Contacts of the strand formed by residues 119 - 126 (chain C) 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 LEU 119 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ILE* 4.0 0.2 - - - -
34C PRO* 3.2 26.9 - - + +
46C VAL* 5.1 2.5 - - + -
49C GLN* 3.8 31.9 - - + +
50C ALA* 3.8 24.9 - - + +
53C SER* 3.5 22.2 + - - +
76C VAL* 4.5 3.1 - - + -
77C PHE 3.1 12.6 - - - +
78C ILE* 4.1 9.2 - - + -
87C ILE* 4.1 22.2 - - + -
113C LEU* 3.4 6.3 - - - +
117C VAL* 3.3 7.9 - - - +
118C LYS* 1.3 84.7 - - + +
120C GLU* 1.3 61.7 + - - +
121C ILE* 4.0 22.2 - - + -
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Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B SER* 3.5 15.9 - - - -
107B CYS 2.7 42.8 + - - +
108B VAL* 4.1 6.6 - - - +
31C GLY* 3.6 25.4 - - - +
32C GLN 3.3 6.5 - - - +
33C ILE* 3.9 11.8 - - + +
76C VAL* 3.7 1.2 - - - -
77C PHE* 2.8 41.0 + - + +
113C LEU* 3.6 21.3 - - + +
114C PRO* 3.6 11.0 - - - +
119C LEU* 1.3 75.9 - - - +
121C ILE* 1.3 65.1 + - - +
122C GLU 4.3 0.2 - - - -
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Residues in contact with ILE 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C SER 3.9 0.3 - - - +
31C GLY* 3.5 1.3 - - - -
32C GLN 2.8 35.1 + - - +
50C ALA* 5.6 0.2 - - - -
53C SER* 4.0 17.3 - - - -
54C LEU* 3.7 31.9 - - + +
57C VAL* 3.6 18.9 - - + +
74C MET* 3.7 33.9 - - + -
75C THR 3.3 7.6 - - - +
76C VAL* 4.1 21.3 - - + -
87C ILE* 5.9 0.9 - - + -
91C TYR* 4.8 2.9 - - + -
119C LEU* 4.0 21.8 - - + -
120C GLU* 1.3 79.0 - - - +
122C GLU* 1.3 63.0 + - - +
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Residues in contact with GLU 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LYS* 2.8 27.7 + - - +
75B THR* 4.2 3.8 + - - -
106B SER* 2.7 36.6 + - - +
29C THR* 3.9 12.8 - - - +
31C GLY* 4.0 5.8 - - - -
57C VAL* 5.2 0.2 - - - -
73C LYS* 5.1 0.3 + - - -
74C MET* 3.2 8.5 - - - +
75C THR* 3.0 57.8 + - - +
77C PHE* 4.4 12.5 - - + -
120C GLU* 4.3 0.4 - - - +
121C ILE* 1.3 75.7 - - - +
123C ALA* 1.3 61.1 + - - +
124C ILE* 6.1 2.8 - - - +
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Residues in contact with ALA 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LYS* 5.8 0.7 + - - -
28C PHE* 3.7 1.0 - - - +
29C THR* 2.9 42.1 + - + +
57C VAL* 3.7 18.4 - - + -
61C VAL* 5.0 1.6 - - + -
71C ILE* 4.2 9.9 - - + -
73C LYS 3.3 7.2 - - - +
74C MET* 3.6 23.3 - - + -
122C GLU* 1.3 75.3 - - - +
124C ILE* 1.3 69.2 + - - +
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Residues in contact with ILE 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.8 26.5 - - + -
124A ILE* 5.9 0.9 - - + -
73B LYS* 5.7 4.3 - - - +
124B ILE* 5.9 0.2 - - + -
26C MET* 3.6 28.9 - - + -
27C VAL 3.3 10.5 - - - +
28C PHE* 3.7 29.6 - - + -
71C ILE* 3.7 3.7 - - - -
72C ILE* 2.9 37.9 + - + +
73C LYS* 2.9 26.0 + - + +
122C GLU* 6.1 2.9 - - - +
123C ALA* 1.3 80.3 - - - +
125C ALA* 1.3 65.1 + - - +
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Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C MET* 3.2 7.6 - - - +
27C VAL* 2.8 36.7 + - + +
29C THR* 6.3 0.2 - - - +
61C VAL* 4.3 20.0 - - + -
66C LEU* 3.9 18.6 - - + -
70C ASP 3.1 20.9 - - - +
71C ILE* 3.9 7.0 - - + +
72C ILE 4.2 0.4 - - - +
124C ILE* 1.3 75.1 - - - +
126C VAL* 1.3 63.1 + - - +
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A LYS* 5.0 7.9 - - + +
23A LEU* 3.4 40.2 - - + -
25C SER 3.5 11.0 - - - +
26C MET* 4.3 7.6 - - + -
66C LEU* 3.9 4.6 - - - +
70C ASP* 2.9 36.7 + - - +
72C ILE* 3.7 30.7 - - + -
125C ALA* 1.3 79.0 - - - +
127C ARG* 1.3 61.3 + - - +
128C SER* 3.9 10.5 + - - +
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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