Contacts of the strand formed by residues 38 - 44 (chain C) in PDB entry 3BSQ
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 GLN 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C LEU* 3.3 4.9 - - - -
35C SER* 2.8 35.1 + - - +
37C ASN* 1.3 79.1 - - - +
39C LEU* 1.3 71.9 + - - +
40C HIS* 4.3 0.7 - - - +
145C PHE* 6.0 6.1 - - + -
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Residues in contact with LEU 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ALA* 4.2 19.1 - - + -
33C LEU 4.4 1.1 - - - +
34C LEU* 3.6 13.0 - - + +
37C ASN 4.0 0.8 + - - -
38C GLN* 1.3 81.4 - - - +
40C HIS* 1.3 60.6 + - - +
41C CYS 3.7 22.0 - - - +
42C GLY* 5.5 0.2 - - - -
71C LEU* 4.4 12.8 - - + -
135C TRP* 3.1 50.5 - - + +
136C GLY* 4.4 0.7 - - - -
145C PHE* 4.5 13.9 - - + -
189C GLY* 3.9 25.7 - - - +
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Residues in contact with HIS 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C SO4 4.1 10.9 + - - -
33C LEU* 2.9 19.3 + - - +
34C LEU 4.6 0.2 - - - -
35C SER* 4.3 14.8 - - - +
38C GLN 3.3 1.3 + - - +
39C LEU* 1.3 77.0 - - - +
41C CYS* 1.3 76.1 + - - +
56C HIS 4.9 2.9 - - - -
57C CYS* 3.7 28.3 + - - -
58C LYS 4.3 2.9 - - - -
59C MET* 3.3 44.2 - - + +
62C TYR* 5.6 0.6 - - - -
189C GLY* 4.4 5.5 - - - -
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Residues in contact with CYS 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C SO4 4.8 1.8 - - - -
32C ALA* 3.7 2.9 - - - -
33C LEU* 2.8 40.2 + - + +
39C LEU* 3.7 7.0 - - - +
40C HIS* 1.3 89.9 - - - +
42C GLY* 1.3 60.4 + - - +
53C THR* 4.1 2.7 - - + -
56C HIS* 5.1 2.2 - - - -
57C CYS* 2.1 57.7 - - + -
189C GLY 3.9 10.5 - - - -
191C SER* 3.6 13.7 - - - +
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Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLN* 4.5 4.3 - - - -
31C VAL 3.7 11.4 - - - -
32C ALA* 4.6 0.7 - - - -
33C LEU* 4.4 4.5 - - - +
39C LEU* 5.5 0.4 - - - -
41C CYS* 1.3 74.0 - - - +
43C GLY* 1.3 58.1 + - - -
53C THR* 2.8 26.3 - - - +
134C GLY* 6.3 2.0 - - - -
135C TRP* 5.5 4.0 - - - -
189C GLY 3.7 6.8 + - - -
190C ASP* 4.4 3.1 - - - -
191C SER 2.8 13.3 + - - +
192C GLY 3.5 7.1 - - - +
193C GLY* 4.3 6.3 - - - -
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Residues in contact with GLY 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C GLN* 3.7 9.6 + - - +
31C VAL* 3.0 39.6 + - - +
33C LEU* 5.6 0.2 - - - -
42C GLY* 1.3 73.3 - - - -
44C VAL* 1.3 64.0 + - - +
51C VAL* 4.1 2.5 - - - -
52C LEU 3.4 7.4 - - - -
53C THR 4.0 2.0 - - - -
192C GLY 3.1 14.9 + - - -
193C GLY* 4.0 2.4 - - - -
194C PRO* 4.0 2.7 - - - +
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C TRP* 3.4 14.4 - - + +
31C VAL* 4.5 0.9 - - - -
43C GLY* 1.3 76.7 - - - +
45C LEU* 1.3 61.2 + - - +
46C VAL 3.4 0.9 + - - -
51C VAL* 3.2 18.9 - - - +
52C LEU* 2.6 39.9 + - + +
117C VAL* 3.6 32.8 - - + -
192C GLY 4.6 0.2 - - - +
194C PRO* 3.7 26.7 - - + -
201C LEU* 3.9 14.6 - - + -
204C LEU* 3.7 26.0 - - + -
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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