Contacts of the strand formed by residues 19 - 26 (chain C) in PDB entry 3OAD
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 GLN 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C THR 3.4 2.5 - - - +
14C ASN* 3.6 2.9 - - - +
15C TYR* 2.7 67.3 + - + +
18C THR* 1.3 90.1 + - - +
20C TYR* 1.3 62.3 + - - +
21C TYR* 4.1 8.2 - - + -
121C LEU 3.9 14.8 + - - -
122C ALA* 4.4 2.1 - - - +
123C GLU* 2.8 34.4 + - - +
124C PHE* 3.5 15.0 - - + -
167C LPO 3.4 27.5 - - + +
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Residues in contact with TYR 20 (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 LEU* 4.4 7.1 - - + +
13C THR 3.3 6.7 - - - -
14C ASN* 3.0 28.8 + - + -
17C ASP* 3.2 10.5 + - - -
18C THR 4.5 0.2 - - - -
19C GLN* 1.3 78.0 - - - +
21C TYR* 1.3 61.7 + - - +
36C VAL* 3.6 24.2 - - - +
37C PHE* 4.9 1.0 + - - -
162C TYR* 3.5 52.9 + + + +
163C ASN 2.7 20.9 + - - -
167C LPO 3.3 9.8 + - - +
173D GLY 3.5 25.6 - - - -
317D ALA* 3.5 31.2 - - + -
321D ARG* 2.9 24.9 + - - +
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Residues in contact with TYR 21 (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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54A LEU* 3.0 28.8 + - + +
55A TYR* 3.6 14.4 - - - -
12C LEU* 3.9 9.0 - - - +
13C THR* 2.6 67.5 + - + +
15C TYR* 4.0 16.8 - - + -
19C GLN* 4.1 7.2 - - + -
20C TYR* 1.3 77.5 - - - +
22C GLY* 1.3 54.0 + - - +
34C LYS* 3.7 36.8 - - + -
35C VAL 3.2 23.1 - - - +
36C VAL* 4.1 2.5 - - + +
37C PHE* 5.6 0.4 - - - -
123C GLU* 3.7 24.7 - - + +
124C PHE* 3.9 22.4 - + + -
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Residues in contact with GLY 22 (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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54A LEU* 4.9 4.7 - - - -
10C VAL* 4.3 1.1 - - - -
11C ILE 3.8 17.0 - - - -
12C LEU* 3.7 11.7 - - - +
21C TYR* 1.3 73.0 - - - +
23C GLU* 1.3 65.5 + - - -
34C LYS* 3.2 6.6 - - - +
35C VAL* 2.8 34.9 + - - -
37C PHE* 4.2 5.4 - - - -
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Residues in contact with GLU 23 (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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53A ARG* 2.9 38.2 + - - -
54A LEU* 3.9 24.1 - - + +
10C VAL* 4.2 15.0 - - - +
11C ILE 4.8 1.6 + - - -
22C GLY* 1.3 77.5 - - - +
24C ILE* 1.3 70.7 + - - +
32C THR* 4.4 19.0 + - + -
33C PHE 3.2 10.4 - - - +
34C LYS* 4.4 12.1 + - + +
98C THR 4.9 0.3 - - - +
99C VAL* 5.2 3.8 - - - +
100C GLY 5.3 1.9 + - - -
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Residues in contact with ILE 24 (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 GLU* 1.3 80.6 - - - +
25C GLY* 1.3 59.0 + - - +
26C ILE* 3.8 32.1 - - + -
31C GLN 3.8 0.5 - - - +
32C THR* 3.4 5.8 - - - -
33C PHE* 2.9 40.1 + - + +
35C VAL* 3.7 34.3 - - + -
37C PHE* 4.0 7.4 - - + -
44C VAL* 5.0 3.4 - - + -
46C VAL* 5.0 1.1 - - + -
97C ILE* 3.9 15.7 - - + -
98C THR 3.5 9.4 - - - +
99C VAL* 3.8 27.4 - - + -
128C VAL* 4.3 13.0 - - + -
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Residues in contact with GLY 25 (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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24C ILE* 1.3 73.0 - - - +
26C ILE* 1.3 60.6 + - - -
27C GLY 5.4 0.2 - - - -
30C PRO* 4.2 14.6 - - - -
31C GLN 3.6 6.3 - - - -
32C THR* 4.5 3.1 - - - -
96C ILE 4.4 0.4 - - - -
97C ILE* 3.1 11.7 - - - +
98C THR* 2.9 46.7 + - - -
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Residues in contact with ILE 26 (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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24C ILE* 3.8 23.3 - - + -
25C GLY* 1.3 79.3 - - - +
27C GLY* 1.3 63.2 + - - +
31C GLN* 2.7 45.5 + - - +
33C PHE* 4.3 8.1 - - + -
44C VAL* 5.2 2.0 - - + -
46C VAL* 4.0 32.5 - - + -
64C PHE* 3.3 27.6 - - + -
95C ASP* 3.9 5.8 - - + -
96C ILE 3.4 4.7 - - - +
97C ILE* 4.1 14.8 - - + -
108C PHE* 3.7 29.4 - - + -
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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