Contacts of the strand formed by residues 26 - 34 (chain D) in PDB entry 6P7B
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 THR 26 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ASN 3.6 1.6 - - - +
20D TYR* 4.5 0.4 - - - -
21D ASP* 3.2 43.7 + - - +
24D SER* 3.0 22.7 + - - -
25D ASN* 1.3 74.3 + - - +
27D ILE* 1.3 62.4 + - - +
28D LYS* 3.3 33.0 + - + +
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Residues in contact with ILE 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 5.4 2.9 - - + -
19D ASN 4.1 2.2 - - - +
20D TYR* 3.5 24.9 - - + -
25D ASN* 3.6 10.3 + - - +
26D THR* 1.3 73.6 - - - +
28D LYS* 1.3 71.2 + - - +
29D LEU* 4.9 0.4 - - - +
115D GLU 4.6 1.0 - - - +
116D TYR* 3.2 72.4 - - + +
141D LEU* 4.9 1.3 - - + -
144D MET* 3.4 31.6 - - + -
145D GLU* 4.3 15.5 - - - +
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Residues in contact with LYS 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 3.3 4.0 - - - +
19D ASN* 2.7 66.5 + - + +
21D ASP* 3.2 31.3 + - - -
26D THR* 3.3 23.2 + - + +
27D ILE* 1.3 81.7 - - - +
29D LEU* 1.3 60.6 + - - +
30D ILE* 5.1 3.6 - - + -
116D TYR* 3.9 7.9 - - - +
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PHE* 3.5 36.3 - - + -
27D ILE* 5.8 0.2 - - + -
28D LYS* 1.3 70.3 - - - +
30D ILE* 1.3 66.4 + - - +
31D ALA* 3.8 22.9 - - - +
32D ILE* 4.2 15.5 - - + -
113D ILE* 5.0 9.6 - - + +
116D TYR* 3.3 36.5 + - + +
117D THR* 3.7 33.9 + - + +
137D PHE* 3.8 21.3 - - + -
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ILE* 5.9 0.9 - - + -
17D ILE* 2.8 23.7 + - + +
18D PHE 4.6 1.1 - - - -
19D ASN* 3.1 41.3 - - - +
28D LYS* 3.7 4.7 + - + -
29D LEU* 1.3 80.4 - - - +
31D ALA* 1.3 61.2 + - + +
52D TYR* 3.6 37.0 - - + +
117D THR* 5.3 1.4 + - - -
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D TYR* 4.7 3.6 - - + -
16D ALA* 3.3 4.5 - - - +
17D ILE* 2.9 40.9 + - + +
18D PHE* 4.3 0.5 - - - -
29D LEU* 3.7 8.1 - - - +
30D ILE* 1.3 86.7 - - + +
32D ILE* 1.3 65.1 + - - +
33D GLU* 5.0 11.4 - - + +
52D TYR* 4.8 9.6 - - + -
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Residues in contact with ILE 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ALA* 5.1 0.2 - - + -
15D TYR 3.6 12.1 - - - +
16D ALA* 3.9 12.8 - - + -
29D LEU* 4.2 20.9 - - + -
31D ALA* 1.3 77.9 - - - +
33D GLU* 1.3 84.3 + - - +
123D ILE* 4.6 32.2 - - + +
127D TYR* 4.6 6.1 + - + -
133D ILE* 4.4 25.6 - - + +
136D SER* 3.8 22.0 - - - +
137D PHE* 5.2 8.7 - - + -
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ALA* 3.3 6.0 - - - +
15D TYR* 2.9 65.8 + - + +
31D ALA* 5.0 8.1 - - + +
32D ILE* 1.3 90.6 + - - +
34D LYS* 1.3 60.6 + - - +
35D SER* 3.9 1.1 + - - -
51D ARG* 6.2 1.3 - - - +
123D ILE* 5.1 6.9 - - - +
127D TYR* 2.2 37.7 + - - -
133D ILE* 5.7 1.3 - - - -
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Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D ASN* 4.2 11.2 - - + -
13D PRO 3.6 14.6 - - - +
14D ALA* 4.0 2.7 - - + -
33D GLU* 1.3 73.3 - - - +
35D SER* 1.3 67.0 + - - +
36D ASP* 6.0 1.2 - - - +
127D TYR* 3.7 32.6 + - + -
128D THR 5.7 0.7 - - - -
129D LYS* 3.7 28.9 - - + +
132D ASP* 3.1 31.4 - - - +
133D ILE* 5.2 1.8 - - + -
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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