Contacts of the helix formed by residues 30 - 44 (chain B) in PDB entry 5LDH
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 GLY 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A TYR* 5.6 0.7 - - - -
28B GLY 2.9 1.4 - - - -
29B VAL* 1.3 80.6 - - - +
31B GLN* 1.3 58.4 + - - -
32B VAL 3.6 0.2 - - - -
33B GLY 2.8 3.9 + - - -
34B MET* 2.3 41.2 + - - -
58B LYS* 5.2 7.6 - - - -
62B GLU* 5.1 2.0 - - - -
332B LNC 3.5 31.7 + - - -
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Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TRP* 6.0 0.9 - - - -
30B GLY* 1.3 69.9 - - - +
32B VAL* 1.3 62.8 + - - +
34B MET* 3.5 3.8 - - - +
35B ALA* 2.6 23.7 + - - +
58B LYS* 5.5 8.3 - - - +
244B GLY* 4.4 14.4 - - - +
245B TYR* 5.7 3.5 - - - -
247B ASN* 3.2 19.2 + - + +
332B LNC 2.7 45.1 + - - +
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Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLY* 5.0 1.8 - - - -
31B GLN* 1.3 72.8 - - - +
33B GLY* 1.3 52.6 + - - +
36B CYS* 2.5 53.7 + - - -
97B THR* 3.7 15.7 - - + +
138B VAL* 6.1 1.8 - - + -
247B ASN* 2.8 12.9 + - + +
250B ILE* 3.5 36.1 - - + -
332B LNC 2.3 70.2 + - + +
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Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 3.8 10.2 - - - +
28B GLY* 1.7 44.2 - - - -
30B GLY 2.8 3.4 + - - -
32B VAL* 1.3 82.8 - - - +
34B MET* 1.3 51.1 + - - -
36B CYS* 3.0 2.6 - - - +
37B ALA* 2.5 36.4 + - - +
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Residues in contact with MET 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A TRP* 2.8 36.3 - - + +
26B VAL* 6.1 0.4 - - - -
29B VAL* 2.6 31.9 - - + +
30B GLY 2.3 27.8 + - - +
31B GLN* 3.6 3.4 - - - +
33B GLY* 1.3 63.7 - - - -
35B ALA* 1.3 66.3 + - - +
37B ALA* 3.1 9.1 - - + +
38B ILE* 2.7 29.8 + - - +
51B LEU* 5.2 6.1 - - + -
62B GLU* 2.4 40.2 - - + +
66B LEU* 2.4 46.4 - - + -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 5.6 2.2 - - + +
248A TRP* 4.3 1.2 - - - -
31B GLN 2.6 10.3 + - - -
32B VAL* 3.3 0.7 - - - +
34B MET* 1.3 73.7 - - - +
36B CYS* 1.3 67.4 - - - +
38B ILE* 3.3 6.4 + - - +
39B SER* 3.1 21.6 + - - -
247B ASN* 2.3 52.9 - - - +
248B TRP* 4.3 20.9 - - + +
251B GLY* 4.5 4.0 - - - -
252B LEU* 5.9 1.2 - - + +
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Residues in contact with CYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 4.4 14.4 - - + -
32B VAL* 2.5 42.3 + - - -
33B GLY* 3.0 10.1 - - - +
35B ALA* 1.3 74.8 - - - +
37B ALA* 1.3 65.9 + - - +
39B SER* 3.1 6.2 + - - -
40B ILE* 2.8 25.2 + - - +
95B VAL* 5.8 4.0 - - + -
251B GLY* 3.9 24.9 - - - +
254B VAL* 4.6 16.8 - - + -
255B ALA* 5.4 1.9 - - - +
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL* 5.4 9.1 - - + +
33B GLY 2.5 16.9 + - - +
34B MET* 3.1 29.6 - - + +
36B CYS* 1.3 71.3 - - - +
