Contacts of the strand formed by residues 545 - 549 (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 LEU 545 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500B VAL* 4.1 20.0 - - + -
503B ILE* 3.2 33.2 - - + -
536B LEU* 4.0 7.6 - - + -
539B CYS* 3.3 26.4 + - + -
540B VAL* 4.1 15.7 - - + +
543B GLY* 3.5 2.8 - - - -
544B ASP 1.3 102.9 + - - +
546B LEU* 1.3 62.0 + - - +
547B ILE* 3.4 8.4 - - - +
556B TYR* 3.4 23.3 - - + -
557B TYR 3.2 16.8 - - - +
558B LYS* 4.1 7.6 - - - -
559B ASN* 3.8 7.1 - - - +
17D GLN* 3.2 10.0 + - - -
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Residues in contact with LEU 546 (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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545B LEU* 1.3 73.6 - - - +
547B ILE* 1.3 62.5 + - - +
556B TYR* 3.8 3.0 - - - -
557B TYR* 3.0 37.1 + - + +
558B LYS 4.5 0.4 - - - +
559B ASN* 2.9 50.9 - - + +
561B TYR* 4.9 3.1 - - + -
562B TRP* 3.5 33.4 - - + -
10D PHE* 3.0 38.1 - - + -
12D PRO* 3.6 14.6 - - + +
17D GLN* 2.7 17.9 - - + +
22D THR* 4.2 2.2 - - + -
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Residues in contact with ILE 547 (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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540B VAL* 3.6 35.4 - - + +
545B LEU 3.4 12.6 - - - +
546B LEU* 1.3 74.4 - - - +
548B ASP* 1.3 63.9 + - - +
549B LYS* 3.7 32.5 - - + +
554B ILE* 3.5 23.1 - - + -
555B TYR 3.8 4.7 - - - -
556B TYR* 5.2 2.0 - - + +
12D PRO* 3.0 12.1 - - - +
15D THR* 2.9 7.6 + - - +
16D ARG* 6.2 0.2 - - - +
17D GLN* 2.5 50.0 - - - +
18D PRO* 3.3 24.5 - - + -
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Residues in contact with ASP 548 (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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547B ILE* 1.3 74.4 - - - +
549B LYS* 1.3 60.4 + - - +
550B GLN* 3.2 9.2 + - - +
553B GLY 4.1 0.3 - - - +
555B TYR* 3.0 49.9 + - + +
557B TYR* 4.3 7.4 + - + -
11D PRO* 3.6 20.8 - - - +
12D PRO* 4.0 14.4 - - + -
14D TYR* 5.8 0.3 - - - +
15D THR* 3.5 11.8 - - - +
83D ARG* 2.5 36.5 + - - -
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Residues in contact with LYS 549 (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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163A ASN* 5.6 3.4 - - - +
204A GLU* 3.0 31.9 + - + +
207A ALA* 4.0 17.0 - - + -
208A ASN* 3.7 22.2 + - - +
537B GLN* 5.2 9.7 - - - +
547B ILE* 3.7 19.7 - - + +
548B ASP* 1.3 70.1 - - - +
550B GLN* 1.3 65.4 + - - +
553B GLY 4.1 2.9 - - - -
554B ILE* 3.1 33.1 - - + +
15D THR* 2.9 24.7 - - + +
16D ARG* 4.1 14.7 - - - +
18D PRO* 5.9 4.8 - - - +
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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