Contacts of the strand formed by residues 66 - 71 (chain K) in PDB entry 2XEW
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 66 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4K PHE* 3.3 15.3 - - + +
6K LYS* 3.8 36.9 - - + -
44K ILE 4.7 0.3 - - - +
45K PHE* 3.5 17.9 - - - -
64K GLU 3.5 6.1 + - - -
65K SER* 1.3 75.6 - - - +
67K LEU* 1.3 72.1 + - - +
68K HIS* 4.2 11.2 + - + +
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Residues in contact with LEU 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K ILE* 3.9 24.7 - - + -
4K PHE 2.8 13.3 + - - +
5K VAL* 3.4 15.8 - - + -
6K LYS* 2.8 25.3 + - - -
23K ILE* 5.8 0.2 - - + -
26K VAL* 4.5 11.0 - - + -
43K LEU* 4.6 8.7 - - + -
44K ILE 3.5 7.4 - - - +
45K PHE* 4.0 15.3 - - + -
50K LEU* 4.2 27.1 - - + -
56K LEU* 4.8 4.7 - - + -
61K ILE* 4.0 26.0 - - + -
65K SER* 4.2 6.7 - - - +
66K THR* 1.3 81.8 - - - +
68K HIS* 1.3 66.1 + - - +
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Residues in contact with HIS 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K VAL* 4.6 0.2 - - - -
6K LYS* 3.6 23.2 - - + +
7K THR 4.7 6.0 + - - -
8K LEU* 5.2 13.7 - - + +
42K ARG 3.6 0.9 - - - +
43K LEU* 3.3 9.0 - - - +
44K ILE* 2.8 52.1 + - + +
66K THR* 4.2 10.0 + - + +
67K LEU* 1.3 78.4 - - - +
69K LEU* 1.3 61.7 + - - +
70K VAL* 4.1 7.6 - - + -
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Residues in contact with LEU 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71J LEU* 3.8 28.4 - - + +
73J LEU* 5.8 0.2 - - + -
5K VAL* 3.6 16.8 - - + -
6K LYS 2.7 15.8 + - - +
7K THR* 3.7 14.2 - - + +
8K LEU* 3.4 18.0 - - - +
13K ILE* 4.0 22.7 - - + -
30K ILE* 4.2 7.2 - - + -
36K ILE* 3.9 15.0 - - + -
40K GLN 5.2 0.4 - - - +
41K GLN* 3.9 29.8 - - + +
42K ARG 3.6 4.3 - - - +
43K LEU* 4.1 8.3 - - + -
67K LEU 4.0 0.2 + - - -
68K HIS* 1.3 72.1 - - - +
70K VAL* 1.3 80.1 + - - +
71K LEU* 5.5 0.9 - - + -
1077K EDO 4.6 1.6 + - - -
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Residues in contact with VAL 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J THR* 3.4 20.9 - - + +
11J LYS* 4.8 0.4 - - + -
8K LEU* 3.2 32.8 - - + -
40K GLN 3.6 2.8 - - - +
41K GLN 3.9 0.3 - - - -
42K ARG* 2.9 54.9 + - + +
44K ILE* 4.6 16.4 - - + -
68K HIS* 5.1 3.8 - - + -
69K LEU* 1.3 78.3 - - - +
71K LEU* 1.3 70.7 + - - +
1077K EDO 2.9 24.5 - - - +
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Residues in contact with LEU 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76I GLY 4.3 0.3 - - - -
7J THR* 4.0 18.4 - - + -
11J LYS* 3.5 14.2 + - - +
36J ILE* 4.1 26.0 - - + -
69J LEU* 4.4 12.6 - - + +
71J LEU* 3.1 51.4 - - + +
36K ILE* 5.1 6.7 - - + -
40K GLN* 3.6 13.5 - - + +
42K ARG* 4.5 1.0 + - - -
69K LEU* 5.5 1.1 - - + -
70K VAL* 1.3 85.6 - - - +
72K ARG* 1.3 59.9 + - - +
73K LEU* 3.9 8.7 - - + -
1077K EDO 2.7 33.1 + - - +
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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