Contacts of the strand formed by residues 545 - 551 (chain B) in PDB entry 1GKU
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 TYR 545 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503B LEU 5.7 0.7 - - - -
504B ILE* 3.4 10.1 - - - -
505B LYS* 3.4 25.6 - - + +
507B ALA* 3.6 23.8 - - + -
542B MET* 2.8 34.6 + - - +
544B LYS* 1.3 101.5 - - + +
546B VAL* 1.3 63.5 + - - +
547B LEU* 3.3 11.9 + - + -
625B PHE* 3.4 36.8 - + - -
627B ILE* 4.0 13.0 - - + -
670B LEU* 4.1 26.6 + - + -
673B LEU* 3.9 10.9 - - + +
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Residues in contact with VAL 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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60B ILE* 4.5 17.9 - - + -
63B MET* 5.9 6.5 - - + -
77B THR 5.7 0.4 - - - +
78B ALA* 6.5 0.2 - - - -
79B PRO* 4.4 11.4 - - + -
504B ILE* 3.3 29.8 - - + +
505B LYS 3.0 10.6 + - - +
506B PRO* 3.7 8.4 - - + +
507B ALA 3.2 20.8 + - - -
539B GLU* 5.1 11.7 - - + +
540B ILE 4.6 2.2 - - - +
541B PRO* 3.8 30.7 - - + -
545B TYR* 1.3 72.6 - - - +
547B LEU* 1.3 62.2 + - - +
548B MET* 3.6 8.3 + - + +
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Residues in contact with LEU 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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507B ALA* 3.7 7.6 - - + +
509B PHE* 4.1 30.5 - - + -
520B ILE* 5.2 4.9 - - + -
524B PHE* 3.4 37.7 - - + -
538B TYR 3.3 5.4 - - - +
539B GLU* 3.3 2.9 - - - +
540B ILE* 2.9 37.3 + - + +
542B MET* 3.9 20.0 - - + -
545B TYR* 3.3 22.8 + - + +
546B VAL* 1.3 72.3 - - - +
548B MET* 1.3 61.2 - - - +
549B VAL* 3.6 17.9 - - + -
627B ILE* 5.3 0.7 - - + -
666B ILE* 5.6 1.1 - - + -
670B LEU* 5.0 8.3 - - + -
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Residues in contact with MET 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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63B MET* 3.8 29.8 - - - +
67B ARG* 4.4 12.8 - - - -
506B PRO* 4.0 10.3 - - + -
507B ALA 2.9 17.3 + - - +
508B LEU* 3.1 20.8 - - + +
509B PHE 3.0 19.7 + - - -
537B VAL* 3.8 13.0 - - + -
538B TYR 3.6 4.5 - - - -
539B GLU* 3.8 17.9 - - + +
546B VAL* 4.3 7.6 - - + +
547B LEU* 1.3 72.6 - - - +
549B VAL* 1.3 59.7 + - - +
619B LEU* 4.4 20.6 - - + +
622B ASP* 5.3 1.6 - - + -
623B ALA* 3.5 33.2 - - + +
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Residues in contact with VAL 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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509B PHE* 3.3 29.4 - - + +
511B VAL* 4.7 1.6 - - + -
517B ALA* 3.5 38.4 - - + +
520B ILE* 4.8 11.2 - - + -
521B SER* 4.6 11.9 - - - -
537B VAL* 3.4 2.9 - - - +
538B TYR* 2.9 49.4 + - + +
540B ILE* 5.6 0.7 - - + -
547B LEU* 4.0 27.6 - - + -
548B MET* 1.3 70.9 - - - +
550B THR* 1.3 69.4 + - - +
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Residues in contact with THR 550 (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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508B LEU* 3.4 24.4 - - - +
509B PHE 3.0 7.0 + - - -
510B ILE* 3.5 4.7 - - - -
511B VAL* 2.9 32.8 + - - +
517B ALA* 4.2 4.7 - - - -
535B ALA* 4.5 10.8 - - + -
536B VAL 2.7 34.5 - - - +
537B VAL* 3.8 9.6 - - + +
548B MET 3.7 0.7 + - - -
549B VAL* 1.3 77.1 + - - +
551B ALA* 1.3 75.1 + - - +
612B ARG* 4.8 0.9 - - - +
616B LEU* 4.9 11.2 - - + -
619B LEU* 4.3 7.2 - - + +
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Residues in contact with ALA 551 (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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510B ILE* 4.8 2.2 - - - -
511B VAL* 3.2 6.1 - - - -
512B GLU 4.0 1.1 - - - +
513B SER* 3.6 36.3 - - - +
514B PRO* 3.6 14.6 - - + -
517B ALA* 4.3 3.2 - - + +
536B VAL 4.5 1.4 + - - -
550B THR* 1.3 82.5 - - - +
552B SER* 1.3 53.4 + - - +
553B ILE* 4.1 7.6 - - + -
612B ARG* 2.6 36.1 + - - +
616B LEU* 5.3 1.6 - - - +
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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