Contacts of the strand formed by residues 398 - 404 (chain B) in PDB entry 4PBY
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 ILE 398 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B THR* 4.4 17.7 - - + -
38B HIS 3.9 1.6 - - - +
39B ALA* 4.5 19.1 - - + -
40B LEU* 5.1 0.2 - - - -
372B GLY 5.6 0.2 - - - +
373B HIS* 3.8 15.2 - - - +
374B THR* 5.3 3.1 - - - +
393B VAL* 3.5 2.6 - - - +
394B SER* 2.9 33.2 + - - +
396B ASP* 3.0 30.9 + - - +
397B ASN* 1.3 77.6 - - + +
399B MET* 1.3 63.6 + - - +
400B GLN* 3.8 30.5 - - + +
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Residues in contact with MET 399 (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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36B MET 4.1 0.2 - - - +
37B THR* 3.8 0.5 - - - -
38B HIS* 3.0 40.8 + - + +
40B LEU* 4.0 18.6 - - + -
66B LEU* 3.4 29.4 - - + -
68B LEU* 3.9 26.0 - - + -
82B ALA* 5.6 0.7 - - + -
84B VAL* 4.2 3.8 - - + -
115B ILE* 3.8 31.8 - - + +
391B CYS* 4.1 7.9 - - - -
392B SER 3.5 4.3 - - - -
393B VAL* 4.0 17.5 - - + -
397B ASN 3.4 0.2 + - - -
398B ILE* 1.3 74.0 - - - +
400B GLN* 1.3 67.1 + - - +
401B VAL* 4.0 16.8 - - + -
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Residues in contact with GLN 400 (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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21B TYR* 5.2 2.8 + - - -
24B TRP* 3.8 14.3 - - - -
35B VAL* 5.3 3.6 - - + -
36B MET 3.3 11.0 - - - +
37B THR* 3.5 22.3 + - - +
370B HIS* 2.9 31.8 + - - -
372B GLY* 3.3 27.6 + - - -
373B HIS* 3.6 14.5 + - + +
390B ILE 3.6 0.9 - - - +
391B CYS* 3.2 5.2 - - - +
392B SER* 2.7 36.5 + - - -
398B ILE* 3.8 13.4 - - + +
399B MET* 1.3 78.4 - - - +
401B VAL* 1.3 65.0 + - - +
402B TRP* 3.9 12.1 - - + -
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Residues in contact with VAL 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LEU* 4.2 4.3 - - + +
35B VAL* 3.5 1.0 + - - -
36B MET* 2.8 51.5 + - + +
49B TRP* 4.5 7.4 - - + -
84B VAL* 4.4 11.2 - - + -
86B LEU* 3.9 27.8 - - + -
115B ILE* 5.1 3.1 - - + -
389B VAL* 4.0 17.3 - - + -
390B ILE 3.3 3.8 - - - +
391B CYS* 4.2 11.7 - - + -
399B MET* 4.0 25.4 - - + -
400B GLN* 1.3 79.7 - - - +
402B TRP* 1.3 63.1 + - - +
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Residues in contact with TRP 402 (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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32B TYR* 3.7 23.1 - + + -
34B LEU* 3.1 14.4 - - - +
35B VAL* 4.3 7.6 - - + -
342B LEU* 3.7 17.7 - - + -
344B VAL* 4.4 5.6 - - + -
368B PHE* 3.6 22.4 - + - -
370B HIS* 3.4 47.0 + + + -
388B TRP 3.5 3.1 - - - +
389B VAL* 3.4 4.8 - - - -
390B ILE* 2.9 77.1 + - + +
392B SER* 3.0 23.8 + - - -
400B GLN* 3.8 9.0 - - + -
401B VAL* 1.3 80.2 - - - +
403B GLN* 1.3 63.3 + - - +
404B MET* 4.1 15.5 - - + -
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Residues in contact with GLN 403 (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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32B TYR* 3.3 5.6 - - - -
33B ASP* 2.8 47.3 + - - +
34B LEU* 2.8 27.2 + - + +
386B GLU* 5.2 2.2 - - - +
387B PRO 3.0 22.8 + - - -
388B TRP* 3.5 20.8 - - + +
389B VAL* 3.6 18.4 - - + +
402B TRP* 1.3 77.6 - - - +
404B MET* 1.3 71.9 + - - +
409B TYR* 5.4 4.8 + - - +
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Residues in contact with MET 404 (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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31B LEU 3.4 7.4 - - - +
32B TYR* 4.1 4.7 - - - +
33B ASP* 3.9 3.5 - - - +
344B VAL* 4.0 17.0 - - + -
367B LEU* 4.3 4.9 - - + -
368B PHE* 3.4 42.8 - - + -
382B TRP* 5.9 0.2 - - + -
388B TRP* 3.9 30.4 + - + +
390B ILE* 6.4 0.2 - - + -
402B TRP* 4.1 10.2 - - + -
403B GLN* 1.3 88.4 - - - +
405B ALA* 1.3 73.7 + - - +
406B GLU 3.5 1.7 + - - -
408B ILE* 3.8 36.1 - - + -
409B TYR* 3.8 23.7 + - + -
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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