Contacts of the strand formed by residues 534 - 541 (chain A) in PDB entry 4X61
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 ARG 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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519A PHE* 3.3 37.4 - - + +
520A THR 2.7 32.5 + - - +
521A PHE* 3.4 25.8 - - + +
531A ASP 3.0 27.1 + - - -
532A ASN* 3.5 20.7 + - - +
533A ASN* 1.3 78.5 + - - +
535A TYR* 1.3 64.5 + - - +
603A TRP* 3.4 5.9 - - - +
604A ARG* 2.9 35.6 + - + +
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Residues in contact with TYR 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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519A PHE* 4.3 0.7 - - - -
534A ARG* 1.3 77.1 - - - +
536A CYS* 1.3 62.6 + - - +
537A THR* 3.8 17.0 + - - -
601A ARG* 3.2 36.6 + - + -
602A PHE 3.4 7.9 - - - -
603A TRP* 3.0 48.8 - + + -
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Residues in contact with CYS 536 (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 PRO 4.4 1.1 - - - -
518A CYS* 3.7 26.9 - - - +
519A PHE* 3.5 22.4 - - + -
535A TYR* 1.3 77.5 - - - +
537A THR* 1.3 66.7 + - - +
538A LEU* 3.7 33.7 - - - +
600A VAL 4.0 0.3 - - - +
601A ARG* 3.4 4.7 - - - +
602A PHE* 3.0 32.8 + - - +
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Residues in contact with THR 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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535A TYR* 3.8 9.5 + - - -
536A CYS* 1.3 77.3 - - - +
538A LEU* 1.3 72.5 + - - +
539A GLU* 5.2 6.0 - - + +
599A CYS* 3.7 25.8 - - - -
600A VAL 3.6 2.5 - - - -
601A ARG* 3.5 35.7 + - - +
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Residues in contact with LEU 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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472A LEU* 3.9 32.3 - - + -
516A GLN* 4.0 20.4 - - + +
517A PRO 3.4 26.0 - - - +
518A CYS* 4.6 1.6 - - + -
536A CYS* 3.7 17.5 - - - +
537A THR* 1.3 81.2 - - - +
539A GLU* 1.3 64.2 + - - +
540A PHE* 3.8 31.9 - - + -
598A ILE 3.8 0.7 - - - +
599A CYS* 3.2 7.8 - - - -
600A VAL* 2.9 38.9 + - + +
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Residues in contact with GLU 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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516A GLN* 2.9 23.6 + - - +
537A THR* 5.2 5.2 - - + +
538A LEU* 1.3 78.6 - - - +
540A PHE* 1.3 62.5 + - - +
541A PRO* 3.5 6.7 - - - +
597A THR* 3.8 21.4 - - + +
598A ILE 3.6 3.8 - - - -
599A CYS* 4.5 16.0 - - - +
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Residues in contact with PHE 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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472A LEU* 3.2 33.2 - - + -
474A PRO* 3.4 31.9 - - + -
513A SER* 3.6 15.3 - - - +
514A ALA 3.3 20.2 - - - -
516A GLN* 3.4 20.9 - - + -
538A LEU* 3.8 31.6 - - + -
539A GLU* 1.3 72.5 - - - +
541A PRO* 1.3 66.5 - - - +
542A VAL* 3.4 4.1 + - + +
551A PHE* 4.1 10.8 - + - -
597A THR* 3.4 5.2 - - - +
598A ILE* 2.7 47.4 + - + +
600A VAL* 3.8 16.8 - - + -
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Residues in contact with PRO 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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512A LEU 3.8 1.7 - - - +
513A SER* 2.9 28.3 + - - +
516A GLN* 4.2 6.5 - - - +
539A GLU 3.5 9.9 - - - +
540A PHE* 1.3 79.8 - - - +
542A VAL* 1.3 59.8 + - - +
543A GLU* 4.2 14.7 + - - +
596A GLN 4.1 3.4 - - - +
597A THR* 4.7 8.5 - - + +
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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