Contacts of the strand formed by residues 388 - 392 (chain B) in PDB entry 1I3O
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 CYS 388 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ARG* 3.8 16.8 - - - +
329B TYR 3.7 1.7 - - - +
330B ALA* 5.0 0.2 - - - -
331B TYR* 2.8 41.9 + - + +
333B THR 3.6 21.7 - - - +
334B ALA* 4.1 3.4 - - - -
335B PRO* 4.2 4.9 - - - -
387B PRO* 1.3 75.8 - - - +
389B ILE* 1.3 62.7 + - - +
390B VAL* 4.0 10.1 - - - -
390D VAL* 3.8 15.3 - - - -
392D SER 4.0 2.9 - - - -
393D MET* 3.8 27.8 - - + -
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Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 4.2 12.3 - - + -
329B TYR 4.0 2.0 - - - +
330B ALA* 4.9 3.1 - - + +
367B MET* 4.1 28.9 - - + +
370B LEU* 3.5 48.9 - - + +
371B THR* 3.9 10.8 - - - +
374B ASN* 3.6 20.0 - - - +
387B PRO* 5.8 0.2 - - + -
388B CYS* 1.3 74.2 - - - +
390B VAL* 1.3 61.6 + - - +
392B SER* 3.9 2.9 - - - +
367D MET* 6.1 1.3 - - - -
389D ILE* 3.3 2.0 - - + +
390D VAL* 3.2 5.5 - - - +
392D SER* 2.8 52.7 + - - +
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ARG* 5.4 1.8 - - - +
328B LEU* 3.6 3.6 - - - -
329B TYR* 2.9 47.8 + - + +
331B TYR* 3.7 27.4 - - + -
388B CYS* 4.0 13.5 - - - -
389B ILE* 1.3 75.7 - - - +
392B SER* 1.3 57.9 + - - +
393B MET* 3.4 28.3 - - + -
335D PRO* 5.9 2.0 - - + -
388D CYS* 3.7 16.4 - - - -
389D ILE 3.1 4.0 - - - +
390D VAL* 4.3 10.8 - - + -
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Residues in contact with SER 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B LEU* 3.2 17.9 - - - -
367B MET* 3.9 20.9 - - - +
389B ILE* 3.9 2.4 - - - -
390B VAL* 1.3 71.1 - - - +
393B MET* 1.3 66.4 + - - +
394B LEU* 3.2 26.7 + - - +
371D THR* 5.1 2.8 + - - -
374D ASN* 3.6 6.0 + - - -
389D ILE* 2.8 50.0 + - - +
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Residues in contact with MET 393 (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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324B GLU* 4.3 16.4 - - - +
326B ASP 3.0 18.9 + - - -
327B PHE 2.8 21.2 + - - +
329B TYR* 3.3 31.4 - - + +
390B VAL* 3.4 24.0 - - + -
392B SER* 1.3 78.6 - - - +
394B LEU* 1.3 64.9 + - - +
334D ALA* 4.0 23.8 - - - -
335D PRO* 4.2 12.3 - - + -
374D ASN* 3.6 8.7 - - - +
386D ILE* 3.6 21.8 - - + +
387D PRO 3.8 10.3 - - - +
388D CYS* 3.7 14.4 - - - -
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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
------------------------------------------------------------
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