Contacts of the strand formed by residues 505 - 511 (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 LYS 505 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B ALA* 3.7 19.3 - - + +
502B ASP* 3.2 42.8 + - - +
503B LEU* 3.3 12.2 + - - +
504B ILE* 1.3 75.1 - - - +
506B PRO* 1.3 78.6 - - + +
544B LYS 4.1 3.4 + - - -
545B TYR* 3.4 17.8 - - + +
546B VAL* 3.0 19.8 + - - -
625B PHE* 6.3 0.7 - - + -
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Residues in contact with PRO 506 (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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59B ALA* 3.6 22.0 - - + +
60B ILE* 4.0 25.8 - - + +
63B MET* 3.9 31.0 - - + -
504B ILE 4.6 0.7 - - - +
505B LYS* 1.3 94.1 - - + +
507B ALA* 1.3 60.2 + - - +
546B VAL* 3.7 13.7 - - + +
548B MET* 4.0 7.9 - - + -
622B ASP 5.0 0.4 - - - +
623B ALA* 4.0 18.3 - - - +
625B PHE* 3.8 18.4 - - - +
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Residues in contact with ALA 507 (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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506B PRO* 1.3 76.6 - - - +
508B LEU* 1.3 62.4 + - - +
509B PHE 3.6 0.9 + - - -
545B TYR* 3.6 35.2 - - + -
546B VAL 3.2 6.8 + - - +
547B LEU* 3.7 6.5 - - + +
548B MET* 2.9 30.0 + - - +
623B ALA* 4.4 0.2 - - - -
625B PHE* 3.5 20.2 - - + -
627B ILE* 4.3 10.3 - - + -
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Residues in contact with LEU 508 (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* 1.3 71.4 - - - +
509B PHE* 1.3 53.9 + - - +
510B ILE* 3.7 30.3 - - + -
548B MET* 3.1 26.2 - - + +
550B THR* 3.4 18.8 - - - +
616B LEU* 4.0 9.9 - - + +
619B LEU* 3.9 32.8 - - + +
620B ALA* 4.0 11.0 - - + +
623B ALA* 4.0 12.3 - - + +
625B PHE 2.9 13.8 + - - +
626B VAL* 3.3 14.6 - - + +
627B ILE* 2.6 35.1 + - - +
647B LEU* 4.9 1.1 - - + -
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Residues in contact with PHE 509 (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 3.6 0.6 + - - -
508B LEU* 1.3 70.7 - - - +
510B ILE* 1.3 63.5 + - - +
511B VAL* 3.5 29.2 - - + -
520B ILE* 3.7 17.0 - - + -
547B LEU* 4.1 29.2 - - + -
548B MET 3.0 7.2 + - - +
549B VAL* 3.3 21.9 - - + +
550B THR 3.0 25.5 + - - +
627B ILE* 3.2 30.5 - - + -
629B GLY* 4.5 5.6 - - - -
656B ALA* 4.5 4.5 - - + -
658B PHE* 3.8 25.4 - + - -
666B ILE* 4.5 15.3 - - + -
669B ALA* 6.3 1.1 - - + -
670B LEU* 4.3 16.2 - - + -
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Residues in contact with ILE 510 (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* 3.7 30.5 - - + -
509B PHE* 1.3 75.4 - - - +
511B VAL* 1.3 73.9 + - - +
550B THR* 3.5 7.9 - - - +
552B SER* 4.2 13.5 - - - +
616B LEU* 3.5 28.9 - - + -
626B VAL* 3.9 14.8 - - + -
627B ILE 2.8 11.8 + - - +
628B VAL* 3.6 6.1 - - + +
629B GLY* 2.7 29.9 + - - -
630B THR* 3.8 2.6 + - + +
643B LEU* 4.0 32.3 - - + -
647B LEU* 4.4 8.3 - - + -
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Residues in contact with VAL 511 (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* 3.5 27.8 - - + -
510B ILE* 1.3 75.8 - - - +
512B GLU* 1.3 66.2 + - - +
513B SER 4.0 5.2 - - - +
516B LYS* 3.8 14.4 - - + +
517B ALA* 3.8 35.2 - - + +
520B ILE* 4.0 12.6 - - + -
549B VAL* 4.7 2.7 - - + -
550B THR 2.9 14.6 + - - +
551B ALA* 3.2 2.6 - - - -
552B SER* 2.9 25.4 + - - -
629B GLY 3.4 22.4 - - - +
630B THR* 4.5 2.7 - - - -
658B PHE* 4.4 0.2 - - + -
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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