Contacts of the strand formed by residues 104 - 109 (chain A) in PDB entry 2UYK
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 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A ILE 2.9 15.9 + - - +
73A LYS* 3.3 18.6 - - - +
74A MET* 3.0 22.6 + - - -
103A PRO* 1.3 78.3 - - - +
105A ARG* 1.3 61.7 + - - +
18B VAL* 3.8 6.4 - - - +
20B GLY* 3.5 34.3 - - - -
21B VAL* 3.5 19.5 - - + +
28B PHE* 3.5 15.3 - - + +
29B THR 4.0 1.9 + - - -
30B SER* 3.3 19.5 - - - +
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Residues in contact with ARG 105 (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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73A LYS* 5.5 1.6 - - - -
74A MET 3.1 13.5 - - - +
76A VAL* 4.0 11.4 - - + -
84A PHE* 3.4 25.8 - - - -
87A ILE* 6.1 1.0 - - - +
88A ASN* 2.9 31.9 + - - +
91A TYR* 3.4 53.2 - - - +
104A THR* 1.3 77.3 - - - +
106A SER* 1.3 74.7 + - - +
107A CYS* 4.9 5.1 - - - +
16B PRO* 3.9 7.6 - - - +
17B TYR* 3.8 36.5 - - + +
30B SER* 2.9 14.2 + - - +
31B GLY 3.0 20.3 + - - +
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Residues in contact with SER 106 (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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73A LYS* 5.5 0.6 - - - +
74A MET 3.2 5.7 + - - -
75A THR* 3.6 10.8 - - - +
76A VAL 2.9 26.6 + - - -
105A ARG* 1.3 75.9 + - - +
107A CYS* 1.3 60.8 + - - +
108A VAL* 5.2 0.9 - - - -
29B THR 5.0 0.2 + - - -
30B SER* 4.0 0.3 - - - -
31B GLY* 3.0 24.3 + - - -
77B PHE* 4.4 12.1 - - - -
120B GLU* 3.4 12.8 - - - -
122B GLU* 2.6 31.2 + - - +
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Residues in contact with CYS 107 (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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76A VAL* 3.3 22.4 - - + +
78A ILE* 4.0 23.8 - - - -
81A LEU* 4.7 4.7 - - - -
84A PHE* 3.7 37.0 - - + -
105A ARG* 4.9 7.6 - - - +
106A SER* 1.3 75.9 - - - +
108A VAL* 1.3 64.0 + - - +
114B PRO* 3.5 17.4 - - + +
120B GLU* 2.9 21.9 + - - +
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Residues in contact with VAL 108 (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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75A THR* 5.9 1.3 - - + -
76A VAL 3.2 4.0 + - - +
77A PHE* 3.6 27.0 - - + -
78A ILE* 3.0 29.3 + - - +
81A LEU* 5.3 1.6 - - - -
106A SER 5.2 0.7 - - - -
107A CYS* 1.3 83.6 - - - +
109A GLN* 1.3 58.7 + - - +
110A VAL* 3.7 4.0 + - + -
77B PHE* 3.8 33.0 - - + -
110B VAL* 4.0 20.2 - - + -
112B ARG 4.2 2.7 - - - -
113B LEU* 3.4 25.6 - - + -
114B PRO* 5.0 1.3 - - - -
120B GLU* 3.5 8.1 - - - +
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Residues in contact with GLN 109 (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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78A ILE* 3.1 6.0 - - + +
79A THR 3.4 34.6 + - - +
80A ASP* 3.6 5.4 + - - +
81A LEU* 2.9 33.4 + - + +
108A VAL* 1.3 70.5 - - - +
110A VAL* 1.3 63.6 + - - +
110B VAL* 3.4 4.8 - - - +
111B ALA* 2.8 42.5 + - - +
112B ARG* 3.0 46.8 + - + +
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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