Contacts of the strand formed by residues 38 - 44 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLN* 4.8 17.3 - - + +
34B LEU* 3.2 4.9 - - - -
35B SER* 2.7 37.0 + - - +
37B ASN* 1.3 78.1 - - - +
39B LEU* 1.3 72.0 + - - +
40B HIS* 4.3 0.7 - - - +
145B PHE* 5.9 5.5 - - + -
172C ASN* 3.4 38.3 - - - +
173C SER* 5.6 0.7 - - - -
226C LYS* 3.2 41.8 - - - +
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Residues in contact with LEU 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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93A GLN* 5.1 7.3 + - - +
32B ALA* 4.1 20.0 - - + -
33B LEU 4.4 0.7 - - - +
34B LEU* 3.6 13.1 - - + +
37B ASN 4.0 1.0 + - - -
38B GLN* 1.3 83.1 - - + +
40B HIS* 1.3 60.4 + - - +
41B CYS 3.8 22.7 - - - +
71B LEU* 4.3 12.1 - - + -
135B TRP* 3.2 49.1 - - + +
136B GLY* 4.2 1.1 - - - +
145B PHE* 4.6 12.8 - - + -
189B GLY* 3.8 23.2 - - - +
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Residues in contact with HIS 40 (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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93A GLN* 5.6 8.5 - - - -
10B SO4 5.1 6.1 + - - -
33B LEU* 2.9 17.0 + - + +
34B LEU 4.6 0.4 - - - -
35B SER* 4.3 11.2 - - - +
38B GLN 3.3 6.0 + - - +
39B LEU* 1.3 78.3 - - - +
41B CYS* 1.3 75.3 + - - +
56B HIS 5.0 2.7 - - - -
57B CYS* 3.9 27.1 + - - -
58B LYS 4.4 2.2 - - - -
59B MET* 3.4 43.6 - - + +
62B TYR* 5.8 0.6 - - - -
189B GLY* 4.5 11.1 - - - -
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Residues in contact with CYS 41 (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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10B SO4 6.0 0.7 - - - -
32B ALA* 3.7 2.9 - - - -
33B LEU* 2.8 37.3 + - + +
39B LEU* 3.8 7.6 - - - +
40B HIS* 1.3 91.4 - - - +
42B GLY* 1.3 65.6 + - - +
53B THR* 4.0 2.0 - - + -
56B HIS* 5.1 1.6 - - - -
57B CYS* 2.0 56.3 - - + -
189B GLY 4.0 9.9 - - - -
191B SER* 3.6 12.6 - - - +
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Residues in contact with GLY 42 (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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30B GLN* 4.5 6.3 - - - -
31B VAL 3.7 11.0 - - - -
32B ALA* 4.5 0.9 - - - -
33B LEU* 4.3 5.0 - - - +
41B CYS* 1.3 73.8 - - - +
43B GLY* 1.3 52.2 + - - -
53B THR* 2.7 35.7 + - - +
134B GLY* 6.3 1.8 - - - -
135B TRP* 5.5 4.3 - - - -
189B GLY 3.9 7.3 + - - -
190B ASP* 4.5 2.5 - - - -
191B SER 2.9 12.7 + - - +
192B GLY 3.7 6.1 - - - -
193B GLY* 4.3 5.6 - - - -
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Residues in contact with GLY 43 (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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30B GLN* 3.6 10.1 + - - +
31B VAL* 2.9 39.3 + - - +
33B LEU* 5.6 0.2 - - - -
42B GLY* 1.3 74.4 - - - -
44B VAL* 1.3 63.4 + - - +
51B VAL* 4.1 3.1 - - - -
52B LEU 3.2 8.5 - - - -
192B GLY 3.2 15.8 + - - -
193B GLY* 4.2 2.6 - - - -
194B PRO* 4.0 2.4 - - - +
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Residues in contact with VAL 44 (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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29B TRP* 3.3 12.8 - - + +
31B VAL* 4.6 0.9 - - - -
43B GLY* 1.3 75.3 - - - +
45B LEU* 1.3 62.4 + - - +
46B VAL 3.3 1.4 + - - -
51B VAL* 3.2 26.3 - - - +
52B LEU* 2.7 26.1 + - + +
117B VAL* 3.6 32.8 - - + -
192B GLY 4.6 0.4 - - - +
194B PRO* 3.7 27.4 - - + -
201B LEU* 3.8 15.5 - - + -
204B LEU* 3.6 25.6 - - + -
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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