Contacts of the strand formed by residues 534 - 541 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523A GLU 4.6 0.2 - - - +
524A VAL* 4.1 3.1 - - - +
525A GLU* 2.9 59.9 + - - +
533A PHE* 1.3 78.0 - - - +
535A LEU* 1.3 68.3 + - - +
536A SER* 5.2 4.9 - - - +
586A ALA* 5.0 13.5 - - + -
587A VAL 2.9 18.2 - - - +
588A LEU* 3.7 27.1 - - + +
589A ILE 4.3 0.9 - - - +
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Residues in contact with LEU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A PHE* 3.8 31.2 - - + -
523A GLU 3.7 7.4 - - - +
524A VAL* 4.1 13.2 - - + -
533A PHE* 5.0 2.7 - - + -
534A LYS* 1.3 77.0 - - - +
536A SER* 1.3 61.7 + - - +
537A ILE* 4.0 4.7 - - + -
553A LEU* 4.2 18.2 - - + -
586A ALA* 3.0 5.7 - - - +
587A VAL* 2.6 52.5 + - + +
589A ILE* 3.3 39.9 - - + -
606A PHE* 3.9 24.2 - - + -
608A VAL* 5.0 1.1 - - + -
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Residues in contact with SER 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A PHE* 3.2 1.7 - - - -
523A GLU* 3.1 55.3 + - - +
534A LYS* 5.2 5.5 - - - +
535A LEU* 1.3 75.5 + - - +
537A ILE* 1.3 62.4 + - - +
538A THR* 4.8 5.6 - - - -
584A LYS* 5.0 10.8 - - - -
585A GLU 3.2 6.3 - - - -
586A ALA* 4.5 8.6 - - - +
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Residues in contact with ILE 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A MET* 3.9 24.2 - - + -
521A ASP 3.2 13.9 - - - +
522A PHE* 3.7 15.0 - - + -
535A LEU* 4.2 4.5 - - + +
536A SER* 1.3 73.4 - - - +
538A THR* 1.3 59.3 + - - +
539A PHE* 3.9 25.2 + - + -
553A LEU* 5.3 2.2 - - + -
573A PHE* 3.9 15.3 - - + -
583A LYS 3.6 0.9 - - - +
584A LYS* 2.9 4.9 - - - -
585A GLU* 2.7 58.3 + - + +
587A VAL* 3.7 26.7 - - + -
608A VAL* 4.6 14.8 - - + -
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Residues in contact with THR 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A MET* 3.3 2.1 - - - -
521A ASP* 2.6 35.6 + - - +
523A GLU* 3.5 25.4 + - - +
536A SER 3.5 3.1 + - - +
537A ILE* 1.3 73.8 - - - +
539A PHE* 1.3 61.3 + - - +
540A ARG* 2.6 33.8 + - - -
582A PHE* 3.5 14.8 - - + -
583A LYS 3.1 3.6 - - - -
584A LYS* 3.3 37.9 - - + -
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Residues in contact with PHE 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A VAL* 5.0 1.3 - - + -
519A ASP 3.2 5.4 - - - +
520A MET* 4.0 26.2 - - + +
537A ILE* 4.0 26.5 - - + -
538A THR* 1.3 75.2 - - - +
540A ARG* 1.3 60.2 + - - +
541A ASN 4.3 0.4 - - - -
549A ILE* 4.1 16.4 - - + -
551A ALA* 3.6 32.8 - - + -
573A PHE* 4.4 4.7 - + - -
575A VAL* 4.2 24.2 - - + -
577A LEU* 4.2 18.7 - - + +
582A PHE* 3.5 1.7 - - - -
583A LYS* 2.7 41.8 + - + +
585A GLU* 3.7 25.1 - - + -
610A ALA* 4.2 10.3 - - + -
619A LEU* 5.4 2.0 - - + -
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Residues in contact with ARG 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A ASN 3.9 0.2 - - - +
518A VAL* 3.7 1.1 - - - +
519A ASP* 2.6 68.4 + - + +
520A MET 4.4 1.2 + - - -
521A ASP* 3.3 27.5 + - - +
538A THR* 2.6 44.5 + - - -
539A PHE* 1.3 74.7 - - - +
541A ASN* 1.3 63.6 + - - +
542A ASN* 3.3 12.5 + - - +
577A LEU* 4.2 3.1 - - - +
581A SER 3.5 6.3 - - - +
582A PHE* 3.6 36.4 - - + -
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Residues in contact with ASN 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517A ASN 4.2 4.7 - - - +
518A VAL* 4.8 1.9 - - - +
540A ARG* 1.3 69.1 - - - +
542A ASN* 1.3 61.6 + - - +
543A SER* 2.8 29.6 + - - -
545A ASN 2.5 30.3 + - - -
547A TYR* 3.6 13.9 - - - -
577A LEU* 2.9 32.0 + - + +
578A GLU 2.7 21.7 + - - +
580A LEU* 3.6 5.5 - - - -
581A SER 2.9 29.9 + - - +
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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