Contacts of the strand formed by residues 26 - 29 (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 MET 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A MET* 3.8 21.8 - - + -
22B ASP* 3.8 0.8 - - - -
23B LEU* 2.8 48.0 + - + +
24B GLY 3.4 1.2 + - - -
25B SER* 1.3 89.0 + - - +
27B VAL* 1.3 60.7 + - - +
28B PHE* 3.7 22.7 - - + -
124B ILE* 3.3 29.6 - - + -
125B ALA 3.2 11.4 - - - +
126B VAL* 4.1 11.2 - - + +
127B ARG* 4.7 1.6 - - - +
23C LEU* 5.0 1.3 - - + -
26C MET* 4.4 17.0 - - + +
28C PHE* 4.4 17.7 - - + -
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ILE* 3.6 22.4 - - + -
21B VAL 3.3 3.1 - - - -
22B ASP* 3.7 29.2 - - - +
26B MET* 1.3 76.1 - - - +
28B PHE* 1.3 70.7 + - - +
29B THR* 4.8 10.0 - - + +
61B VAL* 4.9 8.5 - - + -
64B ALA* 3.8 13.0 - - + -
66B LEU* 3.8 23.6 - - + -
123B ALA 4.0 0.2 - - - +
124B ILE* 3.3 6.9 - - - +
125B ALA* 2.8 41.2 + - + +
127B ARG* 4.6 2.2 - - - +
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Residues in contact with PHE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET* 3.8 13.7 - - + -
28A PHE* 5.8 1.3 - + - -
72A ILE* 3.9 16.4 - - + -
73A LYS* 3.4 22.2 - - + -
104A THR* 3.5 16.9 - - + +
124A ILE* 3.9 24.9 - - + -
20B GLY* 3.1 3.8 - - - -
21B VAL* 2.9 34.7 + - + +
23B LEU* 3.8 29.8 - - + -
26B MET* 3.7 28.9 - - + -
27B VAL* 1.3 78.8 - - - +
29B THR* 1.3 62.9 + - - +
123B ALA 3.7 2.0 - - - -
124B ILE* 3.6 31.9 - - + -
28C PHE* 5.7 1.3 - + - -
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Residues in contact with THR 29 (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* 5.0 6.2 - - - -
104A THR* 4.0 9.3 + - - -
106A SER* 5.0 0.2 + - - -
19B GLN 3.5 9.0 - - - -
20B GLY* 4.2 0.2 - - - -
27B VAL* 4.8 3.4 - - + -
28B PHE* 1.3 78.1 - - - +
30B SER* 1.3 74.4 + - - +
32B GLN* 4.8 1.1 - - - -
57B VAL* 4.5 8.2 - - + +
60B ILE* 3.8 28.5 - - + -
61B VAL* 4.1 22.4 - - + -
121B ILE 4.5 1.0 + - - -
122B GLU* 3.8 12.0 - - - +
123B ALA* 2.9 41.1 + - + +
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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