Contacts of the strand formed by residues 24 - 29 (chain A) in PDB entry 2YUW
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 VAL 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A SER 4.1 4.5 - - - +
19A VAL* 4.3 8.3 - - + +
23A THR* 1.3 80.2 - - - +
25A THR* 1.3 62.8 + - - +
26A MET* 4.8 9.1 - - + +
67A PHE 3.9 0.3 - - - +
68A THR* 3.1 24.8 - - - +
69A ILE* 3.1 32.3 + - + -
72A LEU* 3.8 10.8 - - + -
78A ILE* 4.2 8.1 - - + -
80A VAL* 5.3 0.4 - - + -
100A ILE* 4.4 19.5 - - + +
102A VAL* 3.7 38.1 - - + +
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Residues in contact with THR 25 (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 VAL* 3.0 27.2 - - - +
17A ASP* 3.3 12.4 + - + -
18A SER* 2.8 31.2 + - - +
20A THR* 5.7 1.4 + - - -
23A THR* 4.5 1.1 + - - -
24A VAL* 1.3 72.0 - - - +
26A MET* 1.3 66.8 + - - +
66A LYS* 3.1 42.2 - - - +
67A PHE 3.6 3.4 - - - +
68A THR* 3.1 19.5 + - - +
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Residues in contact with MET 26 (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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14A LEU* 3.8 16.6 - - + -
15A THR 3.9 8.1 - - - +
16A VAL* 3.4 34.5 - - + -
17A ASP 4.4 0.2 - - - +
24A VAL* 4.8 8.1 - - + -
25A THR* 1.3 91.9 - - - +
27A ARG* 1.3 61.3 + - - +
28A TRP* 3.9 4.4 - - + -
44A LEU* 4.5 16.4 - - + -
66A LYS* 3.4 3.3 - - - +
67A PHE* 2.8 39.8 + - + +
69A ILE* 5.4 2.5 - - + -
80A VAL* 4.0 28.5 - - + -
96A TYR* 3.7 24.5 - - + -
100A ILE* 3.8 13.7 - - + -
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Residues in contact with ARG 27 (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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13A LEU 3.9 2.0 - - - +
14A LEU* 3.3 11.3 - - - +
15A THR* 3.1 37.5 + - - +
16A VAL 5.2 0.4 - - - -
17A ASP* 3.7 34.0 + - + +
26A MET* 1.3 74.6 - - - +
28A TRP* 1.3 65.4 + - - +
29A ARG* 3.1 45.0 - - - +
65A THR 3.7 4.7 - - - -
66A LYS* 3.6 21.1 - - + +
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Residues in contact with TRP 28 (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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11A PRO* 4.5 17.7 - - + +
12A THR 4.1 7.2 - - - +
13A LEU 3.7 8.1 - - - -
14A LEU* 4.0 13.7 - - + -
26A MET* 3.9 11.9 - - + -
27A ARG* 1.3 80.8 + - - +
29A ARG* 1.3 82.3 + - - +
30A PRO* 4.4 1.7 - - + +
42A TYR* 4.1 29.4 - + + -
44A LEU* 3.7 22.7 - - + -
62A ILE* 3.6 46.7 - - + -
64A LYS 3.7 2.5 - - - -
65A THR* 3.1 54.6 + - + +
67A PHE* 3.8 13.2 - - + -
82A VAL* 4.1 18.6 - - + -
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Residues in contact with ARG 29 (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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11A PRO* 4.0 3.3 - - - +
12A THR* 3.3 24.8 + - - +
13A LEU* 3.7 42.6 + - + +
27A ARG* 3.1 38.8 - - - +
28A TRP* 1.3 93.5 + - - +
30A PRO* 1.3 78.1 - - + +
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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