Contacts of the strand formed by residues 38 - 44 (chain C) in PDB entry 3G65
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 LYS 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C ARG* 3.8 3.3 - - - +
35C SER* 3.0 36.6 + - - +
37C ASP* 1.3 92.9 - - + +
39C LEU* 1.3 66.6 + - - +
40C ASN* 5.0 8.2 + - - +
57C GLU* 2.8 36.0 + - + +
58C LEU 3.0 17.3 - - - +
59C GLU* 3.6 30.3 + - + +
60C GLN* 3.8 3.8 - - - +
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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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3C PHE* 4.8 6.7 - - + -
16C PHE* 4.7 11.2 - - + -
32C LEU* 3.7 20.6 - - + -
33C ARG 3.4 13.5 - - - +
34C ILE* 3.7 26.7 - - + -
38C LYS* 1.3 75.4 - - - +
40C ASN* 1.3 72.9 + - - +
41C PHE* 5.5 7.0 - - + -
56C CYS 3.6 0.2 - - - +
58C LEU* 2.8 46.3 + - + +
60C GLN* 4.5 1.7 - - + +
64C PHE* 3.8 34.1 - - + -
67C PHE* 4.3 14.1 - - + -
103C ILE* 6.5 1.3 - - + -
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Residues in contact with ASN 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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31C THR 3.2 4.0 - - - +
32C LEU* 3.3 5.5 - - - +
33C ARG* 2.8 85.5 + - + +
38C LYS* 5.0 5.9 + - - +
39C LEU* 1.3 90.0 - - - +
41C PHE* 1.3 63.8 + - - +
42C ILE* 4.0 11.2 - - + -
55C TRP* 3.6 19.1 - - + -
56C CYS 3.0 14.5 - - - +
57C GLU* 3.2 15.6 - - - +
58C LEU 3.9 0.3 + - - -
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Residues in contact with PHE 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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16C PHE* 5.1 13.5 - + - -
19C ILE* 4.1 21.8 - - + -
20C SER* 5.8 2.2 - - - -
23C ILE* 3.3 39.3 - - + -
30C CYS* 4.3 9.4 - - - -
31C THR 3.3 2.5 - - - -
32C LEU* 4.0 26.9 - - + -
39C LEU* 5.5 5.2 - - + -
40C ASN* 1.3 77.0 - - - +
42C ILE* 1.3 60.1 + - - +
54C MET* 3.4 14.4 - - + +
55C TRP* 3.6 0.7 - - - -
56C CYS* 3.1 51.5 + - + -
58C LEU* 4.4 16.2 - - + -
83C LEU* 5.8 0.4 - - + -
88C LEU* 4.2 25.1 - - + -
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Residues in contact with ILE 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 CYS* 3.8 1.7 - - - -
31C THR* 2.8 46.9 + - + +
33C ARG* 3.9 25.6 - - + -
40C ASN* 4.2 4.9 - - + -
41C PHE* 1.3 80.4 - - - +
43C LEU* 1.3 77.1 + - - +
44C CYS* 6.2 0.4 - - + -
54C MET* 3.4 9.2 - - - +
55C TRP* 3.4 34.8 - - + -
80C TYR* 4.1 10.3 - - + -
146C LEU* 3.1 46.4 - - + +
147C GLN 4.8 2.7 - - - +
149C PRO* 5.6 2.7 - - + -
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Residues in contact with LEU 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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26C LEU 5.1 1.6 - - - +
27C ALA* 3.5 23.3 - - + -
29C THR* 3.3 31.4 - - - +
30C CYS* 4.8 2.7 - - - -
31C THR* 5.3 5.4 - - - +
42C ILE* 1.3 85.6 - - - +
44C CYS* 1.3 72.2 + - - +
45C ASP* 4.1 20.6 - - - +
52C VAL* 5.4 4.7 - - + +
53C SER* 3.3 7.0 - - - -
54C MET* 3.2 38.5 + - + +
146C LEU* 5.3 6.1 - - + -
149C PRO* 5.8 0.2 - - - +
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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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42C ILE* 6.2 0.7 - - + -
43C LEU* 1.3 84.7 - - - +
45C ASP* 1.3 77.7 + - - +
51C GLY 5.7 1.1 - - - -
52C VAL 3.7 2.2 - - - -
53C SER* 3.2 20.6 - - - +
145C ASP 5.1 11.4 - - - +
146C LEU* 5.6 4.8 - - + +
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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