Contacts of the strand formed by residues 42 - 49 (chain C) in PDB entry 5FQD
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 GLU 42 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371B ILE* 4.5 10.6 - - - +
372B GLY* 6.2 4.0 - - - -
20C VAL* 6.4 0.2 - - + -
33C LEU* 3.9 23.0 - - + +
34C ALA 3.4 7.0 - - - +
35C ILE* 4.4 13.6 - - + +
40C GLY 3.4 8.2 + - - +
41C GLU* 1.4 77.3 - - - +
43C VAL* 1.3 66.3 + - - +
77C ARG* 4.8 0.5 + - - -
92C LEU* 3.7 34.6 + - + +
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Residues in contact with VAL 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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17C TYR* 3.7 26.9 - - + -
33C LEU* 3.6 8.5 - - - +
34C ALA* 2.9 49.9 + - + +
41C GLU* 3.8 26.9 - - + +
42C GLU* 1.3 79.7 - - - +
44C ALA* 1.3 58.9 + - - +
45C VAL* 4.3 0.4 - - + -
77C ARG* 3.9 23.3 - - + +
89C VAL* 3.7 12.8 - - + -
90C MET 3.4 12.6 - - - +
92C LEU* 3.9 9.8 - - - +
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Residues in contact with ALA 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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23C ILE* 4.6 2.0 - - + -
31C ILE* 4.3 14.6 - - + -
32C TYR 3.3 7.6 - - - +
43C VAL* 1.3 74.3 - - - +
45C VAL* 1.3 62.0 + - - +
46C LYS 4.2 1.1 - - - +
89C VAL* 3.5 3.5 - - - +
90C MET* 2.9 44.5 + - + +
91C ASP 3.8 18.2 - - - +
92C LEU* 4.0 15.3 - - + +
93C LEU 5.3 0.4 - - - +
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Residues in contact with VAL 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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13C VAL* 4.0 8.3 - - + -
17C TYR* 4.6 0.4 - - + -
19C LEU* 4.0 17.5 - - + -
30C ASP 3.8 0.2 - - - +
31C ILE* 3.4 2.7 - - - -
32C TYR* 2.8 42.5 + - + +
34C ALA* 3.5 26.9 - - + -
43C VAL* 4.3 0.2 - - + -
44C ALA* 1.3 76.9 - - - +
46C LYS* 1.3 60.0 + - - +
47C LEU* 3.7 18.4 + - + -
87C VAL* 3.6 29.4 - - + -
88C LEU 3.4 2.9 - - - -
89C VAL* 3.9 22.9 - - + -
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Residues in contact with LYS 46 (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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28C PHE* 3.1 40.1 - - + -
30C ASP 3.5 5.6 - - - -
31C ILE* 3.9 24.5 - - + +
44C ALA 5.8 0.2 - - - -
45C VAL* 1.3 73.4 - - - +
47C LEU* 1.3 59.0 + - - +
56C GLN* 4.1 1.6 - - - +
57C LEU* 3.5 14.8 - - + +
60C GLU* 2.9 30.6 + - - +
64C TYR* 5.6 1.3 - - - -
87C VAL* 3.5 3.3 - - - -
88C LEU* 2.8 58.6 + - + +
90C MET* 3.9 22.2 - - + -
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Residues in contact with LEU 47 (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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11C PHE* 4.0 27.6 - - + -
13C VAL* 4.4 1.3 - - + -
19C LEU* 4.1 6.7 - - + -
28C PHE* 3.5 3.6 - - - -
29C GLY* 3.4 5.5 - - - -
30C ASP* 2.9 32.9 + - + +
32C TYR* 3.7 30.5 - - + +
45C VAL* 3.7 24.9 + - + -
46C LYS* 1.3 71.7 - - - +
48C GLU* 1.3 59.4 + - - +
85C TYR* 3.8 32.5 - - + -
86C ASN 3.6 1.1 - - - +
87C VAL* 3.8 24.7 - - + -
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Residues in contact with GLU 48 (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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28C PHE* 3.1 36.4 - - + +
29C GLY* 4.7 0.4 - - - -
47C LEU* 1.3 74.3 - - - +
49C SER* 1.3 72.9 + - - +
52C ALA* 4.0 3.8 - - + -
55C PRO* 3.3 21.1 - - - +
56C GLN 2.8 26.7 + - - -
57C LEU* 3.2 29.9 + - + +
58C LEU 4.9 1.6 + - - -
85C TYR* 3.3 5.7 - - - -
86C ASN* 2.8 58.7 + - + +
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Residues in contact with SER 49 (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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28C PHE 4.0 5.3 + - - -
29C GLY* 5.5 0.4 - - - -
48C GLU* 1.3 85.0 - - - +
50C GLN* 1.3 76.5 + - - +
51C LYS 4.5 2.5 + - - -
52C ALA* 3.2 31.9 + - - +
55C PRO* 5.8 0.2 - - - +
84C ASP* 3.5 17.5 + - - -
85C TYR* 3.8 15.4 - - - -
86C ASN* 4.2 0.2 + - - -
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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