Contacts of the strand formed by residues 57 - 64 (chain A) in PDB entry 1UY2
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 THR 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A THR* 2.6 33.3 + - - -
33A ASN* 2.8 29.4 + - - +
55A GLY 3.7 9.6 - - - +
56A ASN* 1.3 78.8 - - - +
58A VAL* 1.3 61.4 + - - +
59A THR* 5.2 2.1 + - - -
91A PRO* 4.4 19.4 - - + +
127A VAL* 3.7 16.4 - - + -
128A LEU 3.2 4.0 - - - -
129A VAL* 4.1 22.9 - - + -
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 3.3 40.8 - - + -
31A SER 3.6 4.7 - - - +
32A THR* 3.7 2.7 - - - +
34A SER* 4.8 0.9 - - - +
37A LEU* 3.6 27.6 - - + -
49A ILE* 4.4 4.3 - - + -
56A ASN* 5.3 0.9 - - + -
57A THR* 1.3 81.4 - - - +
59A THR* 1.3 61.3 + - - +
60A TYR* 3.5 24.4 - - + +
127A VAL* 3.4 1.0 - - - -
128A LEU* 2.8 34.9 + - + -
130A PHE* 3.8 25.1 - - + -
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Residues in contact with THR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 3.7 2.3 - - - +
30A ASN* 2.7 35.7 + - + -
31A SER* 2.9 31.3 + - - +
32A THR* 5.8 0.2 - - - -
57A THR* 5.2 2.9 + - - -
58A VAL* 1.3 72.9 - - - +
60A TYR* 1.3 68.0 + - - +
61A SER* 4.2 1.8 - - - +
89A ASP 5.8 0.4 - - - +
91A PRO* 5.3 2.9 - - - +
125A ASP* 4.1 22.2 - - + +
126A ILE 3.3 9.2 - - - +
127A VAL* 3.5 24.8 - - + +
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Residues in contact with TYR 60 (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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18A ARG* 3.9 13.2 - - - +
24A ILE* 4.1 5.2 - - + -
25A GLU 3.8 11.9 - - - -
26A ALA* 2.7 40.1 + - - +
29A TYR* 3.5 18.4 - - - -
30A ASN* 3.4 4.9 - - - -
49A ILE* 3.8 5.4 - - - +
58A VAL* 3.5 37.6 - - + +
59A THR* 1.3 75.0 - - - +
61A SER* 1.3 61.4 + - - +
63A ILE* 4.0 20.3 - - + +
125A ASP* 3.3 3.1 - - - -
126A ILE* 2.8 46.1 + - + +
128A LEU* 4.0 13.6 - - + +
139A PHE* 3.6 33.6 - + + -
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Residues in contact with SER 61 (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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15A PRO 4.7 0.9 - - - +
16A ILE* 2.9 31.2 + - - +
17A ARG* 3.8 4.9 - - - -
18A ARG* 4.5 1.8 + - - +
30A ASN* 2.9 34.0 + - - +
59A THR* 5.5 1.3 - - - -
60A TYR* 1.3 72.7 - - - +
62A ASN* 1.3 77.0 + - - +
63A ILE* 3.3 9.2 + - - +
125A ASP* 3.3 16.2 - - - -
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Residues in contact with ASN 62 (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 ILE* 2.8 37.1 + - - +
17A ARG* 3.4 25.1 - - + +
18A ARG 3.1 20.3 + - - +
60A TYR 3.9 0.8 + - - -
61A SER* 1.3 77.0 + - - +
63A ILE* 1.3 64.1 + - - +
64A ASP* 3.6 1.4 + - - +
123A VAL* 3.6 24.9 - - + +
124A HIS* 3.9 2.9 + - - -
125A ASP* 2.9 21.4 + - - +
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Residues in contact with ILE 63 (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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18A ARG* 3.3 26.5 - - + +
20A ALA* 3.7 26.7 - - + +
24A ILE* 4.2 17.9 - - + -
60A TYR* 4.0 22.4 - - + +
61A SER 3.6 13.5 - - - +
62A ASN* 1.3 70.3 - - - +
64A ASP* 1.3 60.9 + - - +
65A PHE* 3.4 29.6 - - + -
123A VAL* 3.3 2.2 - - - -
124A HIS 2.9 39.3 + - - +
126A ILE* 4.0 15.9 - - + -
139A PHE* 6.0 0.7 - - + -
141A PHE* 4.5 2.2 - - + -
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Residues in contact with ASP 64 (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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18A ARG 2.8 18.1 + - - +
19A ASP* 4.1 8.2 - - - +
20A ALA* 3.0 24.6 + - - +
21A PHE* 4.2 1.9 - - - -
62A ASN 3.6 1.9 + - - +
63A ILE* 1.3 71.1 - - - +
65A PHE* 1.3 60.9 + - - +
66A GLY* 2.9 27.3 + - - -
122A GLY* 3.8 7.7 - - - +
123A VAL* 4.0 20.9 - - + +
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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