Contacts of the strand formed by residues 45 - 50 (chain A) in PDB entry 1LUK
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 TYR 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A ASN* 4.6 4.7 - - + +
5A ASN* 3.6 26.6 + - - -
6A LEU* 2.7 39.9 - - + -
12A TYR* 3.4 17.3 - + + -
36A VAL* 3.1 22.7 - - + -
37A ARG 3.5 3.4 - - - -
38A ASP* 3.2 37.9 - - + +
43A GLY 4.7 7.7 + - - -
44A THR* 1.3 81.8 + - - +
46A THR* 1.3 51.2 + - - +
65A HIS* 2.4 20.6 + - - -
66A ILE* 2.4 33.1 + - - +
76A TYR* 4.7 10.4 - + - -
87A ILE* 3.0 26.2 - - + -
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Residues in contact with THR 46 (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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36A VAL* 2.3 45.5 - - - +
37A ARG* 2.3 75.8 + - - +
39A SER* 4.0 2.8 - - - -
45A TYR* 1.3 69.0 - - - +
47A VAL* 1.3 57.2 + - - +
63A HIS* 4.1 22.2 - - + +
64A TYR 3.1 7.6 - - - +
65A HIS* 2.7 28.9 + - + +
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Residues in contact with VAL 47 (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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34A PHE* 2.6 33.4 - - + -
35A MET 2.6 4.0 - - - -
36A VAL* 3.2 19.7 - - + -
46A THR* 1.3 69.1 - - - +
48A SER* 1.3 57.5 + - - +
49A VAL* 3.3 17.2 + - + -
62A LYS 3.1 2.4 - - - +
63A HIS* 3.0 3.4 - - - -
64A TYR* 2.2 62.9 + - + +
66A ILE* 3.0 29.6 - - + -
78A VAL* 5.0 1.3 - - + -
90A LEU* 5.0 2.2 - - + -
91A ILE* 3.3 11.2 - - + -
101A LEU* 5.8 1.8 - - + -
105A LEU* 3.9 2.9 - - + -
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Residues in contact with SER 48 (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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21A ALA* 2.8 13.0 - - - +
25A LEU* 2.6 35.2 - - - +
33A ALA 3.2 1.6 - - - +
34A PHE* 2.9 3.8 - - - -
35A MET* 2.2 60.8 + - - -
36A VAL* 4.1 1.2 - - - +
37A ARG* 6.2 1.1 - - - +
46A THR* 4.2 0.8 - - - +
47A VAL* 1.3 64.6 - - - +
49A VAL* 1.3 60.8 + - - +
61A ILE* 3.5 1.2 - - - +
62A LYS 3.1 3.4 - - - -
63A HIS* 2.7 27.1 + - - -
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Residues in contact with VAL 49 (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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32A GLY 5.1 1.8 - - - +
33A ALA 2.8 6.5 - - - +
34A PHE* 3.9 1.3 - - + -
47A VAL* 3.3 28.5 - - + -
48A SER* 1.3 65.5 - - - +
50A PHE* 1.3 57.0 + - - +
60A CYS 4.5 0.2 - - - -
61A ILE* 3.5 0.2 - - - -
62A LYS* 2.4 50.7 + - + +
64A TYR* 2.9 25.4 - - + -
101A LEU* 5.1 7.9 - - + -
102A VAL* 2.9 43.2 - - + +
104A ARG 5.6 1.3 - - - +
105A LEU* 3.9 21.8 - - + +
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Residues in contact with PHE 50 (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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25A LEU* 2.4 36.1 - - + +
26A LEU* 3.7 4.9 - - - -
28A THR* 3.2 8.7 - - + -
29A GLY* 3.4 7.9 - - - -
30A LYS 3.0 27.3 - - - +
32A GLY 2.8 0.3 + - - -
33A ALA* 2.3 83.3 + - + -
49A VAL* 1.3 71.8 - - - +
51A THR* 1.3 58.8 + - - +
52A LYS* 3.9 7.4 - - + -
59A PRO* 3.1 32.3 - - + -
60A CYS 2.4 28.5 - - - +
61A ILE* 2.8 35.9 - - + -
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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