Contacts of the strand formed by residues 51 - 59 (chain A) in PDB entry 5H8Q
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 GLY 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.5 24.4 - - - -
42A VAL 3.1 12.8 - - - -
43A LYS* 4.0 0.4 - - - -
44A ILE* 3.9 7.0 - - - -
49A ASN 3.7 2.4 + - - -
50A GLU* 1.3 80.3 - - - +
52A MET* 1.3 75.6 + - - +
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Residues in contact with MET 52 (chain A).
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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40A LYS 3.4 1.0 - - - +
41A PHE* 4.2 3.6 - - - -
42A VAL* 2.8 34.0 + - + +
44A ILE* 3.6 21.8 - - + -
50A GLU* 6.3 1.3 - - + -
51A GLY* 1.3 83.6 - - - +
53A ASN* 1.3 70.9 + - - +
54A VAL* 3.4 10.1 + - + +
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Residues in contact with ASN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 3.9 42.2 + - + +
40A LYS 3.6 4.2 - - - -
41A PHE* 3.8 28.8 + - - +
52A MET* 1.3 77.3 - - - +
54A VAL* 1.3 60.4 + - - +
55A LYS* 4.1 4.8 + - + +
301A ACT 5.4 0.2 - - - +
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 3.2 6.7 - - - -
40A LYS* 2.8 35.1 + - + +
42A VAL* 3.7 30.1 - - + -
52A MET* 3.9 11.0 - - + +
53A ASN* 1.3 74.8 - - - +
55A LYS* 1.3 71.9 + - - +
56A LYS* 3.5 25.5 + - + +
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Residues in contact with LYS 55 (chain A).
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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24A ILE* 3.8 38.7 - - + +
29A GLU 5.8 1.6 - - - +
37A PRO* 6.5 1.3 - - + -
38A CYS 4.1 2.7 - - - -
39A ARG* 4.7 7.4 - - + +
53A ASN* 5.1 4.7 - - + +
54A VAL* 1.3 78.5 - - - +
56A LYS* 1.3 66.0 + - - +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 3.8 26.2 - - + -
22A GLU 3.6 15.0 - - - +
23A ASP* 2.8 35.6 + - - +
24A ILE* 4.5 4.0 - - - +
31A CYS* 3.4 10.1 - - - -
37A PRO* 3.7 1.2 - - - +
38A CYS* 2.8 35.7 + - - +
40A LYS* 4.7 29.2 - - + +
54A VAL* 3.9 27.9 - - + +
55A LYS* 1.3 78.0 + - - +
57A CYS* 1.3 64.6 + - - +
81A LEU* 4.9 1.1 - - + -
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Residues in contact with CYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ILE 3.8 0.2 - - - +
21A VAL* 3.5 3.3 - - - +
22A GLU* 2.7 44.1 + - + +
23A ASP 4.6 2.0 - - - +
24A ILE* 3.7 23.8 - - - -
25A ASP 5.0 0.7 - - - -
30A THR 4.4 0.4 - - - -
31A CYS* 2.0 51.4 - - - -
35A THR* 3.6 20.4 - - + +
36A VAL 3.5 4.0 - - - -
38A CYS* 3.5 2.5 - - - -
56A LYS* 1.3 74.3 - - - +
58A CYS* 1.3 60.9 + - - +
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Residues in contact with CYS 58 (chain A).
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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12A THR* 4.6 5.8 - - - -
19A VAL* 4.5 8.5 - - + -
20A ILE 3.3 3.8 - - - +
21A VAL* 3.9 22.0 - - - -
35A THR* 3.2 4.3 - - - -
36A VAL* 2.8 33.2 + - + +
38A CYS* 2.0 47.8 - - + -
57A CYS* 1.3 74.0 - - - +
59A LYS* 1.3 61.8 + - - +
63A ILE* 3.8 24.2 - - + +
79A LEU* 4.2 6.1 - - + -
81A LEU* 4.6 1.6 - - - -
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Residues in contact with LYS 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A VAL* 3.5 0.3 - - - -
20A ILE* 2.8 61.2 + - + +
22A GLU* 2.8 32.6 + - + +
34A ASN* 3.7 39.2 + - - +
35A THR* 4.1 12.6 - - + -
58A CYS* 1.3 75.4 - - - +
60A GLY* 1.3 61.1 + - - +
63A ILE* 3.5 20.2 - - - +
278A TRP* 4.1 11.2 - - + -
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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