Contacts of the helix formed by residues 22 - 31 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20I LYS 3.4 15.7 + - - +
21I VAL* 1.3 82.8 - - - +
23I GLU* 1.3 64.6 + - - +
24I GLU* 4.0 7.1 + - - +
25I LEU* 3.2 32.9 + - - +
26I LEU* 3.2 13.1 + - - +
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Residues in contact with GLU 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I THR* 1.3 75.3 - - - +
24I GLU* 1.3 62.0 + - - +
26I LEU* 3.4 5.5 + - - +
27I PHE* 3.1 21.8 + - - +
39I VAL* 3.9 35.3 - - + +
41I ILE* 5.3 14.8 - - + +
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Residues in contact with GLU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I THR* 3.3 7.4 + - - +
23I GLU* 1.3 78.7 - - - +
25I LEU* 1.3 61.9 + - - +
27I PHE* 3.5 8.7 + - - +
28I GLU* 3.3 20.6 + - - +
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Residues in contact with LEU 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21I VAL* 4.4 17.3 - - + -
22I THR* 3.2 23.7 + - - +
24I GLU* 1.3 78.6 - - - +
26I LEU* 1.3 62.0 + - - +
28I GLU* 3.4 6.1 + - + +
29I LEU* 3.1 20.8 + - - +
75I LEU* 4.6 9.6 - - + -
76I TYR* 4.0 21.1 - - + +
292J SER* 5.2 1.3 - - - +
294J GLU* 4.2 11.9 - - + +
295J LEU* 3.7 45.7 - - + +
298J ALA* 3.8 21.5 - - + -
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Residues in contact with LEU 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I VAL* 4.6 8.3 - - + -
17I LEU* 3.7 24.7 - - + -
21I VAL* 3.9 9.4 - - + -
22I THR 3.2 11.4 + - - +
23I GLU* 3.4 6.7 + - - +
25I LEU* 1.3 73.4 - - - +
27I PHE* 1.3 61.1 + - - +
29I LEU* 4.2 5.2 - - + -
30I PHE* 2.8 60.7 + - + +
39I VAL* 4.1 15.0 - - + -
53I ALA* 3.6 31.6 - - + -
55I VAL* 6.1 0.2 - - + -
75I LEU* 4.0 26.9 - - + -
80I ILE* 5.4 0.7 - - + -
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Residues in contact with PHE 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I GLU 3.1 13.6 + - - +
24I GLU* 3.6 13.0 - - - +
26I LEU* 1.3 76.7 - - - +
28I GLU* 1.3 61.1 + - - +
30I PHE* 4.1 0.2 - - - -
31I HIS* 2.9 39.8 + - + +
36I VAL* 3.1 52.2 - - + +
37I ILE 3.6 15.0 - - - -
38I LYS* 4.4 4.3 - - - -
39I VAL* 4.0 15.3 - - + +
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Residues in contact with GLU 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I GLU 3.3 10.3 + - - +
25I LEU* 3.8 8.7 - - + +
26I LEU 3.3 0.2 - - - -
27I PHE* 1.3 84.4 - - - +
29I LEU* 1.3 63.1 + - - +
31I HIS* 3.5 15.6 + - - +
32I GLN* 3.8 10.7 + - - +
291J ILE* 6.0 0.2 - - - +
292J SER* 5.3 9.9 - - - +
295J LEU* 4.3 14.4 - - + +
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Residues in contact with LEU 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25I LEU 3.1 17.3 + - - +
26I LEU* 3.6 14.8 - - + +
28I GLU* 1.3 77.2 - - - +
30I PHE* 1.3 71.3 + - + +
32I GLN* 3.2 24.9 + - - +
70I LEU* 3.9 18.2 - - + +
73I ILE* 5.1 5.4 - - + -
75I LEU* 3.8 34.3 - - + -
80I ILE* 4.5 10.3 - - + -
295J LEU* 4.0 22.8 - - + +
299J LEU* 4.5 4.5 - - + -
309J PHE* 3.8 31.2 - - + -
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Residues in contact with PHE 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I VAL* 3.5 33.9 - - + -
26I LEU* 2.8 45.2 + - + +
27I PHE* 5.3 0.2 - - - -
29I LEU* 1.3 80.9 - - + +
31I HIS* 1.3 61.2 + - - +
32I GLN 3.0 5.8 - - - -
33I ALA* 3.0 16.0 + - - +
34I GLY 3.3 10.4 + - - +
36I VAL* 3.7 15.7 - - + -
39I VAL* 5.9 0.2 - - + -
55I VAL* 4.5 12.6 - - + -
57I PHE* 3.6 26.3 - + + -
66I ALA* 3.6 9.2 - - + -
70I LEU* 3.5 20.4 - - + -
80I ILE* 4.4 4.9 - - + -
82I ILE* 3.6 31.9 - - + -
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Residues in contact with HIS 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27I PHE* 2.9 31.0 + - + +
28I GLU* 3.6 11.2 - - - +
29I LEU 3.2 0.6 - - - -
30I PHE* 1.3 75.9 - - - +
32I GLN* 1.3 56.7 + - - +
33I ALA 3.2 0.2 - - - -
34I GLY 3.4 11.3 + - - +
36I VAL* 3.7 6.9 - - + +
286J PHE* 5.2 0.3 - - - -
322J TRP* 2.8 44.2 + - + -
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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