Contacts of the strand formed by residues 534 - 541 (chain B) in PDB entry 1GGT
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 534 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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524B VAL* 4.1 0.3 - - - -
525B GLU* 3.1 38.6 + - + +
533B PHE* 1.3 81.6 - - - +
535B LEU* 1.3 62.9 + - - +
536B SER* 3.9 9.4 + - - +
586B ALA* 5.7 8.3 - - + -
587B VAL 3.4 15.0 - - - +
588B LEU* 4.0 18.2 - - + -
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Residues in contact with LEU 535 (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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522B PHE* 3.1 40.4 - - + -
523B GLU 3.6 2.9 - - - -
524B VAL* 3.7 16.6 - - + +
533B PHE 4.1 0.4 + - - -
534B LYS* 1.3 73.0 - - - +
536B SER* 1.3 61.8 + - - +
537B ILE* 3.5 5.6 + - + +
553B LEU* 3.8 26.5 - - + -
587B VAL* 3.1 36.6 + - + +
589B ILE* 3.9 26.2 - - + -
606B PHE* 3.8 33.0 - - + -
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Residues in contact with SER 536 (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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522B PHE* 3.0 5.3 - - - +
523B GLU* 2.9 47.7 + - - +
525B GLU* 5.8 1.6 + - - +
534B LYS* 4.7 9.5 + - - +
535B LEU* 1.3 71.0 + - - +
537B ILE* 1.3 59.8 + - - +
584B LYS* 3.3 37.8 + - - -
585B GLU 3.8 5.6 - - - -
586B ALA* 4.5 7.3 - - - +
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Residues in contact with ILE 537 (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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520B MET* 4.9 1.1 - - - -
521B ASP 3.9 8.7 - - - +
522B PHE* 3.6 11.4 - - + -
535B LEU* 4.2 14.4 - - + +
536B SER* 1.3 75.3 - - - +
538B THR* 1.3 67.2 + - - +
539B PHE* 3.4 29.6 - - + -
551B ALA* 5.5 4.0 - - + -
552B TYR 5.7 1.1 - - - +
553B LEU* 4.6 4.9 - - + -
573B PHE* 3.8 37.0 - - + -
583B LYS 4.3 0.2 - - - +
584B LYS* 3.5 1.6 - - - +
585B GLU* 2.8 40.5 + - + +
587B VAL* 4.4 4.9 - - + -
608B VAL* 4.4 26.7 - - + -
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Residues in contact with THR 538 (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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520B MET* 2.7 11.8 - - - -
521B ASP* 2.6 55.6 + - - +
522B PHE 3.6 1.4 + - - -
523B GLU* 3.6 21.2 + - - +
537B ILE* 1.3 82.6 - - - +
539B PHE* 1.3 61.5 + - - +
540B ARG* 4.0 9.0 + - - +
583B LYS 4.2 2.2 - - - -
584B LYS* 4.1 24.2 - - + +
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Residues in contact with PHE 539 (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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518B VAL* 4.4 1.8 - - + -
519B ASP 3.1 7.0 - - - +
520B MET* 3.8 20.4 - - + -
537B ILE* 3.4 26.7 - - + -
538B THR* 1.3 77.3 - - - +
540B ARG* 1.3 61.0 + - - +
541B ASN 3.8 0.7 - - - -
549B ILE* 3.4 42.6 - - + -
551B ALA* 3.6 26.9 - - + -
573B PHE* 6.1 0.7 - + - -
575B VAL* 4.6 22.2 - - + -
577B LEU* 3.4 24.0 - - + -
581B SER 3.9 0.2 - - - +
582B PHE* 3.3 4.0 - - - +
583B LYS 2.9 44.5 + - - +
585B GLU* 4.6 5.8 - - + -
610B ALA* 4.7 4.0 - - + -
619B LEU* 5.5 0.7 - - + -
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Residues in contact with ARG 540 (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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519B ASP* 2.8 63.8 + - + +
520B MET 4.5 1.2 + - - +
521B ASP* 2.7 44.7 + - - +
538B THR* 4.3 8.8 + - - +
539B PHE* 1.3 73.9 - - - +
541B ASN* 1.3 62.5 + - - +
542B ASN* 3.0 22.8 + - - +
577B LEU* 4.0 1.1 - - - -
582B PHE* 4.3 24.5 - - + -
621B LYS* 5.4 2.8 - - - +
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Residues in contact with ASN 541 (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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517B ASN 4.5 3.2 - - - +
518B VAL* 4.9 4.3 - - - +
540B ARG* 1.3 69.7 - - - +
542B ASN* 1.3 58.1 + - - +
543B SER* 2.9 29.3 + - - +
545B ASN 2.8 24.5 + - - -
547B TYR* 4.3 10.7 - - - -
577B LEU* 2.9 45.5 + - + +
578B GLU 2.9 8.4 + - - -
580B LEU* 3.1 22.5 - - - -
581B SER 3.6 18.4 + - - +
582B PHE* 3.2 10.8 - - - -
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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