Contacts of the strand formed by residues 32 - 39 (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 TYR 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A ARG* 2.9 9.5 + - - -
24B TRP* 2.8 33.3 + + - -
28B THR* 3.1 28.5 + - + +
29B PRO 3.6 0.2 - - - +
31B LEU* 1.3 92.9 - - + +
33B ASP* 1.3 57.1 + - - +
34B LEU 3.6 10.8 - - - +
35B VAL* 3.1 31.4 - - + -
98B TYR* 2.7 29.0 + - + -
368B PHE* 3.6 18.3 - + - -
369B ILE 4.6 0.2 + - - -
370B HIS* 2.7 30.0 + + - -
371B GLY 3.8 0.3 + - - -
402B TRP* 3.7 30.1 - + + -
403B GLN 3.3 14.1 - - - +
404B MET 4.3 0.9 - - - -
405B ALA 3.9 0.9 - - - -
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Residues in contact with ASP 33 (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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15A ARG* 2.8 32.5 + - - -
19A GLU* 5.6 1.1 - - - -
32B TYR* 1.3 71.6 - - - +
34B LEU* 1.3 58.8 + - - +
93B PHE* 4.0 13.8 - - + -
97B HIS* 3.3 30.0 + - - +
98B TYR* 4.0 8.1 - - - -
403B GLN* 2.8 28.8 + - - +
404B MET 3.9 2.4 - - - +
405B ALA* 3.5 12.4 - - - +
406B GLU* 3.2 26.2 + - - +
409B TYR* 5.3 0.7 + - - -
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Residues in contact with LEU 34 (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* 3.4 1.0 - - - +
33B ASP* 1.3 81.6 - - - +
35B VAL* 1.3 69.5 + - - +
36B MET* 4.1 17.5 - - + -
86B LEU* 3.8 27.4 - - + -
87B PRO* 4.2 26.0 - - + -
96B SER 5.4 0.2 - - - +
97B HIS* 3.5 28.3 - - + +
98B TYR* 5.4 0.4 - - - -
389B VAL* 4.8 9.6 - - + -
401B VAL* 4.3 15.5 - - + +
402B TRP* 3.1 3.2 - - - -
403B GLN* 2.8 51.4 + - + +
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Residues in contact with VAL 35 (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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24B TRP* 4.2 25.1 - - + -
28B THR* 4.5 10.5 - - + -
32B TYR* 3.1 49.4 - - + -
34B LEU* 1.3 72.2 - - - +
36B MET* 1.3 63.9 + - - +
37B THR* 4.4 11.9 - - - +
97B HIS 2.9 18.0 + - - +
98B TYR* 3.8 11.7 - - + +
99B ASP* 3.6 16.6 + - - -
370B HIS* 5.9 0.4 - - + -
400B GLN* 5.2 4.5 - - + +
401B VAL 3.5 3.8 - - - -
402B TRP* 4.3 5.2 - - + -
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Residues in contact with MET 36 (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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34B LEU* 4.1 17.9 - - + -
35B VAL* 1.3 77.3 - - - +
37B THR* 1.3 65.3 + - - +
84B VAL* 4.0 13.7 - - + -
85B GLN 3.7 16.4 - - - +
86B LEU* 3.9 24.0 - - - -
87B PRO* 5.6 1.1 - - - -
96B SER 5.6 2.2 - - - +
97B HIS 5.0 0.7 - - - +
99B ASP* 3.6 14.4 - - - +
112B SER* 5.5 2.9 - - - -
113B GLY* 3.4 32.3 - - - +
115B ILE* 4.0 16.8 - - + -
399B MET 4.1 0.4 - - - +
400B GLN* 3.3 8.0 - - - +
401B VAL* 2.8 50.3 + - + +
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Residues in contact with THR 37 (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* 5.6 5.4 + - - +
24B TRP* 5.2 1.4 - - - -
35B VAL* 4.4 8.0 - - - +
36B MET* 1.3 75.9 - - - +
38B HIS* 1.3 70.4 + - - +
39B ALA 5.2 0.2 - - - +
99B ASP* 2.9 21.0 + - - +
115B ILE* 4.6 3.6 - - - +
398B ILE* 4.4 20.4 - - + -
399B MET 3.8 3.1 - - - +
400B GLN* 3.5 29.4 + - + +
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Residues in contact with HIS 38 (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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37B THR* 1.3 82.6 - - - +
39B ALA* 1.3 87.9 + - - +
40B LEU* 3.4 21.5 + - + +
115B ILE* 3.5 58.7 + - + +
117B ILE* 5.0 11.1 - - + +
398B ILE* 4.8 1.3 - - - -
399B MET* 3.0 41.7 + - + +
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Residues in contact with ALA 39 (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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37B THR* 5.2 0.8 - - - +
38B HIS* 1.3 88.0 + - - +
40B LEU* 1.3 65.0 + - - +
41B GLU 4.0 0.5 + - - -
397B ASN* 4.0 9.4 - - + -
398B ILE* 4.5 16.2 - - + +
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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