Contacts of the strand formed by residues 39 - 47 (chain A) in PDB entry 2YRY
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 TRP 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE* 2.9 51.5 - - + -
30A LYS 4.0 2.0 - - - -
31A GLN* 3.2 43.5 - - + +
38A GLN* 1.3 88.0 + - - +
40A ASN* 1.3 67.8 + - - +
41A LYS 4.1 1.4 + - - -
82A ILE* 3.4 42.0 - - + +
83A SER* 5.7 2.8 - - - +
84A ARG* 3.9 42.2 - - - +
87A THR* 4.5 4.3 - - + -
99A PHE* 4.6 4.0 - - + -
100A PHE* 4.4 3.1 - - - -
101A SER* 3.7 22.9 - - - -
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Residues in contact with ASN 40 (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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29A PHE* 4.5 0.7 - - - -
30A LYS* 3.1 35.6 + - + +
32A ALA* 3.9 16.6 - - - +
36A VAL* 5.9 0.2 - - - +
38A GLN* 3.8 25.8 + - - +
39A TRP* 1.3 80.8 + - - +
41A LYS* 1.3 65.3 + - - +
42A ARG* 3.3 34.8 + - + +
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Residues in contact with LYS 41 (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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27A TRP* 3.5 49.8 + - + +
28A LEU 3.6 8.7 - - - +
29A PHE* 3.5 42.1 - - + -
39A TRP 4.1 2.4 + - - -
40A ASN* 1.3 69.3 - - - +
42A ARG* 1.3 72.3 + - - +
55A LYS 5.3 0.5 - - - +
103A GLU* 3.5 21.2 + - - -
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Residues in contact with ARG 42 (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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27A TRP* 3.3 14.4 - - - -
28A LEU 3.0 30.9 + - - +
30A LYS* 5.4 3.8 - - + -
40A ASN* 3.3 32.6 + - + +
41A LYS* 1.3 80.2 + - - +
43A TRP* 1.3 62.0 + - - +
44A PHE* 3.6 16.7 + - + -
53A TYR* 5.0 14.5 - - + -
54A TYR 3.9 4.5 - - - +
55A LYS* 3.9 34.1 + - - +
63A LEU* 4.9 10.8 - - - +
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Residues in contact with TRP 43 (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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25A ALA* 3.4 22.2 - - + -
26A GLY* 3.1 16.2 - - - -
27A TRP* 2.9 75.5 - + + -
42A ARG* 1.3 73.7 - - - +
44A PHE* 1.3 61.1 + - - +
45A VAL* 3.2 29.4 - - + +
52A PHE 3.9 0.3 - - - +
53A TYR* 3.1 3.5 - - - -
54A TYR* 2.8 44.1 + + - +
56A ASP 3.7 18.2 - - - +
57A GLU* 3.7 23.5 - - + +
59A GLU* 3.7 19.6 + - + -
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Residues in contact with PHE 44 (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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25A ALA* 3.4 0.9 - - - -
26A GLY 3.1 42.3 + - - +
28A LEU* 3.9 31.2 - - + -
30A LYS* 3.9 29.2 - - + -
42A ARG* 3.6 17.7 + - + -
43A TRP* 1.3 76.5 - - - +
45A VAL* 1.3 68.4 + - - +
51A LEU* 3.2 34.3 - - + -
52A PHE 3.8 2.0 - - - -
53A TYR* 3.7 17.7 - + + -
66A ILE* 6.4 0.2 - - + -
100A PHE* 3.1 44.4 - + - -
111A TRP* 4.1 7.6 - - + -
115A MET* 4.7 0.9 - - + -
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Residues in contact with VAL 45 (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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16A ARG* 3.5 22.9 - - - +
22A VAL* 3.7 24.5 - - + -
24A LYS 3.6 3.6 - - - +
25A ALA* 4.2 3.8 - - + -
43A TRP* 3.2 31.6 - - + +
44A PHE* 1.3 80.5 - - - +
46A LEU* 1.3 60.8 + - - +
47A VAL* 3.8 8.7 + - + -
51A LEU* 3.6 3.9 - - - +
52A PHE* 2.7 50.8 + - - +
54A TYR* 4.1 11.0 - - + -
59A GLU* 3.7 10.3 - - - +
111A TRP* 5.1 1.1 - - - -
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Residues in contact with LEU 46 (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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22A VAL* 3.7 0.3 - - - -
23A THR* 2.6 61.7 + - + +
24A LYS* 2.7 23.9 + - + +
45A VAL* 1.3 71.1 - - - +
47A VAL* 1.3 59.0 + - - +
49A ARG* 4.7 3.6 - - - -
50A CYS 3.1 28.0 - - - +
51A LEU* 4.0 4.7 - - + +
68A LEU* 3.4 31.2 - - + -
111A TRP* 4.6 6.5 - - + -
114A ALA* 4.0 30.5 - - + +
115A MET* 4.4 7.2 - - + +
118A ALA* 4.4 7.6 - - + -
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Residues in contact with VAL 47 (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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16A ARG* 3.3 50.3 - - + +
20A ALA* 3.4 31.6 - - + +
21A PRO 4.3 2.2 - - - +
22A VAL* 3.5 23.1 - - - +
23A THR* 4.0 3.4 - - - -
45A VAL* 3.8 8.1 + - + -
46A LEU* 1.3 79.9 - - - +
48A ASP* 1.3 77.7 + - + +
49A ARG 3.4 2.0 - - - -
50A CYS* 2.8 19.4 + - - +
52A PHE* 3.1 15.1 - - + -
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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