Contacts of the helix formed by residues 30 - 40 (chain A) in PDB entry 8LDH
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 ALA 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLY* 1.3 71.2 - - - -
31A VAL* 1.3 63.1 + - + +
33A MET* 3.8 2.4 + - - +
34A ALA* 3.0 27.9 + - - +
244A TYR* 3.5 42.0 - - + -
245A THR 4.2 3.6 - - - +
246A SER* 3.2 8.3 - - - -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 1.3 77.9 - - + +
32A GLY* 1.3 55.5 + - - +
34A ALA* 3.4 4.5 + - - +
35A CYS* 2.7 43.2 + - - -
95A THR* 4.3 11.7 - - - +
136A VAL* 3.4 33.7 - - + -
245A THR* 3.7 19.5 - - - +
246A SER* 4.6 2.0 - - - +
249A ILE* 4.1 22.4 - - + -
250A GLY* 4.7 0.2 - - - -
330A CIT 4.3 17.3 - - - +
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Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 4.0 10.8 - - - +
27A GLY 3.2 26.0 - - - -
29A GLY* 4.3 3.3 + - - +
30A ALA 3.4 0.2 - - - -
31A VAL* 1.3 74.3 - - - +
33A MET* 1.3 62.0 + - - +
34A ALA 3.1 1.1 - - - -
35A CYS* 3.2 3.5 + - - +
36A ALA* 2.8 29.8 + - - +
95A THR* 3.6 15.5 + - - -
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Residues in contact with MET 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY 4.4 0.2 + - - -
28A VAL* 3.8 29.8 - - - +
29A GLY 3.4 22.7 + - - +
30A ALA* 4.6 2.9 - - - +
31A VAL 3.5 0.2 - - - -
32A GLY* 1.3 78.1 - - - +
34A ALA* 1.3 57.5 + - - +
36A ALA* 3.7 5.6 - - + +
37A ILE* 3.1 31.8 + - + +
50A LEU* 3.9 9.2 - - + -
61A GLU* 3.7 37.7 - - + +
65A LEU* 3.1 42.0 - - + -
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA 3.0 21.2 + - - +
31A VAL 3.6 3.8 - - - +
32A GLY 3.1 0.6 - - - -
33A MET* 1.3 75.6 - - - +
35A CYS* 1.3 64.5 + - - +
37A ILE* 3.7 5.7 + - - +
38A SER* 3.3 28.2 + - - -
246A SER* 3.2 35.7 - - - +
247A TRP* 4.2 14.8 - - + +
250A GLY* 3.8 5.1 - - - -
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Residues in contact with CYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 4.6 9.2 - - + -
31A VAL* 2.7 40.0 + - - +
32A GLY* 3.6 5.2 - - - +
34A ALA* 1.3 78.1 - - - +
36A ALA* 1.4 60.2 + - - +
38A SER* 3.4 1.2 + - - -
39A ILE* 3.1 33.4 + - + +
93A VAL* 4.3 12.3 - - + -
95A THR* 4.4 3.6 - - - -
136A VAL* 4.7 1.6 - - - -
249A ILE* 4.9 0.4 - - - -
250A GLY* 3.7 19.9 - - - +
253A VAL* 3.8 33.4 - - + -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 4.3 10.5 - - + -
32A GLY 2.8 21.2 + - - +
33A MET* 3.9 16.6 - - + +
34A ALA 3.3 0.2 - - - -
35A CYS* 1.4 73.5 - - - +
37A ILE* 1.3 53.7 + - - +
39A ILE* 3.8 4.5 + - - +
40A LEU* 2.8 44.5 + - + +
48A VAL* 4.9 3.3 - - + +
50A LEU* 3.8 28.7 - - + -
65A LEU* 4.6 0.7 - - + -
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Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A MET 3.1 17.7 + - - +
34A ALA* 4.2 7.4 - - - +
36A ALA* 1.3 75.1 - - - +
38A SER* 1.3 67.2 + - - +
39A ILE 3.3 0.2 - - - -
40A LEU* 3.8 8.1 - - + -
41A MET* 3.1 53.1 + - + +
65A LEU* 3.9 26.0 - - + -
72A LEU* 5.8 2.0 - - + -
247A TRP* 5.1 13.7 - - + -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA 3.3 18.6 + - - -
35A CYS 4.2 1.8 - - - -
37A ILE* 1.3 80.2 - - - +
39A ILE* 1.3 67.8 + - - +
41A MET* 3.9 6.0 - - - +
42A LYS* 3.0 26.1 + - - +
247A TRP* 5.2 0.5 + - - -
250A GLY* 4.3 8.5 - - - -
251A LEU* 3.8 27.3 + - - +
254A ALA* 3.9 21.7 - - - +
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.9 42.2 - - + -
25A VAL* 4.3 14.4 - - + -
35A CYS* 3.1 26.6 + - + +
36A ALA* 4.1 4.0 - - - +
38A SER* 1.3 80.0 - - - +
40A LEU* 1.3 59.2 + - + +
42A LYS* 3.0 23.2 + - - +
43A ASP 3.4 5.9 + - - -
44A LEU* 3.8 25.2 + - + -
45A ALA* 4.5 9.4 + - + +
48A VAL* 4.6 10.8 - - + -
93A VAL* 4.5 12.8 - - + -
253A VAL* 5.0 2.9 - - + -
254A ALA* 4.5 12.8 - - - +
257A ALA* 4.7 4.7 - - + -
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ALA* 2.8 31.3 + - + +
37A ILE* 3.8 13.2 - - + +
38A SER 3.2 0.4 - - - -
39A ILE* 1.3 73.1 - - - +
41A MET* 1.3 55.2 + - - +
42A LYS 3.0 8.5 + - - -
43A ASP* 3.3 19.9 + - - +
48A VAL* 3.9 25.4 - - + -
65A LEU* 4.1 30.5 - - + -
72A LEU* 3.9 26.1 - - + +
74A THR* 3.1 39.2 - - + +
77A ILE* 3.8 22.2 - - + -
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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