Contacts of the strand formed by residues 538 - 544 (chain A) in PDB entry 3HR4
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 538 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536A ARG 3.7 4.2 + - - +
537A VAL* 1.3 84.4 - - - +
539A VAL* 1.3 63.7 + - - +
540A THR* 5.6 1.3 - - - +
566A ASN* 3.6 29.1 - - - +
582A GLU* 4.4 19.6 + - - -
583A GLU* 6.2 0.2 - - - +
584A ARG* 3.9 19.9 + - + +
585A LEU 4.4 2.1 + - - -
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Residues in contact with VAL 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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537A VAL* 3.6 3.6 - - + +
538A ARG* 1.3 81.8 - - - +
540A THR* 1.3 68.6 + - - +
541A ILE* 4.5 6.3 - - + -
561A PHE* 4.3 7.4 - - + -
565A PHE* 3.5 37.9 - - + -
566A ASN 3.3 6.6 + - - +
567A PRO* 3.3 12.2 - - + +
568A LYS* 2.9 28.9 + - - +
583A GLU* 6.2 0.2 - - - -
585A LEU* 3.7 36.6 - - + +
587A LEU* 4.1 19.1 - - + -
684A PHE* 6.2 0.2 - - + -
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Residues in contact with THR 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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538A ARG* 5.6 1.6 - - - +
539A VAL* 1.3 73.1 - - - +
541A ILE* 1.3 58.6 + - - +
542A LEU* 4.0 17.3 - - + -
568A LYS* 3.8 8.8 - - + +
570A VAL* 4.8 8.7 - - + -
575A TYR* 4.0 17.9 - - + -
583A GLU* 3.0 41.1 + - - +
585A LEU 3.1 8.9 + - - -
586A LEU* 3.5 5.5 - - + +
587A LEU* 2.8 33.4 + - - +
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Residues in contact with ILE 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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539A VAL* 4.5 8.7 - - + -
540A THR* 1.3 76.0 - - - +
542A LEU* 1.3 61.5 + - - +
543A PHE 4.1 0.2 + - - -
554A ALA* 3.9 29.8 - - + +
557A LEU* 3.8 26.9 - - + +
558A GLY* 3.6 37.0 - - - +
561A PHE* 5.0 1.8 - - + -
567A PRO* 4.3 11.9 - - + -
568A LYS 2.8 16.6 + - - +
569A VAL* 3.4 8.7 - - + +
570A VAL 2.7 32.4 + - - -
587A LEU* 3.3 17.7 - - + +
589A VAL* 4.7 3.4 - - + -
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Residues in contact with LEU 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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540A THR* 4.0 9.2 - - + -
541A ILE* 1.3 73.1 - - - +
543A PHE* 1.3 61.3 + - - +
570A VAL* 3.1 20.6 - - + +
571A CYS 4.5 1.8 - - - +
572A MET* 4.5 7.9 - - + -
575A TYR* 3.5 48.5 - - + -
586A LEU* 3.7 28.5 - - + -
587A LEU 2.7 13.1 + - - +
588A VAL* 3.4 15.9 - - + +
589A VAL* 2.8 28.8 + - - +
605A LEU* 3.9 24.2 - - + -
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Residues in contact with PHE 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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542A LEU* 1.3 75.4 - - - +
544A ALA* 1.3 61.3 + - - +
545A THR* 3.8 16.2 - - + -
550A SER 4.3 2.5 - - - +
551A GLU* 3.3 57.9 - - + -
554A ALA* 3.7 17.9 - - + -
555A TRP* 4.2 11.2 - + - -
569A VAL* 3.9 14.4 - - + -
570A VAL 3.3 8.7 + - - -
571A CYS* 3.4 44.4 - - + -
572A MET* 2.8 27.7 + - - -
589A VAL 3.2 13.2 - - - +
590A THR* 5.3 0.2 - - - -
601A ASN* 4.7 2.9 - - - -
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Residues in contact with ALA 544 (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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543A PHE* 1.3 75.0 - - - +
545A THR* 1.3 64.9 + - - +
550A SER* 3.3 14.2 + - - -
572A MET* 3.4 26.7 - - + +
589A VAL 3.4 3.2 + - - -
590A THR* 3.2 27.6 + - - +
591A SER 3.7 1.2 + - - -
599A PRO* 3.8 13.5 - - + -
601A ASN* 3.1 13.9 - - - +
602A GLY* 4.2 5.6 - - - -
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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