Contacts of the helix formed by residues 41 - 46 (chain D) in PDB entry 5YL4
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 ASP 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D TYR* 5.0 0.2 - - - -
39D ASP 4.8 3.9 - - - +
40D SER* 1.3 72.2 + - - +
42D LEU* 1.3 59.8 + - + +
43D GLN 3.2 0.9 - - - -
44D LEU* 3.1 23.6 + - - +
45D GLU* 3.2 16.6 + - - +
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D SER* 3.2 14.8 - - - +
41D ASP* 1.3 75.4 - - + +
43D GLN* 1.3 62.6 + - - +
44D LEU 3.3 0.6 + - - -
45D GLU* 3.8 23.4 + - - +
46D ARG 4.8 0.5 + - - -
241D ARG 4.7 3.8 - - - +
242D PHE* 3.5 27.0 - - + -
243D PRO* 3.8 31.6 - - + +
355D ASP* 4.8 15.3 - - + +
356D ILE* 4.6 19.3 - - + -
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Residues in contact with GLN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ASP 4.6 1.6 + - - -
27D GLU 3.2 25.6 + - - +
28D HIS* 2.8 43.5 + - - +
29D GLY* 3.6 16.4 - - - +
36D TYR* 2.8 28.5 + - + -
38D GLY* 3.6 5.5 - - - -
39D ASP* 3.2 20.0 + - - -
40D SER* 3.2 21.8 + - - +
41D ASP 3.2 0.4 - - - -
42D LEU* 1.3 79.9 - - + +
44D LEU* 1.3 58.2 + - - +
46D ARG 5.4 0.2 - - - -
47D ILE* 3.4 12.0 + - - +
242D PHE* 4.4 7.0 - - + -
356D ILE* 6.1 3.8 - - + -
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 5.3 0.7 - - + -
36D TYR* 3.6 54.7 - - + -
40D SER 5.1 0.9 - - - +
41D ASP* 3.1 11.5 + - - +
43D GLN* 1.3 76.2 - - - +
45D GLU* 1.3 65.7 - - - +
46D ARG 3.4 2.2 - - - -
47D ILE* 3.2 34.2 - - + +
48D ASN* 5.0 0.5 - - - +
59D TYR* 3.7 36.3 - - + +
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Residues in contact with GLU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASP* 3.2 15.1 + - - +
42D LEU* 3.8 20.0 + - - +
43D GLN 3.7 1.6 - - - -
44D LEU* 1.3 78.5 - - - +
46D ARG* 1.3 64.4 + - + +
47D ILE 3.9 0.3 + - - -
48D ASN* 4.6 7.3 - - - +
243D PRO* 3.2 34.6 - - + +
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Residues in contact with ARG 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D MET 4.2 16.6 + - - -
2D ARG* 5.0 2.0 - - - +
28D HIS* 5.1 2.2 + - - -
42D LEU 4.8 1.6 + - - -
43D GLN 5.2 0.9 + - - -
45D GLU* 1.3 87.6 - - + +
47D ILE* 1.3 62.8 + - - +
48D ASN* 3.2 5.1 + - - +
49D VAL* 3.4 33.2 + - + +
131D GLN* 4.4 4.9 - - - +
239D CYS 3.3 18.0 + - - -
240D LEU 3.4 12.8 + - - -
241D ARG* 3.6 26.1 + - - +
242D PHE* 4.0 20.5 + - - -
243D PRO* 4.5 6.7 - - + +
244D GLY 5.2 2.6 + - - +
248D ALA* 3.0 41.1 + - - +
249D ASP* 4.8 1.8 - - - +
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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