38B ILE* 1.3 53.2 + - + +
40B ILE* 2.8 4.3 - - - +
41B LEU* 2.4 59.8 + - + +
51B LEU* 6.1 3.4 - - + -
66B LEU* 4.8 7.4 - - + -
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 5.6 2.5 - - - +
38A ILE* 2.8 40.6 - - + -
39A SER* 4.6 9.4 - - - +
248A TRP* 3.1 40.6 - - + -
252A LEU* 4.6 15.3 - - + -
34B MET 2.7 23.7 + - - +
35B ALA* 3.6 6.1 - - - +
37B ALA* 1.3 68.9 - - - +
39B SER* 1.3 70.0 + - - +
41B LEU* 4.5 4.0 - - + -
42B GLY* 2.5 26.6 + - - -
66B LEU* 4.3 17.0 - - + -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 4.6 6.4 - - - +
35B ALA 3.1 7.8 + - - -
36B CYS* 3.1 10.2 + - - -
38B ILE* 1.3 81.0 - - - +
40B ILE* 1.3 54.6 + - - +
42B GLY* 5.1 0.2 - - - -
43B LYS* 2.7 44.5 + - - +
252B LEU* 3.8 31.9 - - - +
255B ALA* 3.6 23.7 - - - +
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Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.9 39.9 - - + -
36B CYS 2.8 17.4 + - - +
37B ALA* 2.8 13.9 - - - +
38B ILE 3.0 0.4 + - - -
39B SER* 1.3 71.4 - - - +
41B LEU* 1.3 110.6 + - + +
42B GLY 2.9 2.3 + - - -
43B LYS* 3.8 5.3 + - - -
44B SER* 4.0 9.0 + - - -
45B LEU* 4.4 37.3 + - + +
46B THR* 4.8 13.2 - - + +
49B LEU* 4.9 2.2 - - + -
75B THR* 5.6 0.3 - - - +
255B ALA* 4.9 4.8 - - + +
258B ILE* 5.2 13.2 - - + -
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ALA* 2.4 59.7 + - + +
38B ILE* 3.9 4.3 - - - +
40B ILE* 1.3 96.2 - - + +
42B GLY* 1.3 49.9 + - - +
44B SER* 5.7 0.2 - - - -
46B THR* 4.4 2.0 - - + -
49B LEU* 2.9 35.9 - - + -
51B LEU* 6.3 1.6 - - + -
66B LEU* 4.8 18.2 - - + -
73B LEU* 1.9 61.6 - - + +
75B THR* 3.8 17.1 - - + +
78B ILE* 5.6 2.7 - - + -
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Residues in contact with GLY 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLY 6.4 2.2 - - - -
43A LYS* 6.2 0.3 - - - -
38B ILE* 2.5 23.0 + - - -
39B SER* 3.5 0.4 - - - -
40B ILE 2.9 1.0 - - - -
41B LEU* 1.3 77.5 - - - +
43B LYS* 1.3 66.8 + - - +
73B LEU* 3.9 11.9 - - - +
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Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A GLY 6.2 0.4 - - - -
72A PHE* 4.5 22.3 + - - +
39B SER* 2.7 23.0 + - - +
40B ILE 3.8 0.4 + - - -
42B GLY* 1.3 76.0 - - - +
44B SER* 1.3 71.9 + - - +
45B LEU* 3.8 17.5 - - + -
73B LEU* 5.6 0.2 - - - +
252B LEU* 4.7 3.0 + - - +
255B ALA* 4.1 25.3 - - + +
256B ASP* 4.1 17.4 - - - +
259B GLU* 4.9 14.8 - - + +
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Residues in contact with SER 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE 4.0 2.8 + - - -
41B LEU 5.7 0.9 - - - -
42B GLY 3.7 1.2 - - - -
43B LYS* 1.3 86.4 - - - +
45B LEU* 1.3 75.1 + - - +
73B LEU* 5.7 4.3 - - - -
75B THR* 6.5 0.2 - - - -
263B LYS* 3.9 15.9 + - - -
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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