Contacts of the strand formed by residues 10 - 17 (chain A) in PDB entry 5UWS
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 GLN 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 1.3 83.8 - - - +
11A PHE* 1.3 71.0 + - - +
60A LYS* 3.2 39.8 + - + +
62A ASN* 2.6 29.7 + - - +
84A GLN* 3.9 7.3 + - - +
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Residues in contact with PHE 11 (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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9A VAL* 4.8 13.0 - - + -
10A GLN* 1.3 80.6 - - - +
12A LYS* 1.3 63.4 + - - +
13A LEU 3.6 0.2 + - - -
59A ILE* 3.6 39.7 - - + -
60A LYS 2.9 8.1 + - - +
61A PHE* 3.4 10.8 - + + +
62A ASN* 2.8 29.8 + - - -
84A GLN* 3.2 31.0 - - + +
85A CYS* 4.8 0.7 - - - -
168A LEU* 3.8 48.2 - - + -
169A ILE* 3.9 16.8 - - + -
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Residues in contact with LYS 12 (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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10A GLN 4.5 0.2 + - - -
11A PHE* 1.3 70.9 - - - +
13A LEU* 1.3 62.5 + - - +
14A VAL* 3.9 9.6 - - - -
62A ASN* 3.7 8.9 - - + +
64A TRP* 3.5 51.6 - - + +
79A TYR 2.8 28.3 + - - -
81A ILE 2.6 24.6 + - - +
82A GLN* 3.6 26.2 - - + +
83A ALA* 3.7 5.6 - - + -
84A GLN* 2.8 36.2 + - - +
85A CYS* 3.2 10.3 + - - +
24C TYR* 4.5 4.8 - - - -
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Residues in contact with LEU 13 (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 PHE 3.6 0.8 + - - -
12A LYS* 1.3 74.3 - - - +
14A VAL* 1.3 75.0 + - - +
15A LEU* 4.1 5.6 - - + +
61A PHE* 3.7 17.9 - - + -
62A ASN 3.0 9.4 + - - +
63A VAL* 3.4 21.5 - - + -
64A TRP* 2.6 34.7 + - - +
85A CYS* 3.4 18.8 - - - +
86A ALA* 4.4 1.6 - - - -
87A ILE* 4.2 17.7 - - + -
161A PHE* 3.6 29.6 - - + -
164A LEU* 3.7 24.5 - - + -
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Residues in contact with VAL 14 (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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12A LYS* 3.9 8.3 - - - -
13A LEU* 1.3 78.6 - - - +
15A LEU* 1.3 60.5 + - - +
16A VAL* 4.1 4.8 - - + +
64A TRP* 3.7 10.5 - - + +
66A THR* 5.3 1.1 - - + -
79A TYR* 3.4 27.6 - - + +
80A TYR* 4.1 12.1 - - + -
83A ALA* 3.7 21.8 - - + -
85A CYS 3.1 6.4 + - - +
86A ALA* 3.0 26.3 - - + +
87A ILE 2.9 24.6 + - - +
108A LEU* 3.7 21.3 - - + -
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Residues in contact with LEU 15 (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* 4.2 10.5 - - + -
14A VAL* 1.3 74.1 - - - +
16A VAL* 1.3 56.2 + - - +
23A LYS* 3.6 39.3 - - + +
26A PHE* 4.8 5.8 - - + -
27A VAL* 3.3 34.3 - - + -
63A VAL* 4.4 6.1 - - + -
64A TRP 3.1 13.1 + - - +
65A ASP* 4.0 9.0 - - - +
66A THR* 2.8 32.2 + - - -
87A ILE* 3.4 35.0 - - + +
89A MET* 4.0 12.6 - - + -
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Residues in contact with VAL 16 (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 VAL* 4.7 5.8 - - + +
15A LEU* 1.3 80.3 - - - +
17A GLY* 1.3 60.0 + - - +
23A LYS* 3.4 9.8 - - - +
66A THR* 3.5 14.6 - - + +
80A TYR* 3.4 38.4 - - + +
87A ILE 3.0 13.4 + - - +
88A ILE* 3.4 19.1 - - + -
89A MET* 2.9 24.1 + - - +
104A TRP* 3.8 31.2 - - + +
108A LEU* 4.8 9.2 - - + -
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Residues in contact with GLY 17 (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* 1.3 78.9 - - - +
18A ASP* 1.3 66.3 + - - -
21A THR* 4.3 0.2 - - - -
23A LYS* 2.8 21.1 + - - +
68A GLY* 3.1 13.0 - - - -
88A ILE* 5.2 0.7 - - - -
89A MET 3.4 15.9 - - - -
104A TRP* 3.5 23.4 - - - -
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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