Contacts of the strand formed by residues 537 - 543 (chain A) in PDB entry 1EUQ
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 VAL 537 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A GLU* 3.9 25.1 - - + +
470A ARG* 3.6 27.8 - - + +
526A LEU* 2.9 11.9 - - - +
527A ASP* 2.6 57.5 + - + +
530A HIS* 4.2 10.8 - - + +
531A SER* 2.9 27.7 - - - +
535A LYS* 3.4 17.3 - - + +
536A PRO* 1.3 72.8 - - - +
538A PHE* 1.3 55.1 + - - +
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Residues in contact with PHE 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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465A LEU* 5.6 0.2 - - + -
467A VAL* 3.2 27.6 - - + -
468A GLU 3.3 9.6 + - - +
469A ILE* 3.6 8.0 - - + +
470A ARG 3.1 23.0 + - - -
507A LEU* 3.5 38.1 - - + -
510A ALA* 3.7 18.8 - - + -
516A PHE* 4.0 12.1 - + - -
518A PHE* 2.9 42.2 - + + -
524A PHE* 4.1 7.8 - - + -
525A CYS 2.9 14.6 - - - +
526A LEU* 3.8 15.3 - - + -
536A PRO* 4.0 9.6 - - + -
537A VAL* 1.3 78.7 - - - +
539A ASN* 1.3 63.0 + - - +
540A ARG 3.9 0.3 + - - -
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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
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288A PRO* 4.1 5.5 - - - +
298A ARG 3.3 18.5 + - - +
299A ARG* 4.4 4.5 - - - +
470A ARG* 3.8 6.3 - - - +
472A TYR* 2.7 38.4 + - + -
524A PHE* 3.0 8.1 - - - +
525A CYS* 2.4 47.3 + - - -
527A ASP* 2.6 46.5 + - - +
537A VAL 4.0 0.8 + - - -
538A PHE* 1.3 71.8 - - - +
540A ARG* 1.3 60.2 + - - +
541A THR 3.4 0.2 + - - -
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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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299A ARG* 3.0 16.4 + - - +
470A ARG 3.1 17.9 + - - +
471A LEU* 3.3 41.9 - - + +
472A TYR* 3.1 34.7 + - - +
473A ASP* 5.4 2.6 - - - +
497A VAL* 5.2 2.0 - - - +
521A GLU* 5.0 5.6 + - - -
523A TYR 3.6 5.6 - - - +
524A PHE* 3.5 33.3 - - + -
539A ASN* 1.3 71.7 - - - +
541A THR* 1.3 65.7 + - - +
542A VAL* 3.9 13.6 - - - +
543A GLY* 3.9 23.7 - - - +
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Residues in contact with THR 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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299A ARG* 2.5 56.2 + - - +
300A GLY* 3.3 28.8 + - - +
301A TYR* 4.6 10.3 + - + -
331A ILE* 3.7 24.9 - - + -
335A LEU* 4.5 2.9 - - + -
515A ALA* 4.9 2.3 - - - +
523A TYR* 2.9 19.7 + - - -
524A PHE 4.5 1.0 - - - -
525A CYS* 3.7 11.1 + - - +
539A ASN 3.4 2.6 + - - -
540A ARG* 1.3 70.1 - - - +
542A VAL* 1.3 64.8 + - + +
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Residues in contact with VAL 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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299A ARG* 5.2 1.3 - - - +
301A TYR* 5.0 3.4 - - - +
328A GLU* 4.4 24.7 - - + +
331A ILE* 3.5 28.7 - - + -
332A ARG* 3.5 34.5 - - + +
522A GLY* 3.6 0.2 - - - -
523A TYR* 2.9 36.5 + - + +
540A ARG* 3.9 6.7 - - - +
541A THR* 1.3 85.5 - - + +
543A GLY* 1.3 69.8 + - - +
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Residues in contact with GLY 543 (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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332A ARG* 2.6 37.4 + - - +
521A GLU 3.8 11.9 - - - -
522A GLY* 4.0 1.8 - - - -
523A TYR* 4.6 1.3 - - - -
540A ARG* 3.9 17.5 - - - +
542A VAL* 1.3 83.6 - - - +
544A LEU* 1.3 58.1 + - - -
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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