Contacts of the helix formed by residues 25 - 37 (chain B) in PDB entry 3LDZ
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 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B LYS 5.9 1.1 - - - +
16B ALA* 5.4 5.1 + - - +
21B ASN* 5.7 8.2 - - - +
23B ALA 3.5 5.0 + - - +
24B GLU* 1.3 69.8 - - - +
26B TRP* 1.3 56.7 + - - +
27B GLY* 3.3 14.7 + - - -
28B LEU* 3.3 32.4 + - + +
29B ILE* 3.1 31.2 + - - +
8E LEU* 4.8 9.7 - - - +
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Residues in contact with TRP 26 (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 GLU* 3.4 43.8 + - + +
25B ASP* 1.3 70.2 + - - +
27B GLY* 1.3 57.9 + - - +
29B ILE* 3.7 29.0 - - + +
30B LEU* 3.0 36.5 + - + +
67B THR* 3.6 29.8 - - + -
71B ALA* 4.4 2.0 - - + -
8E LEU* 5.1 5.0 - - + +
44E ILE* 3.8 21.3 - - + -
46E ALA* 5.0 0.4 - - - -
47E GLY* 3.6 38.6 - - - -
68E HIS* 4.1 37.6 - + + -
70E VAL* 3.4 24.6 - - + +
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Residues in contact with GLY 27 (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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25B ASP* 3.2 9.3 + - - -
26B TRP* 1.3 77.5 - - - +
28B LEU* 1.3 54.4 + - - +
31B ASP* 3.0 37.5 + - - +
8E LEU* 5.4 1.2 - - - +
42E ARG* 3.7 9.3 + - - -
70E VAL* 3.6 27.4 - - - +
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Residues in contact with LEU 28 (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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12B ASP* 4.1 30.7 - - + +
15B LYS* 3.6 36.3 - - + +
16B ALA* 3.6 24.7 - - + +
25B ASP* 3.3 32.1 + - + +
27B GLY* 1.3 74.1 - - - +
29B ILE* 1.4 63.4 + - - +
31B ASP* 3.2 12.9 + - + +
32B ILE* 3.0 23.1 + - + +
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Residues in contact with ILE 29 (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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16B ALA* 4.4 20.0 - - + +
24B GLU* 4.5 8.7 - - + -
25B ASP 3.1 33.3 + - - +
26B TRP* 3.4 31.6 + - + +
28B LEU* 1.4 73.1 - - - +
30B LEU* 1.4 58.2 + - + +
32B ILE* 3.0 21.6 + - - +
33B CYS* 3.2 13.4 + - - -
64B GLN 5.7 1.3 - - - +
67B THR* 4.6 10.8 - - + -
68B LEU* 3.9 28.7 - - + +
71B ALA* 3.5 32.3 - - + -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TRP* 3.0 21.6 + - + +
27B GLY 4.0 1.6 - - - +
29B ILE* 1.4 78.1 - - + +
31B ASP* 1.3 56.6 + - - +
32B ILE 3.3 0.2 - - - -
33B CYS* 3.5 6.8 + - + +
34B ASP* 3.0 35.7 + - - +
75B ASN* 4.0 18.2 - - - +
42E ARG* 3.5 33.9 - - + +
44E ILE* 3.7 30.7 - - + -
47E GLY 4.5 3.1 - - - +
49E GLN* 3.4 45.3 - - + +
70E VAL* 5.0 2.5 - - + -
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Residues in contact with ASP 31 (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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27B GLY 3.0 28.8 + - - +
28B LEU* 3.2 17.0 + - + +
30B LEU* 1.3 73.2 - - - +
32B ILE* 1.4 59.6 + - - +
34B ASP* 3.5 7.9 + - - +
35B LYS* 3.1 28.6 + - - +
42E ARG* 3.4 21.8 + - - -
72E ARG* 5.3 1.0 + - - -
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Residues in contact with ILE 32 (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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9B PHE* 3.9 7.9 - - + -
12B ASP* 3.5 46.2 - - + +
13B VAL* 4.1 3.6 - - + +
16B ALA* 3.7 18.6 - - + -
28B LEU* 3.0 20.4 + - + +
29B ILE 3.0 6.7 + - - +
31B ASP* 1.4 73.5 - - - +
33B CYS* 1.4 63.4 + - - +
35B LYS* 3.2 9.3 + - - +
36B VAL* 3.1 25.5 + - - +
46B CYS* 3.6 28.5 - - - -
68B LEU* 3.9 29.4 - - + -
72B CYS* 4.4 3.1 - - - -
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Residues in contact with CYS 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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29B ILE* 3.2 23.2 + - - -
30B LEU* 3.7 9.4 - - + +
31B ASP 3.4 0.2 - - - -
32B ILE* 1.4 75.7 - - - +
34B ASP* 1.3 64.4 + - - +
36B VAL* 3.3 17.5 + - - +
37B GLY 3.6 3.5 + - - -
71B ALA* 3.8 34.3 - - - -
72B CYS* 4.1 14.1 - - - -
75B ASN* 3.9 20.4 - - + +
76B CYS* 3.7 20.7 - - - +
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Residues in contact with ASP 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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30B LEU 3.0 22.8 + - - +
31B ASP* 3.8 8.4 - - - +
33B CYS* 1.3 77.1 - - - +
35B LYS* 1.4 61.9 + - - +
37B GLY* 3.3 12.8 + - - -
38B GLN* 3.7 17.2 + - - +
42E ARG* 3.8 16.6 + - - -
49E GLN* 4.4 10.8 + - - +
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Residues in contact with LYS 35 (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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8B PRO* 2.8 40.4 + - - +
9B PHE* 3.7 31.3 - - + +
12B ASP* 3.5 21.4 + - + +
31B ASP 3.1 17.8 + - - +
32B ILE* 3.2 8.7 + - - +
34B ASP* 1.4 71.9 - - - +
36B VAL* 1.4 64.5 + - - +
38B GLN* 3.1 27.8 + - + +
39B SER* 4.1 4.7 + - - -
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Residues in contact with VAL 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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9B PHE* 3.9 9.0 - - + -
32B ILE* 3.1 21.8 + - + +
33B CYS 3.3 10.1 - - - +
35B LYS* 1.4 76.1 - - - +
37B GLY* 1.3 56.5 + - - +
38B GLN 3.3 3.8 + - - -
39B SER 3.4 18.0 + - - +
42B GLY* 3.8 3.0 - - - +
43B PRO* 3.7 36.4 - - + +
46B CYS* 3.7 34.8 - - + -
72B CYS* 4.8 1.6 - - - -
76B CYS* 3.9 30.5 - - + -
79B ILE* 5.3 2.4 - - + +
80B PHE* 4.2 2.9 - - + -
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Residues in contact with GLY 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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33B CYS 3.6 3.8 + - - -
34B ASP 3.3 11.4 + - - -
36B VAL* 1.3 76.3 - - - +
38B GLN* 1.3 65.7 + - - +
39B SER 3.5 2.3 + - - -
79B ILE* 6.1 4.0 - - - -
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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