Contacts of the strand formed by residues 119 - 126 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ILE* 4.1 0.2 - - - -
34B PRO* 3.3 27.4 - - + +
46B VAL* 5.2 3.4 - - + +
49B GLN* 3.7 32.3 - - + +
50B ALA* 3.9 17.3 - - + +
53B SER* 3.6 16.8 - - - +
76B VAL* 4.3 3.8 - - + -
77B PHE 3.1 13.7 - - - +
78B ILE* 4.0 8.1 - - + -
87B ILE* 4.1 25.4 - - + -
113B LEU* 3.4 5.2 - - - -
117B VAL* 3.3 8.1 - - - +
118B LYS* 1.3 81.4 - - + +
120B GLU* 1.3 59.9 + - - +
121B ILE* 3.8 26.9 - - + -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A SER* 3.4 17.0 - - - -
107A CYS 2.9 39.9 + - - +
108A VAL* 4.0 6.4 - - - +
31B GLY* 3.6 23.8 - - - +
32B GLN 3.4 7.0 - - - +
33B ILE* 3.9 13.1 - - + +
75B THR 3.6 2.1 - - - +
77B PHE* 2.9 38.1 + - + -
113B LEU* 3.5 15.3 - - + +
114B PRO* 3.5 17.4 - - - +
119B LEU* 1.3 75.9 - - - +
121B ILE* 1.3 66.3 + - - +
122B GLU 4.3 0.2 - - - -
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B SER 3.9 0.5 - - - +
31B GLY* 4.0 1.1 - - - -
32B GLN* 2.7 40.3 + - - +
50B ALA* 4.7 0.4 - - + +
53B SER* 3.9 14.6 - - - -
54B LEU* 3.8 26.7 - - + +
57B VAL* 3.6 13.0 - - + +
74B MET* 3.7 35.7 - - + -
75B THR 3.3 6.7 - - - +
76B VAL* 4.2 19.3 - - + -
87B ILE* 5.9 0.4 - - + -
91B TYR* 4.8 5.2 - - + -
119B LEU* 3.8 27.8 - - + -
120B GLU* 1.3 79.0 - - - +
122B GLU* 1.3 63.9 + - - +
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Residues in contact with GLU 122 (chain B).
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* 3.0 37.1 + - - +
75A THR* 4.3 5.9 + - - +
106A SER* 2.6 40.4 + - - +
29B THR* 3.8 13.6 - - - +
30B SER 4.1 0.4 - - - -
31B GLY* 3.9 4.0 - - - -
74B MET* 3.2 8.0 - - - +
75B THR* 3.0 55.1 + - - +
77B PHE* 4.4 10.2 - - + -
120B GLU 4.3 0.4 + - - -
121B ILE* 1.3 75.8 - - - +
123B ALA* 1.3 61.1 + - - +
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Residues in contact with ALA 123 (chain B).
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* 5.3 1.5 + - - -
28B PHE* 3.7 1.0 - - - +
29B THR* 2.9 41.0 + - + +
57B VAL* 3.6 19.1 - - + -
61B VAL* 5.1 1.6 - - + -
71B ILE* 4.2 9.6 - - + -
73B LYS 3.3 6.7 - - - +
74B MET* 3.5 25.1 - - + -
122B GLU* 1.3 77.3 - - - +
124B ILE* 1.3 69.0 + - - +
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Residues in contact with ILE 124 (chain B).
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* 4.3 12.8 - - - +
124A ILE* 6.0 0.2 - - + -
26B MET* 3.3 32.1 - - + -
27B VAL 3.3 9.0 - - - +
28B PHE* 3.6 28.7 - - + -
71B ILE* 3.6 2.9 - - - -
72B ILE* 2.8 39.1 + - + +
73B LYS* 2.9 27.4 + - + +
123B ALA* 1.3 78.3 - - - +
125B ALA* 1.3 64.3 + - - +
28C PHE* 3.6 28.0 - - + -
124C ILE* 5.9 0.4 - - + -
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Residues in contact with ALA 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B MET* 3.2 5.7 - - - +
27B VAL* 2.8 36.2 + - + +
61B VAL* 4.2 20.6 - - + -
66B LEU* 3.9 19.3 - - + -
70B ASP 3.2 20.6 - - - +
71B ILE* 4.0 6.1 - - + +
72B ILE 4.2 0.4 - - - +
123B ALA 4.3 0.2 - - - -
124B ILE* 1.3 74.2 - - - +
126B VAL* 1.3 67.5 + - - +
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Residues in contact with VAL 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B SER 3.5 10.3 - - - +
26B MET* 4.1 10.8 - - + -
66B LEU* 3.9 4.4 - - - +
70B ASP* 2.9 33.3 + - - +
72B ILE* 3.8 29.4 - - + -
125B ALA* 1.3 80.8 - - - +
127B ARG* 1.3 63.5 + - - +
128B SER* 3.5 16.0 + - - +
2C LYS* 4.4 6.7 - - + -
23C LEU* 3.6 38.4 - - + -
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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