Contacts of the strand formed by residues 40 - 45 (chain C) in PDB entry 5BOU
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 VAL 40 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL 3.4 19.7 - - - +
35C LYS* 4.0 6.7 - - + -
39C CYS* 1.3 80.7 - - - +
41C VAL* 1.3 69.8 + - - +
42C LEU* 4.8 0.2 - - + -
134C ALA* 3.8 20.2 - - + -
135C GLY 4.4 2.7 - - - +
136C PHE* 4.3 9.2 - - + -
143C PRO* 3.6 20.6 - - + -
144C LYS 3.7 20.2 - - - +
145C LEU* 4.4 10.5 - - + -
212C VAL* 3.8 1.9 - - - +
213C VAL* 2.9 46.9 + - + +
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Residues in contact with VAL 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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32C VAL 3.9 0.5 - - - +
33C GLY* 3.4 4.2 - - - -
34C VAL* 2.7 36.5 + - - +
39C CYS* 4.5 5.6 - - - -
40C VAL* 1.3 77.7 - - - +
42C LEU* 1.3 66.5 + - - +
43C GLY 4.1 0.2 + - - -
186C VAL 5.0 0.2 - - - +
189C CYS* 3.5 23.3 - - + -
190C VAL* 3.9 24.2 - - + +
193C THR* 3.5 32.2 + - + +
210C ILE* 3.8 28.0 - - + -
211C THR 3.5 3.6 - - - +
212C VAL* 4.3 8.7 - - + -
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Residues in contact with LEU 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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32C VAL 3.4 3.6 - - - +
33C GLY* 3.9 17.0 - - - -
40C VAL* 4.8 0.9 - - + -
41C VAL* 1.3 81.3 - - - +
43C GLY* 1.3 60.2 + - - +
44C CYS* 4.3 0.8 + - - -
62C VAL* 4.1 26.1 - - + +
70C VAL* 3.5 29.6 - - + -
72C SER* 3.8 29.6 - - - +
132C LEU* 4.4 8.5 - - + +
134C ALA* 4.0 23.1 - - + -
145C LEU* 4.2 8.1 - - + -
209C GLU 3.9 0.5 - - - +
210C ILE* 3.6 1.6 - - - -
211C THR* 2.9 39.4 + - - +
213C VAL* 5.5 2.2 - - + -
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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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32C VAL* 2.8 51.5 + - - +
42C LEU* 1.3 74.3 - - - +
44C CYS* 1.3 66.6 + - - -
72C SER* 5.5 0.2 + - - -
193C THR* 3.9 3.6 - - - +
197C LEU* 3.9 3.1 - - - -
209C GLU 3.3 9.0 - - - -
210C ILE* 3.9 13.2 - - - -
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Residues in contact with CYS 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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30C CYS 3.6 5.4 - - - +
31C ALA* 4.3 9.0 - - - -
42C LEU* 4.3 0.6 + - - -
43C GLY* 1.3 80.9 - - - -
45C GLU* 1.3 62.2 + - - +
46C ARG 3.9 0.2 + - - -
61C LYS* 3.9 32.5 - - + -
62C VAL* 3.9 26.5 - - - -
72C SER* 4.0 16.4 - - - -
197C LEU* 3.9 8.3 - - - +
207C ASN 3.5 2.3 - - - +
208C ILE* 3.6 2.4 - - - -
209C GLU* 2.9 44.5 + - + +
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Residues in contact with GLU 45 (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 THR* 3.4 22.0 + - - +
30C CYS* 2.8 51.0 + - + +
44C CYS* 1.3 76.2 - - - +
46C ARG* 1.3 70.0 - - - +
47C ARG* 4.9 0.9 - - - -
61C LYS* 4.8 5.0 - - - +
164C ARG* 2.7 42.3 + - - +
197C LEU* 4.5 8.0 - - + +
200C VAL* 4.5 12.9 - - - +
201C VAL* 4.1 29.0 - - + +
207C ASN 3.4 4.3 - - - -
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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