Contacts of the strand formed by residues 32 - 38 (chain C) in PDB entry 5CTR
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 ALA 32 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C GLN* 2.2 39.7 - - + +
30C ARG 4.1 0.2 - - - +
31C GLY* 1.3 76.3 - - - +
33C GLN* 1.3 55.5 + - - +
34C TRP* 3.4 18.1 - - - +
120C LYS* 2.5 43.2 - - - +
121C VAL* 3.3 9.7 + - + +
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Residues in contact with GLN 33 (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 GLY 4.1 6.0 + - - +
32C ALA* 1.3 75.5 - - - +
34C TRP* 1.3 64.9 + - - +
35C TYR* 4.3 2.0 - - - +
97C PRO* 4.2 0.5 - - - +
98C THR* 3.1 45.9 + - + +
118C VAL* 3.6 25.3 - - + +
119C ARG 3.8 2.0 - - - +
120C LYS* 4.6 15.5 - - + +
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Residues in contact with TRP 34 (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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23C LEU* 5.3 2.7 - - + -
26C THR* 3.6 44.2 - - + -
27C THR 4.1 0.9 - - - -
28C LEU* 4.0 35.5 - - + +
29C GLN 4.4 0.4 - - - +
32C ALA* 3.4 31.4 - - + +
33C GLN* 1.3 80.1 + - - +
35C TYR* 1.3 62.2 + - - +
95C LEU* 4.4 12.1 - - + -
96C VAL 3.3 36.6 - - - -
97C PRO* 3.5 27.1 - - + -
118C VAL* 3.3 4.0 - - - +
119C ARG* 2.4 48.0 + - - +
121C VAL* 4.2 12.3 - - + +
133C VAL* 4.1 23.1 - - + -
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Residues in contact with TYR 35 (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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33C GLN* 4.1 1.1 - - - +
34C TRP* 1.3 79.7 - - - +
36C LEU* 1.3 66.3 + - - +
95C LEU* 3.4 30.8 - - - +
96C VAL* 3.1 19.5 + - + +
97C PRO 4.0 1.3 - - - -
98C THR* 3.7 39.5 + - + +
101C TRP* 3.1 44.9 - + + +
116C PRO* 4.1 17.9 - - + -
117C ILE 3.2 9.4 - - - +
118C VAL* 3.5 41.0 - - + +
119C ARG* 5.2 0.7 - - - -
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Residues in contact with LEU 36 (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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35C TYR* 1.3 86.1 - - - +
37C ILE* 1.3 67.8 + - - +
71C ASN* 2.9 16.0 + - - -
74C LEU* 4.9 7.6 - - + -
83C LEU* 4.0 20.9 - - + -
87C LEU* 5.4 6.1 - - + -
93C TYR* 3.4 47.1 - - + -
94C VAL 4.5 0.2 - - - -
95C LEU* 3.6 10.8 - - + -
101C TRP* 4.6 6.2 + - - -
117C ILE* 3.2 45.7 + - + +
119C ARG* 4.7 6.5 - - + -
135C VAL* 4.8 15.5 - - + -
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Residues in contact with ILE 37 (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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36C LEU* 1.3 80.9 - - - +
38C ASP* 1.3 74.9 + - - +
41C TRP* 4.1 21.1 - - + -
42C PHE* 4.3 13.5 - - + -
69C ILE* 4.8 7.6 - - + -
71C ASN* 3.3 10.8 - - - +
74C LEU* 4.3 1.1 - - - -
93C TYR* 3.2 4.8 - - - -
94C VAL* 2.9 42.5 + - + +
96C VAL* 3.5 31.6 - - + -
101C TRP* 4.4 9.4 - - + +
104C LEU* 3.8 35.7 - - + -
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Residues in contact with ASP 38 (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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37C ILE* 1.3 73.0 - - - +
39C SER* 1.3 74.0 + - - +
40C ARG* 3.3 39.3 + - - +
41C TRP* 3.2 8.4 + - + +
42C PHE* 3.1 17.2 + - - +
70C ASP 3.7 13.6 - - - +
71C ASN* 2.9 25.1 + - - +
73C GLY* 5.5 5.4 + - - -
74C LEU* 3.7 24.2 - - + +
92C ASP* 3.0 17.1 - - - +
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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