Contacts of the helix formed by residues 22 - 31 (chain E) in PDB entry 5LXY
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 22 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E LYS 3.4 15.3 - - - +
21E VAL* 1.3 82.7 - - - +
23E GLU* 1.3 63.5 + - - +
24E GLU* 3.7 7.1 + - - +
25E LEU* 3.1 27.9 + - + +
26E LEU* 3.2 19.6 + - - +
76E TYR* 5.5 3.1 + - - +
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Residues in contact with GLU 23 (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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22E THR* 1.3 72.3 - - - +
24E GLU* 1.3 63.9 + - - +
26E LEU* 3.6 3.1 + - - -
27E PHE* 3.3 15.6 + - - +
39E VAL* 3.6 41.1 - - + +
40E LYS* 5.3 0.4 - - - -
41E ILE* 5.0 16.9 - - + +
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Residues in contact with GLU 24 (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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22E THR* 3.3 6.3 + - - +
23E GLU* 1.3 77.4 - - - +
25E LEU* 1.3 63.5 + - - +
27E PHE* 3.4 9.5 + - - +
28E GLU* 3.3 19.9 + - - +
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Residues in contact with LEU 25 (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 VAL* 5.0 5.4 - - + -
22E THR* 3.1 29.6 + - + +
23E GLU 3.2 0.2 - - - -
24E GLU* 1.3 74.0 - - - +
26E LEU* 1.3 66.8 + - - +
28E GLU* 3.1 8.7 + - - +
29E LEU* 3.0 21.5 + - - +
75E LEU* 6.4 1.8 - - + -
76E TYR* 5.8 4.9 - - + +
294F GLU* 6.1 5.8 - - + +
295F LEU* 4.7 18.6 - - + +
298F ALA* 6.0 4.0 - - + -
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Residues in contact with LEU 26 (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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14E VAL* 4.3 9.6 - - + -
17E LEU* 3.8 24.0 - - + -
21E VAL* 3.9 6.1 - - + -
22E THR 3.2 12.3 + - - +
23E GLU* 4.0 8.5 - - - +
24E GLU 3.5 0.4 - - - -
25E LEU* 1.3 79.5 - - - +
27E PHE* 1.3 61.3 + - - +
29E LEU* 3.3 7.1 + - + -
30E PHE* 3.0 50.7 + - + +
39E VAL* 4.1 14.4 - - + -
53E ALA* 3.7 30.3 - - + -
55E VAL* 5.1 1.7 - - + +
75E LEU* 3.8 29.8 - - + -
80E ILE* 5.5 1.1 - - + -
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Residues in contact with PHE 27 (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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23E GLU 3.3 7.3 + - - +
24E GLU* 3.4 14.6 - - - +
25E LEU 3.1 0.6 - - - -
26E LEU* 1.3 78.5 - - - +
28E GLU* 1.3 65.9 + - - +
30E PHE 3.9 0.3 - - - -
31E HIS* 3.0 47.9 + + - +
36E VAL* 3.3 41.5 - - + +
37E ILE 3.7 15.3 - - - -
38E LYS* 4.5 2.5 - - - -
39E VAL* 3.6 28.9 - - + +
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Residues in contact with GLU 28 (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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24E GLU 3.3 8.5 + - - +
25E LEU* 3.1 10.1 + - - +
27E PHE* 1.3 82.5 - - + +
29E LEU* 1.3 64.7 + - - +
31E HIS* 3.4 20.9 - - - +
32E GLN* 3.9 13.3 + - - +
290F VAL 4.0 5.7 - - - +
291F ILE* 3.5 9.4 - - + -
292F SER* 3.1 38.9 + - - +
295F LEU* 3.6 22.6 - - + +
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Residues in contact with LEU 29 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25E LEU 3.0 13.0 + - - +
26E LEU* 3.7 17.0 - - + +
28E GLU* 1.3 77.8 - - - +
30E PHE* 1.3 76.4 + - + +
32E GLN* 3.0 31.4 + - - +
70E LEU* 3.8 18.2 - - + +
73E ILE* 5.6 6.3 - - + -
75E LEU* 4.6 16.8 - - + -
80E ILE* 4.4 19.3 - - + -
295F LEU* 4.3 20.4 - - + -
309F PHE* 3.4 35.9 - - + -
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Residues in contact with PHE 30 (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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12E LEU* 3.8 20.9 - - + -
14E VAL* 3.5 28.5 - - + -
26E LEU* 3.0 47.7 + - + +
29E LEU* 1.3 82.6 - - + +
31E HIS* 1.3 62.9 + - - +
32E GLN 3.0 2.2 - - - -
33E ALA* 3.1 11.1 + - - +
34E GLY 3.2 12.1 + - - +
36E VAL* 3.4 17.7 - - + +
55E VAL* 3.9 26.7 - - + -
57E PHE* 3.4 27.3 - + + -
66E ALA* 4.2 4.3 - - + -
70E LEU* 3.6 26.2 - - + -
80E ILE* 4.9 8.5 - - + -
82E ILE* 5.6 3.4 - - + -
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Residues in contact with HIS 31 (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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27E PHE* 3.0 41.8 + + - +
28E GLU* 3.4 17.7 - - - +
29E LEU 3.1 0.6 - - - -
30E PHE* 1.3 75.6 - - - +
32E GLN* 1.3 65.9 + - - +
34E GLY 3.3 5.0 + - - +
35E PRO* 4.2 2.2 - - + -
36E VAL* 3.5 25.8 + - - +
286F PHE* 3.7 5.9 - + - -
322F TRP* 3.1 60.8 + + - -
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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