Contacts of the strand formed by residues 38 - 45 (chain C) in PDB entry 3SE3
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 HIS 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C PRO* 4.3 0.2 - - - +
37C THR* 1.3 99.1 + - + +
39C TYR* 1.3 62.0 + - - +
60C ASN* 2.8 36.5 + - + +
61C THR 3.5 7.3 - - - -
62C THR* 5.2 5.2 - - - -
85C GLY* 3.4 1.0 - - - -
86C PHE* 2.9 52.6 + - + +
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Residues in contact with TYR 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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27C TRP* 3.9 30.7 - + + -
29C LEU* 4.7 9.9 - - + +
35C VAL* 4.4 9.7 - - - +
36C PRO* 3.4 40.9 + - + +
37C THR 4.4 4.9 - - - -
38C HIS* 1.3 75.5 - - - +
40C THR* 1.3 58.0 + - - +
58C CYS 3.4 4.3 - - - +
60C ASN* 2.6 28.6 + - - -
61C THR* 3.0 19.6 + - - +
62C THR 2.9 28.9 - - - -
63C ARG 3.7 14.6 - - - -
64C SER* 4.4 5.3 - - - -
83C LEU* 4.3 18.6 - - + -
84C GLU 3.1 11.7 - - - +
85C GLY* 4.4 1.8 - - - -
86C PHE* 4.5 0.4 - - - -
93C PHE* 6.1 0.9 - + - -
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Residues in contact with THR 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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39C TYR* 1.3 70.9 - - - +
41C LEU* 1.3 62.9 + - - +
42C LEU* 4.1 4.1 - - + +
54C VAL* 4.0 33.2 - - + -
58C CYS 3.8 3.8 - - - -
59C ALA* 4.0 7.9 - - + +
60C ASN* 3.2 16.1 + - - +
82C VAL 3.6 1.7 - - - +
83C LEU* 3.5 4.4 - - - -
84C GLU* 2.7 50.9 + - - +
86C PHE* 3.3 27.1 - - - -
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Residues in contact with LEU 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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14C PHE* 5.3 2.2 - - + -
25C LEU* 3.2 30.3 - - + -
27C TRP* 4.0 23.3 - - + -
40C THR* 1.3 73.6 - - - +
42C LEU* 1.3 79.7 + - - +
43C TYR* 4.7 2.9 - - + +
54C VAL* 3.9 4.3 - - - +
55C VAL* 3.0 47.7 + - + +
58C CYS* 3.7 14.3 + - + +
66C CYS* 4.6 4.3 - - + -
68C LEU* 4.3 14.1 - - + -
81C THR* 4.5 15.0 - - + -
82C VAL 3.4 6.7 - - - +
83C LEU* 4.2 15.0 - - + +
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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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40C THR* 4.1 7.0 - - + +
41C LEU* 1.3 80.8 - - - +
43C TYR* 1.3 62.9 + - - +
52C LEU* 3.9 34.1 - - + +
53C LYS 3.5 7.2 - - - +
54C VAL* 3.4 31.4 - - + +
55C VAL 4.6 0.4 - - - +
81C THR* 3.1 8.7 - - - -
82C VAL* 2.9 49.2 + - + +
84C GLU* 4.0 30.7 - - - +
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Residues in contact with TYR 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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41C LEU* 4.9 2.0 - - + -
42C LEU* 1.3 78.2 - - - +
44C THR* 1.3 77.3 + - - +
45C ILE* 4.8 3.4 - - + -
52C LEU* 3.3 6.5 - - - -
53C LYS* 3.0 49.7 + - + +
55C VAL* 4.9 11.2 - - + -
68C LEU* 5.1 2.7 - - + -
71C GLU* 3.3 46.6 + - + -
72C TRP* 3.0 49.8 - + + -
79C TYR* 3.9 10.5 - + - -
80C VAL 3.1 11.7 - - - +
81C THR* 3.9 1.3 - - + -
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Residues in contact with THR 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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30B LEU* 4.2 17.7 - - + -
33B ARG* 3.2 23.8 + - - +
43C TYR* 1.3 84.5 - - - +
45C ILE* 1.3 75.1 + - - +
50C GLU* 2.9 36.1 + - - +
51C ASP 4.0 5.2 + - - -
52C LEU* 3.9 17.7 - - + -
79C TYR* 3.6 3.1 - - - -
80C VAL* 3.0 27.7 + - + +
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Residues in contact with ILE 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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33B ARG* 3.2 12.6 + - - -
43C TYR* 4.8 4.3 - - + -
44C THR* 1.3 87.3 + - - +
46C MET* 1.3 61.2 + - - +
47C SER* 3.3 24.2 - - - +
48C LYS* 3.2 31.5 - - + +
50C GLU* 4.5 22.4 + - - +
77C GLU* 3.4 27.1 - - + +
78C ALA 3.3 8.1 - - - +
79C TYR* 3.7 30.7 - - + -
80C VAL* 4.8 0.7 - - - +
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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