Contacts of the helix formed by residues 26 - 34 (chain M) 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 LEU 26 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17M LEU* 6.5 0.4 - - + -
21M VAL* 6.4 1.6 - - + -
22M THR 3.0 18.1 + - - +
23M GLU* 4.1 0.9 - - - -
25M LEU* 1.3 76.8 - - - +
27M PHE* 1.3 62.9 + - - +
29M LEU* 3.2 9.2 + - - +
30M PHE* 3.0 39.6 + - + +
39M VAL* 4.3 17.9 - - + -
53M ALA* 5.4 9.2 - - + -
55M VAL* 5.2 2.0 - - + -
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Residues in contact with PHE 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M GLU 4.2 12.1 - - - +
25M LEU 3.2 2.1 - - - +
26M LEU* 1.3 79.8 - - - +
28M GLU* 1.3 56.8 + - - +
30M PHE* 4.3 0.6 - - - +
31M HIS* 2.8 32.7 + - - +
36M VAL* 5.0 3.7 - - + +
39M VAL* 3.7 30.4 - - + +
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Residues in contact with GLU 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M LEU* 3.1 16.1 + - - +
27M PHE* 1.3 77.8 - - - +
29M LEU* 1.3 66.2 + - - +
31M HIS* 3.4 15.0 + - - +
32M GLN* 3.5 12.0 + - - +
290N VAL 4.3 3.0 - - - +
291N ILE* 3.2 12.7 - - - +
292N SER* 2.6 52.0 + - - -
295N LEU* 3.3 16.8 - - - +
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Residues in contact with LEU 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M LEU 3.2 10.1 + - - +
26M LEU* 3.2 12.5 + - - +
28M GLU* 1.3 82.4 - - - +
30M PHE* 1.3 70.6 + - + +
32M GLN* 3.3 22.3 + - - +
33M ALA 3.9 0.9 + - - -
70M LEU* 3.7 27.5 - - + +
73M ILE* 4.9 16.2 - - + -
295N LEU* 6.4 1.8 - - + -
309N PHE* 3.4 38.4 - - + -
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Residues in contact with PHE 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M LEU* 5.0 9.4 - - + -
13M PHE 6.2 0.2 - - - -
14M VAL* 5.2 15.5 - - + -
26M LEU* 3.0 26.9 + - + +
27M PHE* 4.3 2.0 - - - +
29M LEU* 1.3 84.8 - - + +
31M HIS* 1.3 64.0 + - - +
32M GLN 3.0 2.5 + - - -
33M ALA* 3.2 8.2 + - - +
34M GLY 2.8 17.8 + - - +
36M VAL* 4.8 3.1 - - + -
55M VAL* 4.0 31.4 - - + -
57M PHE* 3.3 36.8 - + + -
66M ALA* 4.1 22.0 - - + -
70M LEU* 4.1 25.4 - - + -
82M ILE* 5.6 10.3 - - + -
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Residues in contact with HIS 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M PHE 2.8 19.4 + - - +
28M GLU* 3.6 9.9 - - - +
29M LEU 3.3 0.4 - - - -
30M PHE* 1.3 76.0 - - - +
32M GLN* 1.3 59.2 + - - +
34M GLY 3.1 12.4 + - - +
35M PRO* 5.8 0.4 - - + -
36M VAL* 4.7 9.8 - - + +
286N PHE* 5.0 0.7 - - - -
322N TRP* 2.9 35.3 - - + -
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Residues in contact with GLN 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28M GLU 3.5 7.7 + - - +
29M LEU* 3.3 15.1 + - - +
30M PHE 3.0 0.8 - - - -
31M HIS* 1.3 80.4 - - - +
33M ALA* 1.3 61.9 + - - +
34M GLY 3.4 0.3 + - - -
70M LEU* 6.0 1.7 - - + +
286N PHE* 3.0 40.3 - - + -
287N LYS 3.7 4.3 - - - +
288N PRO* 3.5 3.5 - - + -
289N GLY* 2.6 34.3 + - - -
290N VAL 3.7 14.4 + - - +
291N ILE* 5.9 2.4 - - - +
309N PHE* 3.1 36.8 - - - -
313N MET* 4.0 18.1 - - + +
319N PRO* 3.9 4.2 - - - +
322N TRP* 3.7 1.0 + - - -
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Residues in contact with ALA 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M LEU 3.9 1.0 + - - -
30M PHE 3.2 8.2 + - - +
32M GLN* 1.3 79.3 - - - +
34M GLY* 1.3 55.3 + - - +
57M PHE* 4.9 1.6 - - - -
62M SER* 4.6 4.6 - - - +
65M TYR* 3.2 36.2 - - + +
66M ALA* 3.8 32.8 - - + -
69M LEU* 5.0 3.4 - - + -
70M LEU* 4.2 21.1 - - + +
313N MET* 5.2 2.4 - - - +
319N PRO* 3.4 9.2 - - - +
320N PRO* 5.4 0.2 - - - +
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Residues in contact with GLY 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M PHE 2.8 18.1 + - - +
31M HIS* 3.1 12.6 - - - +
32M GLN 3.2 3.6 - - - -
33M ALA* 1.3 80.2 - - - +
35M PRO* 1.3 78.8 - - - +
36M VAL 3.3 0.5 + - - -
57M PHE* 3.7 3.8 - - - -
62M SER* 3.7 11.4 - - - -
319N PRO* 4.6 0.9 - - - -
321N GLY* 5.4 0.4 - - - -
322N TRP* 3.4 8.5 - - - -
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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