Contacts of the strand formed by residues 484 - 488 (chain B) in PDB entry 1U5T
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 ILE 484 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436B THR* 6.3 0.4 - - - -
478B VAL 3.4 1.2 - - - +
479B LYS* 3.4 6.0 - - - +
480B VAL* 2.9 55.7 + - + +
481B ASN* 5.2 0.7 - - + -
483B ARG* 1.3 78.6 - - + +
485B LEU* 1.3 63.0 + - - +
486B CYS* 4.0 12.8 - - + -
492B PHE* 3.9 24.5 - - + -
531B ILE* 4.7 7.6 - - + -
534B GLU* 2.7 68.6 - - + +
535B VAL* 4.3 0.7 - - - +
538B ASN* 5.0 11.0 - - - +
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Residues in contact with LEU 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU 3.9 14.8 - - - +
145A GLU* 3.8 29.1 + - + +
436B THR* 3.5 5.4 - - - -
437B LEU* 3.0 39.8 + - + +
438B VAL* 6.0 0.3 - - - +
461B ARG* 3.1 35.0 - - - +
477B LEU* 4.0 13.0 - - + -
478B VAL 3.2 21.3 - - - +
479B LYS* 4.2 5.4 - - + +
483B ARG 3.3 5.6 + - - +
484B ILE* 1.3 75.5 - - - +
486B CYS* 1.3 79.0 + - - +
534B GLU* 6.0 0.8 - - - +
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Residues in contact with CYS 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B ILE* 4.1 24.9 - - + -
435B ILE 2.9 27.1 - - - +
436B THR* 3.9 2.2 - - - -
437B LEU 4.0 2.7 - - - +
477B LEU* 3.4 7.2 - - - -
478B VAL* 2.5 42.1 + - - +
480B VAL* 4.0 23.1 - - - -
484B ILE* 4.0 9.9 - - + -
485B LEU* 1.3 84.6 - - - +
487B VAL* 1.3 55.4 + - - +
488B THR* 4.5 2.0 - - - -
492B PHE* 4.6 0.9 - - - -
531B ILE* 4.8 2.2 - - + -
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Residues in contact with VAL 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B THR* 4.9 1.8 - - + -
433B MET 4.3 0.7 - - - +
434B ILE 4.0 0.2 - - - -
435B ILE* 3.0 35.7 + - + +
437B LEU* 3.7 13.2 - - + -
440B LEU* 3.4 35.2 - - + -
464B CYS* 4.8 4.9 - - + -
467B PHE* 5.2 5.2 - - + -
475B LEU* 4.3 25.6 - - + -
476B LYS 2.7 17.0 - - - +
477B LEU* 3.4 19.7 - - + -
486B CYS* 1.3 70.9 - - - +
488B THR* 1.3 62.3 + - - +
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Residues in contact with THR 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B TYR* 6.0 0.2 - - - +
433B MET 3.5 6.6 - - - -
434B ILE* 2.8 42.0 - - + +
475B LEU* 3.0 29.3 - - - +
476B LYS* 2.7 18.2 + - + +
478B VAL* 4.7 13.9 - - + -
486B CYS* 4.0 4.6 + - - -
487B VAL* 1.3 74.6 - - - +
489B SER* 1.3 63.8 + - - +
490B GLU* 2.8 32.5 + - - +
491B LYS 5.0 2.7 - - - -
492B PHE* 5.1 3.8 - - + +
495B VAL* 4.8 3.3 - - + +
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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