Contacts of the strand formed by residues 386 - 390 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369B ILE* 4.3 0.7 - - - -
384B VAL* 3.8 2.6 - - - +
385B SER* 1.3 87.7 - - - +
387B CYS* 1.3 62.4 + - - +
431B LEU* 3.5 31.4 - - + -
453B GLY 3.3 4.3 - - - +
454B GLY 4.0 15.0 - - - +
455B ILE* 3.9 12.3 - - + -
474B VAL* 3.6 33.9 - - + -
475B LEU 4.4 7.9 - - - +
477B THR* 5.9 1.6 - - - -
493B TYR* 3.9 24.0 - - + -
494B LYS 3.7 13.4 + - - +
495B VAL* 3.3 12.4 - - + -
496B ILE* 2.9 28.6 + - - +
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Residues in contact with CYS 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B CYS* 2.0 57.2 - - + -
368B MET* 3.4 27.6 - - - -
369B ILE* 3.8 16.2 - - + -
386B MET* 1.3 76.4 - - - +
388B ILE* 1.3 74.8 + - - +
452B VAL* 3.3 5.0 - - - +
453B GLY 2.8 26.7 + - - +
455B ILE* 3.7 2.1 - - - +
495B VAL* 4.1 0.4 - - - -
496B ILE* 3.2 9.6 - - + +
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Residues in contact with ILE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B CYS* 1.3 82.6 - - - +
389B LEU* 1.3 64.1 + - - +
426B LEU* 5.5 0.9 - - + -
431B LEU* 4.6 13.9 - - + -
434B ALA* 5.0 2.2 - - + -
435B PHE* 3.7 30.7 - - + -
450B LEU* 4.1 21.8 - - + -
451B GLN 3.4 7.0 - - - +
452B VAL* 4.5 2.0 - - + -
455B ILE* 3.9 8.1 - - + -
495B VAL* 4.0 9.1 - - + +
496B ILE 3.2 5.3 + - - +
497B LEU* 3.3 36.1 - - + +
498B PRO* 3.3 17.5 - - - +
501B LEU* 4.1 8.5 - - + -
511B ILE* 4.1 16.6 - - + -
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B GLY* 4.1 12.3 - - - +
364B ILE* 3.7 38.4 - - + -
365B CYS* 4.0 12.1 - - - +
368B MET* 4.7 5.4 - - - -
388B ILE* 1.3 78.0 - - - +
390B ASN* 1.3 78.4 + - - +
391B GLY 3.4 0.2 + - - -
393B GLY* 5.3 6.3 - - - -
394B ILE* 3.8 27.8 - - + -
415B LEU* 5.8 3.6 - - + -
421B PHE* 4.9 4.0 - - + -
450B LEU* 3.6 3.9 - - - +
451B GLN* 2.8 36.7 + - + +
498B PRO* 3.7 25.6 - - + -
501B LEU* 4.4 0.2 - - - -
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Residues in contact with ASN 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B LEU* 1.3 80.8 - - - +
391B GLY* 1.3 59.0 + - - +
392B GLY 3.9 2.4 - - - -
393B GLY* 2.9 43.7 + - - +
394B ILE 3.9 2.1 + - - -
447B GLY 3.3 13.9 - - - +
448B GLU* 4.6 2.5 - - - +
449B PHE 3.6 5.8 - - - +
450B LEU* 4.1 7.2 - - + -
498B PRO* 4.0 11.8 - - - +
500B PHE* 3.4 19.5 - - - -
501B LEU* 3.7 31.5 - - + +
506B ASP* 2.8 22.8 + - - +
508B PHE* 4.9 0.2 - - + -
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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