Contacts of the strand formed by residues 54 - 58 (chain C) in PDB entry 5U07
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 LEU 54 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ALA* 3.6 28.7 - - + +
31C ARG 4.2 4.9 - - - +
32C SER* 3.4 27.1 - - - +
33C ARG 4.0 0.2 - - - -
42C LEU* 4.9 8.5 - - + -
47C VAL* 4.6 17.0 - - + +
50C ARG* 3.3 38.6 + - + +
51C SER 3.1 0.3 - - - +
53C GLU* 1.3 78.7 - - - +
55C SER* 1.3 60.7 + - - +
56C ASP 4.5 3.1 - - - +
57C VAL* 4.2 9.4 - - + -
227C THR* 3.1 19.2 - - - -
228C LEU* 3.0 29.3 - - + +
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Residues in contact with SER 55 (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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31C ARG* 2.4 38.3 + - - +
32C SER* 3.2 6.5 + - - +
33C ARG* 3.2 27.8 - - - +
54C LEU* 1.3 74.1 - - - +
56C ASP* 1.3 65.3 + - - +
224C LEU* 5.7 1.2 - - - +
226C ARG 3.9 9.1 - - - +
227C THR* 3.3 14.0 - - - +
228C LEU* 3.0 17.9 + - - -
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Residues in contact with ASP 56 (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 ALA* 3.4 2.4 - - - +
31C ARG* 2.9 55.7 + - - +
54C LEU* 3.5 1.7 - - - +
55C SER* 1.3 86.8 + - - +
57C VAL* 1.3 73.0 + - - +
58C GLU* 2.7 32.9 - - - +
69C TRP* 3.4 19.1 - - - -
224C LEU* 4.8 11.9 - - + +
228C LEU* 4.4 7.4 - - - +
375C ARG* 3.1 11.2 + - - -
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Residues in contact with VAL 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.6 29.4 - - + -
29C ILE 2.8 11.4 - - - +
30C ALA* 3.5 23.3 - - + -
31C ARG* 5.9 0.2 - - - +
47C VAL* 3.7 17.9 - - + -
54C LEU* 4.2 4.3 - - + -
56C ASP* 1.3 80.8 + - - +
58C GLU* 1.3 76.5 + - - +
68C LEU* 5.3 4.7 - - + +
69C TRP* 4.0 9.7 - - + -
72C LEU* 4.8 8.7 - - + -
228C LEU* 3.5 28.9 - - + +
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Residues in contact with GLU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 5.3 0.4 - - - -
29C ILE* 2.8 43.6 + - + +
31C ARG* 4.1 17.4 - - - +
56C ASP* 2.7 22.6 - - - +
57C VAL* 1.3 82.9 - - - +
59C ILE* 1.3 74.0 + - - +
60C PRO* 4.8 0.2 - - - -
65C ALA* 4.3 13.2 - - - +
69C TRP* 3.1 7.6 + - - -
375C ARG* 2.3 50.2 + - - +
377C PHE* 4.3 0.2 - - - -
216N THR* 5.9 2.7 - - - +
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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