3 + - - +
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Residues in contact with ILE 510 (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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45D ASN* 3.2 2.3 - - - -
46D PHE* 2.8 58.9 + - + +
52D ILE* 5.3 4.5 - - + -
55D VAL* 3.7 32.5 - - + -
62D ILE* 5.1 2.5 - - + -
64D LEU* 4.2 14.6 - - + -
73D LEU* 4.2 12.6 - - + -
78D LEU* 3.7 4.9 - - + +
503D LEU* 3.8 31.0 - - + -
504D VAL 3.1 14.8 - - - +
505D ILE* 4.0 10.8 - - + -
509D LYS* 1.3 76.4 - - - +
511D THR* 1.3 64.9 - - - +
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Residues in contact with THR 511 (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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43D LEU* 3.6 28.0 - - + -
44D PRO 3.4 12.6 - - - +
45D ASN* 3.7 5.0 - - + +
78D LEU* 4.2 2.5 - - - -
481D LEU* 3.8 18.8 - - + +
502D THR 3.0 5.5 - - - +
503D LEU* 3.2 3.4 - - - -
504D VAL 2.8 36.6 + - - -
506D THR* 5.0 0.7 + - - -
509D LYS* 3.2 32.2 + - - +
510D ILE* 1.3 72.6 - - - +
512D LYS* 1.3 62.9 + - - +
513D ILE* 3.8 13.1 + - + +
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Residues in contact with LYS 512 (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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43D LEU* 2.9 26.3 - - - +
44D PRO* 2.8 36.7 + - + +
75D GLU* 3.0 29.9 + - - +
76D GLU* 3.3 17.3 + - - +
78D LEU* 3.8 15.4 - - + +
501D TYR* 3.5 55.5 - - + -
502D THR 3.4 2.7 - - - -
503D LEU* 4.0 5.6 - - + -
511D THR* 1.3 70.9 - - - +
513D ILE* 1.3 58.9 + - - +
514D PRO* 4.3 1.0 - - - +
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Residues in contact with ILE 513 (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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43D LEU* 3.3 16.4 - - + -
462D PHE* 3.6 58.8 - - + -
464D GLN* 4.1 1.6 - - - +
479D PHE* 4.6 8.1 - - + -
481D LEU* 4.5 11.2 - - + -
501D TYR* 3.1 3.5 - - - -
502D THR* 2.8 48.8 + - - +
504D VAL* 4.3 8.3 - - + -
511D THR* 4.0 11.9 - - + +
512D LYS* 1.3 74.8 - - - +
514D PRO* 1.3 81.8 - - + +
518D LEU* 4.5 10.8 - - + -
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Residues in contact with PRO 514 (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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43D LEU* 3.6 17.3 - - + -
464D GLN* 3.3 18.2 + - - -
500D GLY 3.9 9.2 - - - +
501D TYR* 4.3 2.2 - - + -
512D LYS 4.3 1.1 - - - +
513D ILE* 1.3 97.0 - - + +
515D LEU* 1.3 59.4 + - - +
516D ASN* 3.2 8.5 + - + +
517D GLY* 3.7 13.3 + - - +
518D LEU* 3.6 19.3 - - + -
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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