Contacts of the strand formed by residues 533 - 538 (chain A) in PDB entry 1HMU
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 ALA 533 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513A LYS* 4.5 2.2 - - - +
514A ALA* 2.6 43.9 + - - +
529A PHE* 3.9 21.3 - - + -
532A GLY* 1.3 77.5 - - - +
534A ASN* 1.3 60.8 + - - +
535A LEU* 3.2 11.4 + - + -
567A ILE* 4.1 22.0 - - + -
578A TYR* 6.5 0.2 - - - -
579A ALA 5.6 0.7 - - - +
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Residues in contact with ASN 534 (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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511A THR* 5.9 0.7 - - - -
512A PHE 4.0 5.2 - - - -
513A LYS* 3.4 34.6 - - - +
533A ALA* 1.3 70.3 - - - +
535A LEU* 1.3 60.0 + - - +
567A ILE* 3.3 7.3 - - - +
568A ASN* 2.8 61.1 + - + +
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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
----------------------------------------------------------
488A LEU* 4.7 0.2 - - + -
510A THR 4.6 0.2 - - - -
511A THR* 3.3 7.7 - - - +
512A PHE* 2.9 53.4 + - + +
514A ALA* 3.5 24.5 - - + -
518A PHE* 3.8 14.1 - - + -
520A LEU* 4.6 4.9 - - + -
529A PHE* 3.5 46.9 - - + -
533A ALA* 3.2 8.5 + - + +
534A ASN* 1.3 73.9 - - - +
536A SER* 1.3 60.9 + - - +
537A LEU 4.3 0.2 - - - -
565A LEU* 4.0 14.1 - - + -
566A TRP 3.5 14.6 - - - +
567A ILE* 3.9 13.2 - - + -
568A ASN* 4.0 0.9 - - - -
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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
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509A ILE* 5.7 1.8 - - - -
510A THR 3.5 5.4 - - - -
511A THR* 2.9 20.0 + - - +
535A LEU* 1.3 70.8 + - - +
537A LEU* 1.3 60.6 + - - +
565A LEU* 3.4 7.0 - - - +
566A TRP* 3.0 68.8 + - - -
568A ASN* 2.9 22.2 + - - -
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Residues in contact with LEU 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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497A VAL* 3.9 18.6 - - + -
504A THR* 3.8 31.9 - - + +
508A LYS 3.8 0.7 - - - +
509A ILE* 3.2 6.4 - - - +
510A THR* 2.8 53.3 + - + +
512A PHE* 4.7 8.7 - - + -
520A LEU* 4.4 13.2 - - + -
535A LEU 4.3 0.2 - - - -
536A SER* 1.3 74.5 - - - +
538A SER* 1.3 70.3 + - - +
539A THR* 4.5 4.5 - - + -
563A PHE* 3.6 34.5 - - + -
564A LYS 3.7 6.3 - - - +
565A LEU* 4.2 15.3 - - + -
566A TRP* 5.0 0.2 - - - -
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Residues in contact with SER 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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508A LYS 3.3 4.7 - - - -
509A ILE* 4.6 2.7 - - - -
537A LEU* 1.3 78.3 - - - +
539A THR* 1.3 68.9 + - - +
540A GLN* 3.4 32.3 + - - +
542A GLN* 4.8 2.4 + - - -
562A VAL 3.2 3.1 + - - +
563A PHE* 3.6 1.0 - - - -
564A LYS* 2.8 55.9 + - - +
566A TRP* 4.1 16.8 - - - -
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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