Contacts of the strand formed by residues 25 - 36 (chain D) in PDB entry 6B0B
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 HIS 25 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D SER* 3.2 1.0 - - - -
22D VAL* 2.9 38.4 + - + +
23D ASN 3.2 2.7 + - - +
24D GLY* 1.3 74.5 - - - +
26D GLU* 1.3 68.6 + - - +
27D PHE* 3.6 15.8 - + + -
51D GLY* 3.5 34.7 + - - -
54D LEU* 5.2 0.9 - - + -
55D PRO* 3.5 38.5 - - + +
56D PHE* 5.0 0.9 - + - -
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Residues in contact with GLU 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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20D GLY 3.4 7.0 - - - +
21D SER* 4.0 15.9 - - - +
24D GLY 3.4 10.8 + - - +
25D HIS* 1.3 86.4 + - - +
27D PHE* 1.3 64.2 + - - +
50D LYS* 4.7 1.7 - - - +
51D GLY* 4.3 7.4 + - - -
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Residues in contact with PHE 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 MET* 4.5 9.2 - - + -
19D GLU* 3.7 0.3 - - - +
20D GLY* 2.9 61.2 + - - +
21D SER 3.7 0.4 - - - -
22D VAL* 3.6 18.6 - - + -
25D HIS* 3.6 15.0 - + + -
26D GLU* 1.3 75.9 - - - +
28D GLU* 1.3 71.3 + - - +
29D ILE* 3.9 28.9 - - + -
50D LYS* 3.3 22.9 - - - +
51D GLY* 4.9 0.2 - - - -
54D LEU* 3.9 20.2 - - + -
56D PHE* 3.5 35.7 - + - -
61D LEU* 4.5 4.0 - - + -
124D LEU* 4.1 9.4 - - + -
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Residues in contact with GLU 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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17D HIS* 3.2 26.9 - - - -
18D MET 3.2 11.9 - - - +
19D GLU* 4.3 11.1 - - + +
27D PHE* 1.3 81.9 - - - +
29D ILE* 1.3 68.4 + - - +
30D GLU* 4.7 2.5 - - - +
48D VAL* 3.8 3.3 - - - +
49D THR* 3.0 38.9 + - - +
50D LYS* 3.6 24.9 + - + +
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Residues in contact with ILE 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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16D VAL* 3.8 2.5 - - + +
17D HIS* 3.5 1.2 - - - -
18D MET* 2.9 41.9 + - + +
27D PHE* 3.9 22.2 - - + -
28D GLU* 1.3 80.0 - - - +
30D GLU* 1.3 77.2 + - - +
46D LEU* 4.0 30.7 - - + -
47D LYS 3.5 11.0 - - - +
48D VAL* 4.4 11.0 - - + -
54D LEU* 4.4 3.1 - - + -
58D TRP* 3.6 27.6 - - + -
61D LEU* 3.7 18.6 - - + -
65D PHE* 5.6 4.3 - - + -
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Residues in contact with GLU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D VAL 3.5 3.2 - - - +
17D HIS* 2.6 48.9 + - - +
18D MET 3.9 0.2 + - - -
28D GLU* 4.7 1.7 - - - +
29D ILE* 1.3 96.7 + - - +
31D GLY* 1.3 59.1 + - - +
32D GLU* 4.6 7.2 - - - +
47D LYS* 2.9 36.9 + - + +
49D THR* 3.7 26.2 + - + +
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Residues in contact with GLY 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 LYS* 3.4 5.0 - - - +
16D VAL* 2.9 49.0 + - - +
30D GLU* 1.3 75.6 - - - +
32D GLU* 1.3 70.6 + - - +
45D LYS 3.2 13.2 - - - -
46D LEU* 3.7 5.6 - - - -
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Residues in contact with GLU 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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13D ARG* 6.4 0.7 - - - +
14D PHE* 3.3 11.2 - - - +
15D LYS* 4.5 17.4 - - + +
30D GLU* 4.6 6.6 - - - +
31D GLY* 1.3 88.2 + - - +
33D GLY* 1.3 60.6 + - - +
44D ALA* 4.6 0.7 - - - -
45D LYS* 2.9 40.6 + - + +
47D LYS* 4.4 16.3 + - - +
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Residues in contact with GLY 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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13D ARG* 3.2 14.0 + - - +
14D PHE* 3.1 46.7 + - - +
32D GLU* 1.3 76.3 - - - +
34D GLU* 1.3 62.4 + - - +
43D THR 3.2 14.4 - - - -
44D ALA* 3.9 0.7 - - - -
45D LYS* 4.6 0.7 - - - -
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Residues in contact with GLU 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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163A LEU* 5.2 5.2 - - - +
11D PHE* 3.5 29.3 - - + -
12D MET 3.5 7.9 - - - -
13D ARG* 2.4 44.2 + - + +
14D PHE* 4.0 2.7 - - - -
33D GLY* 1.3 74.3 - - - +
35D GLY* 1.3 59.3 + - - +
36D ARG* 4.7 6.9 + - - +
42D GLN* 4.6 2.5 - - - -
43D THR* 2.9 43.3 + - - +
45D LYS* 5.2 9.5 + - - -
72D TYR* 5.0 2.2 - - - -
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Residues in contact with GLY 35 (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 PHE* 3.5 8.0 - - - -
12D MET 3.2 30.5 + - - +
34D GLU* 1.3 78.4 - - - +
36D ARG* 1.3 77.6 + - - +
37D PRO* 3.8 2.7 - - - +
41D THR 3.4 12.1 - - - -
42D GLN* 4.0 5.8 - - - -
72D TYR* 4.4 4.8 - - - -
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Residues in contact with ARG 36 (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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138A PHE* 3.1 38.6 - - + -
163A LEU* 3.4 35.1 - - - +
167A ASP* 5.1 7.5 + - - -
10D GLU* 3.2 18.8 - - + +
11D PHE* 3.2 41.8 - - + -
34D GLU* 4.6 5.5 + - - +
35D GLY* 1.3 87.3 - - - +
37D PRO* 1.3 69.3 - - - +
38D TYR 3.3 1.8 - - - +
39D GLU* 4.1 24.0 - - + +
40D GLY* 3.1 18.0 + - - -
41D THR* 2.9 25.4 + - - +
43D THR* 5.9 0.2 + - - -
72D TYR* 4.4 1.6 - - - +
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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