Contacts of the strand formed by residues 25 - 36 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H SER* 3.3 1.7 - - - -
22H VAL* 2.9 37.8 + - + +
23H ASN* 3.2 3.1 + - + +
24H GLY* 1.3 74.9 - - - +
26H GLU* 1.3 71.6 + - - +
27H PHE* 3.5 16.2 - + + -
51H GLY* 3.5 35.6 + - - -
54H LEU* 4.9 1.1 - - + +
55H PRO* 3.5 36.9 - - + +
56H PHE* 5.1 0.4 - + - -
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Residues in contact with GLU 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H GLY 3.4 7.9 - - - +
21H SER* 4.0 16.1 - - - +
24H GLY 3.4 10.2 + - - +
25H HIS* 1.3 86.2 + - - +
27H PHE* 1.3 64.3 + - - +
50H LYS* 4.7 2.6 - - - +
51H GLY* 4.5 6.1 - - - -
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Residues in contact with PHE 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H MET* 4.6 8.1 - - + -
19H GLU* 4.5 0.3 - - - +
20H GLY* 2.9 60.8 + - - +
21H SER 3.8 0.4 - - - -
22H VAL* 3.6 18.4 - - + -
25H HIS* 3.5 14.6 - + + -
26H GLU* 1.3 76.4 - - - +
28H GLU* 1.3 71.1 + - - +
29H ILE* 3.8 30.5 - - + -
48H VAL* 5.2 0.2 - - + -
50H LYS* 3.3 23.6 - - - +
54H LEU* 3.8 19.5 - - + -
56H PHE* 3.5 36.3 - + - -
61H LEU* 4.6 3.4 - - + -
124H LEU* 4.2 8.7 - - + -
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Residues in contact with GLU 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H HIS* 3.2 28.3 - - - -
18H MET 3.2 12.1 - - - +
19H GLU* 4.2 12.0 - - + +
27H PHE* 1.3 80.4 - - - +
29H ILE* 1.3 66.7 + - - +
30H GLU* 4.7 2.5 - - - +
48H VAL* 3.8 3.5 - - - +
49H THR* 3.0 39.5 + - - +
50H LYS* 3.6 22.1 + - + +
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Residues in contact with ILE 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H VAL* 3.8 2.6 - - + +
17H HIS* 3.6 1.0 - - - -
18H MET* 2.9 42.9 + - + +
27H PHE* 3.8 21.5 - - + -
28H GLU* 1.3 79.4 - - - +
30H GLU* 1.3 78.6 + - - +
46H LEU* 4.1 28.7 - - + -
47H LYS 3.4 11.2 - - - +
48H VAL* 4.4 11.7 - - + -
54H LEU* 4.4 3.8 - - + -
58H TRP* 3.7 28.0 - - + -
61H LEU* 3.8 18.6 - - + -
65H PHE* 5.6 3.8 - - + -
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Residues in contact with GLU 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H VAL 3.5 3.2 - - - +
17H HIS* 2.6 50.1 + - - +
18H MET 3.9 0.3 + - - -
28H GLU* 4.7 1.6 - - - +
29H ILE* 1.3 94.0 + - - +
31H GLY* 1.3 59.1 + - - +
32H GLU* 4.6 8.5 - - - +
46H LEU 3.7 0.2 - - - -
47H LYS* 2.9 37.9 + - + +
49H THR* 3.7 24.7 - - + +
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Residues in contact with GLY 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H LYS* 3.4 4.5 - - - +
16H VAL* 2.9 47.7 + - - +
30H GLU* 1.3 75.7 - - - +
32H GLU* 1.3 72.0 + - - +
45H LYS 3.2 13.5 - - - -
46H LEU* 3.7 5.8 - - - -
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Residues in contact with GLU 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H ARG* 6.3 0.7 - - - +
14H PHE* 3.4 11.9 - - - +
15H LYS* 4.5 17.3 - - + -
30H GLU* 4.6 7.2 - - - +
31H GLY* 1.3 88.1 + - - +
33H GLY* 1.3 60.1 + - - +
44H ALA* 4.6 1.1 - - - -
45H LYS* 2.9 41.5 + - + +
47H LYS* 4.4 16.5 + - - +
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Residues in contact with GLY 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H ARG* 3.3 11.7 + - - +
14H PHE* 3.1 48.0 + - - +
32H GLU* 1.3 77.0 - - - +
34H GLU* 1.3 64.9 + - - +
43H THR 3.3 13.5 - - - -
44H ALA* 3.9 0.9 - - - -
45H LYS* 6.0 0.4 - - - -
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Residues in contact with GLU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E LEU* 5.3 5.6 - - + +
11H PHE* 3.5 22.6 - - + -
12H MET 3.6 8.5 - - - -
13H ARG* 2.4 52.5 + - + -
14H PHE* 4.0 2.7 - - - -
33H GLY* 1.3 75.6 - - - +
35H GLY* 1.3 58.7 + - - +
36H ARG* 4.8 6.5 + - - +
42H GLN* 4.6 2.7 - - - -
43H THR* 2.9 43.5 + - - +
45H LYS* 5.5 5.9 + - - -
72H TYR* 5.1 2.0 - - - -
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Residues in contact with GLY 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H PHE* 3.5 7.5 - - - -
12H MET 3.2 30.7 + - - +
34H GLU* 1.3 78.2 - - - +
36H ARG* 1.3 77.9 + - - +
37H PRO* 3.8 2.5 - - - +
41H THR 3.4 12.6 - - - -
42H GLN* 4.0 6.1 - - - -
72H TYR* 4.4 5.5 - - - -
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Residues in contact with ARG 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E PHE* 3.0 40.3 - - + -
163E LEU* 3.6 34.4 - - - +
167E ASP* 5.0 8.7 + - - -
10H GLU* 3.2 18.6 - - + +
11H PHE* 3.2 41.5 - - + +
34H GLU* 4.6 5.7 + - - +
35H GLY* 1.3 86.9 - - - +
37H PRO* 1.3 68.8 - - - +
38H TYR 3.3 1.6 - - - +
39H GLU* 3.3 24.2 + - + +
40H GLY* 3.1 18.4 + - - -
41H THR* 2.9 24.7 + - - +
72H TYR* 4.4 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