Contacts of the strand formed by residues 386 - 390 (chain A) in PDB entry 4H1S
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 MET 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369A ILE* 4.4 0.2 - - - -
384A VAL* 3.8 2.9 - - - +
385A SER* 1.3 87.3 - - - +
387A CYS* 1.3 61.7 + - - +
431A LEU* 3.5 31.6 - - + -
453A GLY 3.4 3.8 - - - +
454A GLY 3.8 18.2 - - - +
455A ILE* 4.1 11.0 - - + -
474A VAL* 3.6 35.0 - - + -
475A LEU 4.4 7.0 - - - +
477A THR* 6.0 3.6 - - + -
493A TYR* 4.0 25.6 - - + -
494A LYS 3.7 12.5 + - - +
495A VAL* 3.5 12.0 - - + -
496A ILE* 2.9 30.5 + - - +
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Residues in contact with CYS 387 (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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365A CYS* 2.1 57.9 - - + -
368A MET* 3.5 26.5 - - - -
369A ILE* 3.8 15.9 - - + -
386A MET* 1.3 76.2 - - - +
388A ILE* 1.3 71.9 + - - +
452A VAL* 3.3 5.4 - - - +
453A GLY 2.9 27.2 + - - +
455A ILE* 3.8 1.4 - - - +
495A VAL* 4.3 0.9 - - - -
496A ILE* 3.2 8.7 - - + -
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Residues in contact with ILE 388 (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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387A CYS* 1.3 82.7 - - - +
389A LEU* 1.3 64.7 + - - +
426A LEU* 5.6 0.4 - - + -
431A LEU* 4.5 17.7 - - + -
434A ALA* 4.9 2.2 - - + -
435A PHE* 3.8 30.5 - - + -
450A LEU* 4.0 25.4 - - + -
451A GLN 3.4 6.5 - - - +
452A VAL* 4.4 1.6 - - + -
455A ILE* 3.9 7.9 - - + -
495A VAL* 4.0 7.1 - - + +
496A ILE 3.1 6.7 + - - +
497A LEU* 3.5 35.7 - - + +
498A PRO* 3.4 17.2 - - - +
501A LEU* 4.3 5.8 - - + -
508A PHE* 5.5 0.4 - - + -
511A ILE* 4.1 17.0 - - + -
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Residues in contact with LEU 389 (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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361A GLY* 4.1 11.7 - - - +
364A ILE* 3.7 38.8 - - + -
365A CYS* 4.0 12.8 - - - +
368A MET* 4.8 2.9 - - - -
388A ILE* 1.3 79.3 - - - +
390A ASN* 1.3 74.2 + - - +
391A GLY 3.4 0.2 + - - -
393A GLY* 5.1 5.8 - - - -
394A ILE* 3.9 25.6 - - + -
415A LEU* 5.8 4.0 - - + -
421A PHE* 5.0 5.6 - - + -
450A LEU* 4.0 3.9 - - - +
451A GLN* 2.6 39.5 + - + +
498A PRO* 3.7 26.5 - - + -
501A LEU* 4.4 0.4 - - - -
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Residues in contact with ASN 390 (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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389A LEU* 1.3 79.5 - - - +
391A GLY* 1.3 56.1 + - - +
392A GLY 3.6 3.4 - - - -
393A GLY* 2.8 50.3 + - - +
394A ILE 4.0 1.4 + - - -
447A GLY 3.4 11.2 - - - +
448A GLU* 4.6 2.9 - - - -
449A PHE 3.6 5.8 - - - -
450A LEU* 4.0 7.6 - - + -
498A PRO* 4.0 11.8 - - - +
500A PHE* 3.7 16.8 - - - -
501A LEU* 3.7 34.2 - - + +
506A ASP* 2.9 23.3 + - - +
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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