Contacts of the strand formed by residues 61 - 68 (chain C) in PDB entry 6D84
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 ILE 61 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLU* 4.4 18.2 - - + +
18C MET* 4.8 5.8 - - + +
57C GLU* 4.8 0.4 - - - -
58C TYR 2.9 22.7 + - - +
59C LYS* 3.6 12.6 - - + +
60C ASN* 1.3 86.6 - - - +
62C SER* 1.3 61.4 + - - +
63C PHE* 2.9 25.6 + - + -
174C SER* 5.3 2.0 - - - -
177C LEU* 3.7 32.1 - - + -
178C ARG* 5.0 22.0 - - + +
180C GLN* 6.0 2.9 - - - +
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Residues in contact with SER 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLU* 2.4 45.9 + - - +
18C MET 3.1 5.6 - - - +
55C THR* 3.9 15.7 - - - -
56C VAL 3.6 7.2 - - - -
57C GLU* 3.5 21.6 + - - -
60C ASN 4.1 2.0 + - - -
61C ILE* 1.3 69.8 - - - +
63C PHE* 1.3 59.7 + - - +
64C THR* 3.0 14.3 + - - -
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Residues in contact with PHE 63 (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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18C MET 3.8 4.7 - - - -
20C ILE* 4.5 7.0 - - + -
55C THR* 3.9 0.4 - - - -
56C VAL* 3.1 27.3 + - + +
58C TYR* 3.3 49.8 - + + -
61C ILE* 2.9 26.6 + - + -
62C SER* 1.3 66.6 - - - +
64C THR* 1.3 60.4 + - - +
65C VAL* 3.2 24.9 + - + +
170C LEU* 3.7 24.0 - - + -
173C LEU* 3.6 31.2 - - + -
174C SER* 3.6 27.8 - - - -
177C LEU* 3.6 28.9 - - + -
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Residues in contact with THR 64 (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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25B ASP* 4.7 19.0 + - - +
17C GLU* 4.8 2.1 - - - -
18C MET 2.9 16.2 + - - -
19C ARG* 3.4 8.4 - - + -
20C ILE* 2.8 33.8 + - - +
53C VAL* 5.0 2.9 - - + -
54C GLU 4.2 7.9 - - - +
55C THR* 4.3 10.7 + - - -
62C SER* 3.0 15.4 + - - -
63C PHE* 1.3 68.1 - - - +
65C VAL* 1.3 58.4 + - - +
66C TRP* 3.4 30.3 - - + +
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Residues in contact with VAL 65 (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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20C ILE* 3.4 17.5 - - + +
22C MET* 3.7 33.4 - - + -
34C LEU* 3.7 25.6 - - + -
37C LEU* 6.3 2.9 - - + -
53C VAL* 3.3 22.2 - - - +
54C GLU* 3.2 24.9 + - + +
56C VAL* 5.0 12.6 - - + -
63C PHE* 3.3 19.5 - - + +
64C THR* 1.3 71.4 - - - +
66C TRP* 1.3 62.9 + - - +
67C ASP 3.9 1.3 - - - +
89C ILE* 6.3 0.9 - - + -
170C LEU* 6.3 2.0 - - + -
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Residues in contact with TRP 66 (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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25B ASP* 5.4 4.9 + - - -
30B LYS* 5.8 6.7 - - - -
56B ASN* 3.2 50.7 - - + -
57B CYS* 5.1 7.4 - - - -
19C ARG* 4.6 2.2 - - + +
20C ILE 2.8 11.3 + - - +
21C LEU* 3.3 9.4 - - - +
22C MET 3.2 16.0 + - - -
51C PHE* 3.7 20.6 - + - -
52C ASN 3.7 3.6 - - - -
53C VAL* 3.7 31.9 - - + -
64C THR* 3.4 33.1 - - + +
65C VAL* 1.3 73.0 - - - +
67C ASP* 1.3 65.2 + - - +
68C VAL* 3.6 6.3 + - + +
81C TYR* 3.1 50.6 + + + -
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Residues in contact with ASP 67 (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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22C MET* 2.8 26.4 - - - +
30C LYS* 3.3 23.4 - - - +
31C THR* 3.3 24.5 - - - +
34C LEU* 3.6 21.2 - - + +
48C THR* 3.9 6.1 + - - -
51C PHE* 3.2 24.9 - - - +
52C ASN* 3.0 26.8 + - + +
65C VAL* 3.9 3.8 - - - +
66C TRP* 1.3 74.3 - - - +
68C VAL* 1.3 72.2 + - - +
69C GLY 3.8 2.8 + - - -
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Residues in contact with VAL 68 (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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56B ASN* 6.1 0.9 - - - +
86B MET* 3.7 23.6 - - + -
21C LEU* 5.0 6.7 - - + -
22C MET 3.1 9.2 + - - +
23C VAL* 3.5 23.4 - - + +
30C LYS* 3.3 13.3 - - - -
51C PHE* 4.6 10.1 - - + -
66C TRP* 3.6 10.4 + - + +
67C ASP* 1.3 81.4 - - - +
69C GLY* 1.3 66.7 + - - +
77C LEU 5.1 0.9 - - - +
78C TRP* 3.4 38.1 - - + +
81C TYR* 5.1 12.6 - - + -
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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