Contacts of the strand formed by residues 536 - 542 (chain A) in PDB entry 1EJ9
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 536 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A ASP* 3.0 35.8 + - - +
529A PHE 3.3 9.4 - - - +
530A LEU* 3.5 15.7 - - + -
534A SER 3.4 4.2 + - - -
535A ILE* 1.3 74.6 - - - +
537A TYR* 1.3 70.6 + - - +
538A TYR* 3.9 20.2 + - + +
631A ASN* 3.3 14.5 + - - +
633A GLN* 3.9 15.1 + - - +
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Residues in contact with TYR 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A LEU* 4.1 24.0 + - - +
487A LEU* 4.3 16.2 - - + -
527A PHE* 3.7 25.1 - + + -
528A ASP* 2.9 5.7 - - - -
529A PHE* 2.4 80.8 + + + +
531A GLY* 5.9 0.2 - - - -
535A ILE 4.7 2.5 - - - +
536A ARG* 1.3 74.8 - - - +
538A TYR* 1.3 61.3 + - - +
539A ASN* 3.2 36.1 + - + -
629A LEU 5.8 1.8 - - - -
631A ASN* 4.0 29.6 - - + +
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Residues in contact with TYR 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A GLU* 2.8 38.1 + - + -
527A PHE 3.0 24.5 - - - -
528A ASP* 3.6 21.5 - - + +
536A ARG* 3.9 30.2 + - - +
537A TYR* 1.3 79.8 - - - +
539A ASN* 1.3 70.0 + - - +
540A LYS* 3.2 34.5 + - + +
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Residues in contact with ASN 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A LEU* 4.2 7.1 - - - +
525A VAL 3.1 4.5 - - - +
526A GLU* 4.9 0.4 - - - -
527A PHE* 2.8 44.7 + - - +
537A TYR* 3.2 31.3 + - + +
538A TYR* 1.3 81.5 - - - +
540A LYS* 1.3 71.8 + - - +
541A VAL* 3.1 24.3 - - + +
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Residues in contact with LYS 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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518A LEU* 3.8 23.8 - - + -
519A ASP* 5.0 9.2 - - - +
521A GLN* 5.3 5.6 + - - +
524A VAL* 3.7 13.4 - - + +
525A VAL 3.2 4.5 - - - -
526A GLU* 3.5 27.1 - - + +
538A TYR* 3.2 33.2 + - - +
539A ASN* 1.3 79.1 + - - +
541A VAL* 1.3 62.6 + - - +
542A PRO* 3.7 7.4 - - - +
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Residues in contact with VAL 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A LYS* 3.7 21.5 - - + +
485A LEU* 4.1 14.8 - - + -
524A VAL* 3.6 3.0 - - - +
525A VAL 2.5 40.9 + - - +
527A PHE* 3.9 18.4 - - + -
539A ASN* 3.1 40.8 - - - +
540A LYS* 1.3 75.7 - - - +
542A PRO* 1.3 77.5 - - + +
543A VAL* 3.3 16.0 + - + +
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Residues in contact with PRO 542 (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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484A LYS* 2.8 24.0 + - - +
521A GLN* 3.8 38.4 - - + +
522A GLU 4.1 11.4 - - - +
523A TYR 3.2 8.5 - - - +
524A VAL* 4.0 4.3 - - + -
540A LYS 3.7 8.1 - - - +
541A VAL* 1.3 85.1 - - + +
543A VAL* 1.3 62.3 + - - +
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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