Contacts of the strand formed by residues 538 - 545 (chain A) in PDB entry 5HG1
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 PHE 538 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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531A LEU* 4.0 17.0 - - + -
532A ASP 3.2 20.0 - - - +
533A LEU* 4.0 20.0 - - + +
534A GLY 5.6 0.7 - - - +
535A GLY 5.1 0.6 + - - -
536A THR 4.1 2.4 + - - -
537A ASN* 1.3 72.4 - - - +
539A ARG* 1.3 73.2 + - - +
540A VAL* 4.0 17.5 - - + -
559A ILE* 3.5 2.9 - - - +
560A TYR* 2.9 50.2 + + + +
562A ILE* 3.7 34.8 - - + -
578A ILE* 4.0 29.4 - - + -
581A CYS* 3.8 29.8 - - + -
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Residues in contact with ARG 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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531A LEU* 3.7 3.5 - - - -
532A ASP* 3.1 46.8 + - + -
537A ASN* 3.4 27.0 + - - +
538A PHE* 1.3 80.5 - - - +
540A VAL* 1.3 61.3 + - - +
541A LEU* 3.5 21.4 - - + +
557A ASN* 3.1 35.4 + - - +
558A LYS 3.2 21.3 - - - +
559A ILE* 3.1 33.9 - - - +
560A TYR* 4.7 0.7 - - - +
895A ASP 5.8 3.9 + - - -
896A GLY* 6.4 1.6 - - - -
1003A BG6 5.6 5.5 + - - -
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Residues in contact with VAL 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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529A LEU* 4.3 9.2 - - + -
530A ALA 3.6 9.0 - - - +
531A LEU* 3.7 21.1 - - + -
538A PHE* 4.0 13.9 - - + -
539A ARG* 1.3 75.5 - - - +
541A LEU* 1.3 67.2 + - - +
557A ASN* 3.2 5.5 - - - +
558A LYS 3.2 27.8 + - - -
560A TYR* 4.3 9.2 - - + -
581A CYS 4.3 15.9 - - - +
582A ILE* 4.3 13.5 - - + +
585A PHE* 3.6 37.6 - - + -
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Residues in contact with LEU 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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529A LEU* 3.2 12.5 - - - +
530A ALA* 2.9 43.8 + - + +
532A ASP* 4.5 2.7 - - + -
539A ARG* 3.5 34.5 - - + +
540A VAL* 1.3 79.0 - - - +
542A LEU* 1.3 59.1 + - - +
543A VAL* 4.1 7.2 - - + -
555A MET* 3.6 19.5 - - + -
556A HIS 3.3 7.2 - - - +
557A ASN* 4.1 12.1 - - + -
585A PHE* 4.0 4.0 - - - -
895A ASP 4.9 1.8 - - - +
898A GLY* 3.2 44.0 - - - +
899A LYS* 3.3 7.2 - - - +
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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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527A ASP* 4.3 13.9 - - + -
528A PHE 3.3 8.7 - - - +
529A LEU* 4.6 4.0 - - + -
541A LEU* 1.3 74.3 - - - +
543A VAL* 1.3 65.0 + - - +
544A ARG* 3.8 30.5 - - + +
554A GLU 3.6 2.6 - - - +
556A HIS* 2.9 32.5 + - + +
585A PHE* 3.7 18.5 - - + -
589A MET* 4.5 17.0 - - + -
591A MET* 3.7 43.3 - - + -
596A LEU* 4.2 13.9 - - + -
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Residues in contact with VAL 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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527A ASP* 3.9 0.5 - - - -
528A PHE* 3.0 40.0 + - + +
541A LEU* 4.1 8.5 - - + -
542A LEU* 1.3 73.5 - - - +
544A ARG* 1.3 59.9 + - - +
545A VAL* 3.9 6.2 + - + -
553A VAL* 5.6 7.9 - - + -
554A GLU 3.2 6.5 - - - +
555A MET* 3.4 31.6 - - + -
899A LYS* 4.3 15.7 - - + +
902A ALA* 2.9 39.7 - - + -
903A LEU* 5.8 4.9 - - + -
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Residues in contact with ARG 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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526A GLY 4.0 0.7 - - - +
527A ASP* 2.9 38.2 + - - +
542A LEU* 3.8 14.5 - - + +
543A VAL* 1.3 70.7 - - - +
545A VAL* 1.3 57.6 + - - +
546A ARG* 3.9 8.5 + - + +
552A GLY 3.4 3.8 - - - +
553A VAL* 4.4 0.2 - - - -
554A GLU* 2.5 62.0 + - + +
556A HIS* 5.6 4.3 + - - -
589A MET* 5.5 7.5 - - - +
591A MET* 5.4 9.4 - - - -
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Residues in contact with VAL 545 (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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524A GLU* 3.5 32.7 - - + +
525A LYS* 3.5 3.8 - - - +
526A GLY 3.2 32.6 + - - +
528A PHE* 3.4 24.7 - - + -
543A VAL* 4.9 4.7 - - + +
544A ARG* 1.3 71.9 - - - +
546A ARG* 1.3 70.5 + - - +
552A GLY 3.7 2.9 - - - +
553A VAL* 3.9 24.9 - - + +
667A PHE* 5.7 2.5 - - + -
903A LEU* 5.1 10.8 - - + -
906A ALA* 4.9 2.5 - - + -
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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