Contacts of the strand formed by residues 24 - 30 (chain D) in PDB entry 4D2T
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 LYS 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLU* 2.9 43.1 + - - -
95A PHE* 4.4 6.3 - - - -
96A ASP* 3.6 5.5 + - - -
136A GLU* 5.1 2.8 - - - +
4D TYR* 5.6 1.5 + - - +
16D THR* 3.6 25.1 - - + -
18D GLY 3.7 8.5 - - - +
19D THR* 4.4 10.8 - - - -
20D GLY 4.8 2.2 - - - +
21D GLY 5.6 3.1 - - - +
22D PHE 3.6 3.3 + - - +
23D ALA* 1.3 71.6 - - - +
25D VAL* 1.3 65.0 + - - +
26D LYS* 3.5 31.8 + - - +
39D ILE 3.5 2.1 - - - +
40D LYS* 3.6 0.9 - - - -
41D ILE* 2.9 45.7 + - + +
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Residues in contact with VAL 25 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A THR* 5.3 5.8 - - - +
16D THR* 3.7 3.3 - - - +
17D ILE* 2.9 56.1 + - + +
18D GLY* 3.4 12.4 + - - +
23D ALA* 4.8 4.9 - - + +
24D LYS* 1.3 78.2 - - - +
26D LYS* 1.3 65.5 + - - +
27D LEU* 5.8 0.2 - - - -
38D ALA* 4.3 18.8 - - + -
39D ILE 3.4 8.7 - - - +
40D LYS* 3.8 27.1 - - + -
86D LEU* 6.3 0.2 - - + -
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Residues in contact with LYS 26 (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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95A PHE* 4.2 1.8 - - - -
96A ASP* 2.7 27.7 + - - +
99A ILE* 4.0 15.3 - - + +
4D TYR* 4.0 21.2 + - - -
13D LEU* 4.3 21.3 - - + -
14D HIS 4.0 12.6 - - - +
15D GLU 3.8 2.5 - - - -
16D THR* 3.3 20.0 - - + +
24D LYS* 3.5 27.0 + - + +
25D VAL* 1.3 76.2 - - - +
27D LEU* 1.3 65.4 + - - +
38D ALA* 3.8 1.6 - - - -
39D ILE* 2.9 32.7 + - + +
41D ILE* 3.6 27.1 - - + -
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D LEU* 4.0 1.4 - - - +
14D HIS* 2.9 43.9 + - + +
15D GLU* 2.8 43.8 + - + +
17D ILE* 4.7 14.0 - - + +
25D VAL* 4.2 0.6 + - - -
26D LYS* 1.3 80.5 - - - +
28D ALA* 1.4 68.2 + - - +
36D MET* 4.0 28.0 - - + -
37D VAL 4.0 8.3 - - - +
38D ALA* 4.8 3.4 - - + +
88D TYR* 3.7 28.3 - - + +
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Residues in contact with ALA 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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11D TYR* 4.1 10.1 - - + -
12D GLU 3.6 8.1 - - - +
13D LEU* 4.1 6.1 - - + -
14D HIS* 3.9 7.0 - - - +
27D LEU* 1.4 76.8 - - - +
29D CYS* 1.3 60.9 + - - +
30D HIS 4.2 0.2 - - - -
36D MET* 3.6 12.1 - - - +
37D VAL* 3.0 39.7 + - + +
39D ILE* 3.6 31.4 - - + -
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Residues in contact with CYS 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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11D TYR* 3.4 4.7 - - - -
12D GLU* 2.8 54.9 + - + +
14D HIS* 3.9 14.8 - - + -
28D ALA* 1.3 73.5 - - - +
30D HIS* 1.4 65.8 + - - +
31D ILE* 3.4 1.4 + - - -
34D GLY* 3.5 31.2 - - - -
35D GLU 4.0 3.6 - - - -
36D MET* 4.3 17.0 - - - -
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Residues in contact with HIS 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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10D TYR* 4.1 8.1 + - + +
11D TYR* 3.4 41.2 + + + -
28D ALA 4.2 0.6 - - - -
29D CYS* 1.4 72.0 - - - +
31D ILE* 1.4 67.3 + - - +
32D LEU* 3.8 23.2 + - + +
33D THR* 2.8 47.9 + - + +
34D GLY* 3.1 20.6 + - - -
35D GLU* 3.1 18.2 + - + +
37D VAL* 4.8 6.6 - - + +
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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