Contacts of the strand formed by residues 35 - 40 (chain E) in PDB entry 3LNX
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 ILE 35 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E VAL* 3.8 32.8 - - + -
23E THR 3.5 2.5 - - - +
24E GLY 3.7 7.4 - - - +
25E GLY* 3.5 31.0 - - - +
33E GLY 4.6 1.1 - - - +
34E GLY* 1.3 72.7 - - - -
36E TYR* 1.3 61.0 + - - +
57E ARG* 3.4 9.7 - - - +
58E VAL* 2.9 35.0 + - + +
66E LEU* 4.0 39.5 - - + +
69E ALA* 4.5 4.7 - - + +
70E THR 4.8 0.2 - - - +
71E HIS* 5.0 1.1 - - + -
74E ALA* 3.6 27.8 - - + -
78E LEU* 5.5 1.6 - - + -
104E SCN 5.0 2.6 - - - -
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Residues in contact with TYR 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C GLU* 2.8 31.7 + - - -
22E VAL* 3.1 9.8 - - - +
23E THR* 2.8 45.1 + - + -
30E VAL* 3.7 13.7 - - + -
31E ARG* 3.3 52.9 + - + +
32E HIS* 3.4 6.1 + - - -
34E GLY* 3.7 19.3 - - - -
35E ILE* 1.3 75.7 - - - +
37E VAL* 1.3 64.5 + - - +
55E GLY* 3.6 24.5 - - - +
56E ASP 3.4 4.3 - - - +
57E ARG* 3.5 30.5 + - + -
58E VAL* 5.0 0.7 - - - -
90E GLU* 6.3 0.2 - - - -
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Residues in contact with VAL 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ILE* 4.3 13.7 - - + -
21E SER 3.6 5.6 - - - +
22E VAL* 4.6 1.1 - - - +
23E THR* 5.0 0.4 - - - +
36E TYR* 1.3 71.0 - - - +
38E LYS* 1.3 64.4 + - - +
39E ALA 3.7 20.9 - - - +
40E VAL* 3.8 21.5 - - + -
52E ILE* 3.9 20.0 - - + -
53E HIS 3.7 14.1 - - - +
54E LYS* 3.5 3.3 - - - +
55E GLY* 2.9 26.3 + - - -
56E ASP* 2.9 26.1 + - + +
58E VAL* 4.1 19.7 - - + -
89E LEU* 4.5 0.7 - - + -
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Residues in contact with LYS 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E SER* 2.7 32.0 + - - +
22E VAL 3.9 17.9 - - - +
23E THR* 4.1 18.4 - - + +
36E TYR 3.3 2.4 + - - -
37E VAL* 1.3 73.6 - - - +
39E ALA* 1.3 60.9 + - + +
54E LYS* 3.3 27.6 + - - +
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Residues in contact with ALA 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E ILE* 3.4 3.8 - - - -
21E SER* 3.0 37.1 + - - +
37E VAL* 3.5 6.8 - - - +
38E LYS* 1.3 84.7 - - + +
40E VAL* 1.3 67.2 + - - +
41E ILE* 4.0 7.1 + - + -
54E LYS* 4.8 5.4 - - + -
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Residues in contact with VAL 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E GLY 3.5 7.9 - - - +
20E ILE* 4.1 10.1 - - + -
37E VAL* 3.8 18.2 - - + -
39E ALA* 1.3 77.4 - - - +
41E ILE* 1.3 65.6 + - - +
42E PRO* 3.3 8.5 - - - +
46E ALA* 4.6 7.9 - - + -
47E GLU* 4.6 22.8 - - + +
52E ILE* 3.8 24.7 - - + +
53E HIS* 4.1 12.1 - - + -
54E LYS* 4.1 7.2 - - + +
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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