Contacts of the strand formed by residues 78 - 86 (chain C) in PDB entry 3SE4
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 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B MET* 4.1 16.6 - - + -
152B LYS* 5.8 0.2 - - - +
45C ILE* 3.6 19.8 - - - +
46C MET* 3.7 12.9 + - + +
47C SER 6.1 0.2 - - - +
77C GLU* 1.3 73.9 + - - +
79C TYR* 1.3 63.3 + - - +
80C VAL* 3.5 3.5 + - - +
98C ASN* 4.8 3.6 - - + +
99C PHE 3.7 5.4 - - - +
100C TRP* 3.1 44.2 - - + +
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Residues in contact with TYR 79 (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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43C TYR* 3.8 13.5 - + - -
44C THR 3.4 5.8 - - - +
45C ILE* 4.0 11.0 - - + -
71C GLU 3.9 6.8 + - - -
72C TRP* 3.1 70.8 - + + -
73C ARG 3.5 5.5 + - - -
74C SER* 3.2 49.5 + - - -
77C GLU* 3.8 23.5 - - + +
78C ALA* 1.3 70.1 - - - +
80C VAL* 1.3 62.0 + - - +
81C THR* 4.0 0.4 - - - +
98C ASN* 3.0 4.7 - - - -
99C PHE* 3.0 38.7 + - - +
101C LEU* 5.0 7.0 - - + -
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PRO* 4.3 4.3 - - + -
29B PHE* 3.9 42.4 - - + +
32B LEU* 3.5 28.5 - - + -
43C TYR* 3.2 1.4 - - - -
44C THR* 2.8 45.5 + - + +
45C ILE* 4.5 0.4 - - - -
46C MET* 4.0 22.2 - - + -
52C LEU* 4.4 2.2 - - + +
78C ALA 5.0 0.2 - - - +
79C TYR* 1.3 73.3 - - - +
81C THR* 1.3 62.5 + - - +
82C VAL* 6.0 0.2 - - + -
97C HIS 3.5 10.1 - - - +
98C ASN* 3.8 11.2 - - + -
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Residues in contact with THR 81 (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* 4.9 6.2 - - - -
25C LEU* 4.7 4.3 - - + +
41C LEU* 4.2 11.8 - - + +
42C LEU 3.0 11.2 - - - -
43C TYR* 3.3 11.2 - - + +
72C TRP* 3.1 42.2 - - + -
79C TYR 4.0 4.5 - - - +
80C VAL* 1.3 79.2 - - - +
82C VAL* 1.3 62.6 + - - +
83C LEU 4.1 0.2 - - - -
95C CYS 3.9 0.2 - - - +
96C SER* 3.1 7.9 - - - -
97C HIS* 2.7 39.3 + - - +
99C PHE* 3.4 13.7 - - + -
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Residues in contact with VAL 82 (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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29B PHE* 3.5 36.8 - - + -
41C LEU* 3.3 3.6 - - - +
42C LEU* 2.7 47.9 + - + +
52C LEU* 4.0 28.5 - - + -
80C VAL 5.7 0.2 - - - -
81C THR* 1.3 75.4 - - - +
83C LEU* 1.3 61.3 + - - +
84C GLU* 4.7 5.6 - - - +
94C SER* 3.1 28.5 - - - +
95C CYS 3.3 11.0 - - - +
96C SER* 4.9 0.2 - - - -
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Residues in contact with LEU 83 (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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12C CYS* 4.5 6.3 - - + -
14C PHE* 4.0 26.2 - - + -
27C TRP* 3.5 69.1 - - + +
29C LEU* 5.2 0.9 - - + -
39C TYR* 4.2 14.8 - - + -
40C THR 3.6 11.2 - - - +
41C LEU* 4.2 11.2 - - + -
81C THR 4.1 1.0 + - - -
82C VAL* 1.3 74.9 - - - +
84C GLU* 1.3 62.8 + - - +
93C PHE* 4.7 4.7 - - + -
94C SER* 3.3 5.0 + - - -
95C CYS* 2.8 43.1 + - - +
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Residues in contact with GLU 84 (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* 3.2 6.3 - - - +
40C THR* 2.7 48.0 + - - +
42C LEU* 4.0 21.9 - - + +
82C VAL* 4.7 3.6 - - - +
83C LEU* 1.3 75.6 - - - +
85C GLY* 1.3 57.2 + - - +
86C PHE* 3.5 33.2 - - + -
91C THR* 5.2 6.0 - - + +
93C PHE* 3.4 16.4 - - - +
94C SER* 4.2 14.6 + - - -
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Residues in contact with GLY 85 (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 PRO* 3.7 18.4 - - - -
38C HIS 3.2 9.6 - - - -
39C TYR* 3.8 9.4 - - - -
84C GLU* 1.3 73.4 - - - +
86C PHE* 1.3 62.1 + - - -
91C THR* 3.9 1.0 - - - +
92C LEU* 2.9 31.0 + - - +
93C PHE* 3.5 13.5 + - - +
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Residues in contact with PHE 86 (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 PRO* 4.1 1.1 - - - -
37C THR* 3.3 2.1 + - - -
38C HIS* 2.7 44.9 + - + +
40C THR* 3.2 34.3 - - - -
60C ASN* 4.0 15.3 - - - -
84C GLU* 3.5 38.6 - - + -
85C GLY* 1.3 74.3 - - - -
87C SER* 1.3 60.6 + - - +
88C GLY 3.8 8.1 + - - +
90C THR 2.8 19.1 - - - +
91C THR* 3.0 31.4 - - - -
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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