Contacts of the helix formed by residues 30 - 44 (chain A) in PDB entry 3LDH
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 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A GLY 2.7 16.4 + - - +
29A CYS* 1.3 74.0 - - - +
31A ALA* 1.3 58.6 + - - +
32A VAL* 3.8 3.8 + - - +
33A GLY 3.3 9.4 + - - -
34A MET* 2.1 62.6 + - - +
58A LYS* 4.3 14.6 - - - +
62A GLU* 5.3 0.9 - - - -
97A THR* 5.2 1.2 + - - -
332A NAD 2.0 63.3 + - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 1.3 88.2 + - - +
32A VAL* 1.3 65.2 + - - +
34A MET* 4.3 2.5 - - - -
35A ALA* 2.6 21.7 + - - +
101A ARG* 5.3 0.2 - - - +
246A TYR* 3.5 30.3 - - + +
247A VAL 3.6 3.8 - - - +
248A ALA* 4.4 6.3 - - - +
332A NAD 2.3 35.9 - - - +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 3.8 2.2 + - - +
31A ALA* 1.3 78.1 - - - +
33A GLY* 1.3 55.9 + - - +
35A ALA* 3.5 5.5 + - - +
36A ASP* 2.2 40.9 + - - +
97A THR* 2.6 31.0 - - + -
138A HIS* 2.3 60.8 - - + +
247A VAL* 4.4 8.1 + - + -
248A ALA 5.7 0.9 - - - -
332A NAD 2.8 42.8 + - + +
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Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 4.2 16.6 - - - +
28A GLY 3.5 18.5 + - - -
30A ASP* 3.3 5.7 + - - -
31A ALA 2.7 4.9 + - - -
32A VAL* 1.3 75.5 - - - +
34A MET* 1.3 58.1 + - - -
36A ASP* 2.7 10.0 + - - +
37A ALA* 2.6 36.7 + - - +
97A THR* 4.9 2.9 - - - +
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Residues in contact with MET 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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29A CYS* 3.8 7.0 - - - -
30A ASP* 2.1 63.7 + - - +
31A ALA* 2.7 2.4 + - - +
33A GLY* 1.3 66.7 - - - +
35A ALA* 1.3 50.9 + - - +
37A ALA* 3.2 17.8 - - + +
38A ILE* 2.7 40.7 + - + +
51A LEU* 5.0 7.2 - - + -
62A GLU* 3.4 38.1 - - + +
66A LEU* 4.0 23.3 - - + -
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 2.6 19.8 + - - +
32A VAL* 3.5 6.3 - - - +
34A MET* 1.3 68.6 - - - +
36A ASP* 1.3 68.6 + - - +
38A ILE* 2.7 29.4 - - - +
39A SER* 2.8 8.2 + - - -
248A ALA 3.2 32.5 - - - +
249A TRP* 4.0 17.0 - - + -
251A GLY* 4.1 9.0 - - - +
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Residues in contact with ASP 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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26A VAL* 5.6 7.2 - - + -
32A VAL* 2.2 32.6 + - - +
33A GLY* 2.7 15.0 + - - +
35A ALA* 1.3 69.4 - - - +
37A ALA* 1.3 55.4 + - - +
39A SER* 2.5 31.5 + - - -
40A VAL* 2.8 20.4 + - + +
95A VAL* 4.9 10.1 - - + +
138A HIS* 3.2 18.4 + - - -
251A GLY* 4.1 10.8 - - - +
254A VAL* 2.9 38.2 - - - +
255A ALA* 4.6 2.0 + - - +
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Residues in contact with ALA 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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26A VAL* 5.4 11.9 - - + +
33A GLY 2.6 15.1 + - - +
34A MET* 3.2 17.5 - - + +
36A ASP* 1.3 72.5 - - - +
38A ILE* 1.3 53.6 + - - +
40A VAL* 4.9 2.9 - - - -
41A LEU* 2.6 55.2 + - + +
51A LEU* 5.3 7.9 - - + -
66A LEU* 3.9 23.3 - - + -
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Residues in contact with ILE 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 MET* 2.7 20.3 + - + +
35A ALA* 2.7 13.7 - - - +
37A ALA* 1.3 74.0 - - - +
39A SER* 1.3 76.2 + - - +
41A LEU* 4.7 1.6 - - - -
42A MET* 3.2 41.4 + - + +
66A LEU* 3.9 26.0 - - + -
249A TRP* 3.5 38.4 - - + -
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA* 2.9 11.3 + - - +
36A ASP 2.5 13.2 + - - -
38A ILE* 1.3 83.9 - - - +
40A VAL* 1.3 57.4 + - - -
42A MET* 4.1 4.0 - - - +
43A LYS* 3.0 35.9 + - - +
249A TRP* 5.5 1.6 - - - -
251A GLY* 3.6 27.9 + - - -
252A CYS* 4.0 6.8 + - - -
255A ALA* 3.9 14.4 - - - -
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Residues in contact with VAL 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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24A ILE* 3.0 38.1 - - + -
36A ASP* 2.8 22.1 + - + +
37A ALA* 4.5 1.6 - - - +
39A SER* 1.3 75.1 - - - +
41A LEU* 1.3 69.3 + - + +
43A LYS* 4.1 5.2 - - - +
44A ASP* 3.1 24.3 + - - -
45A LEU* 3.7 24.9 + - + +
46A ALA* 5.4 0.7 - - + +
49A VAL* 5.9 1.1 - - + -
93A LEU* 6.5 0.9 - - + -
255A ALA* 4.3 23.3 - - + +
258A ALA* 5.8 4.7 - - + -
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Residues in contact with LEU 41 (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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24A ILE* 5.8 0.7 - - + -
37A ALA* 2.6 44.8 + - + +
38A ILE* 4.4 2.0 - - - +
40A VAL* 1.3 81.0 - - + +
42A MET* 1.3 52.8 + - + +
44A ASP* 3.8 7.2 + - - +
49A VAL* 4.0 39.3 - - + -
51A LEU* 6.2 0.4 - - + -
66A LEU* 3.8 29.6 - - + +
67A GLU* 5.8 1.3 - - - +
70A SER* 6.1 4.0 - - - -
73A LEU* 2.7 36.9 - - + +
75A THR* 4.5 15.0 + - - +
78A ILE* 5.1 13.5 - - + -
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Residues in contact with MET 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.2 30.4 + - + +
39A SER* 4.1 3.6 - - - +
41A LEU* 1.3 78.1 - - - +
43A LYS* 1.3 72.7 + - + +
44A ASP* 3.3 7.4 - - - +
73A LEU* 2.8 22.0 - - + +
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Residues in contact with LYS 43 (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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39A SER* 3.0 21.3 + - - +
40A VAL* 4.1 4.0 - - - +
42A MET* 1.3 84.2 - - + +
44A ASP* 1.3 79.3 + - - +
45A LEU* 4.4 21.1 - - + -
255A ALA* 5.0 16.4 - - + +
259A GLN* 2.4 41.3 - - + +
263A LYS* 6.3 0.2 - - - +
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Residues in contact with ASP 44 (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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40A VAL 3.1 8.3 + - - -
41A LEU 3.8 10.9 - - - +
42A MET 3.3 11.7 - - - +
43A LYS* 1.3 96.1 - - - +
45A LEU* 1.3 72.9 + - - +
73A LEU* 4.1 11.4 - - - +
74A HIS* 3.9 34.3 + - - +
75A THR* 5.5 2.4 + - - -
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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