Contacts of the helix formed by residues 41 - 55 (chain D) 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 THR 41 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D SER* 4.1 7.3 + - - -
40D ARG* 1.3 87.0 - - + +
42D GLY* 1.3 55.0 + - - +
43D PRO 3.5 1.8 - - - -
44D LYS* 3.3 10.0 + - - +
45D ASP* 2.8 54.9 + - - -
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Residues in contact with GLY 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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9D PHE* 3.7 18.5 - - - -
36D VAL* 3.9 12.1 - - - -
39D SER* 3.2 24.8 + - - -
41D THR* 1.3 75.8 - - - +
43D PRO* 1.3 67.6 - - - +
45D ASP* 4.7 0.2 - - - -
46D CYS* 2.9 27.7 + - - +
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Residues in contact with PRO 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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36D VAL* 3.5 25.6 - - + +
39D SER 3.8 10.8 - - - +
40D ARG 3.8 7.6 - - - +
41D THR 3.8 2.7 - - - -
42D GLY* 1.3 85.5 - - - +
44D LYS* 1.4 56.3 + - - +
47D LEU* 2.9 32.4 + - - +
79D ILE* 3.6 39.5 - - + +
80D PHE* 3.6 18.2 - - + +
83D GLU* 3.7 21.8 - - + +
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Residues in contact with LYS 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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41D THR* 3.3 10.1 + - - +
43D PRO* 1.4 74.6 - - - +
45D ASP* 1.4 66.9 + - - +
47D LEU* 4.0 2.9 - - + +
48D ARG* 3.0 66.1 + - + +
83D GLU* 3.7 37.4 + - + +
86D SER* 5.8 3.6 + - - -
88D ASP* 3.6 22.2 + - - +
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Residues in contact with ASP 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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7D ASN* 2.8 34.1 + - - +
8D PRO* 3.8 24.5 - - - +
9D PHE* 3.6 17.6 - - + -
39D SER* 5.3 0.5 + - - -
41D THR* 2.8 45.8 + - - +
42D GLY* 3.7 1.5 + - - +
44D LYS* 1.4 74.1 - - - +
46D CYS* 1.3 56.5 + - - +
48D ARG* 3.4 2.9 + - - +
49D SER* 3.0 14.7 + - - -
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Residues in contact with CYS 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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9D PHE* 3.6 24.2 - - + -
13D VAL* 4.6 2.9 - - - -
32D ILE* 3.7 28.0 - - - -
36D VAL* 3.8 18.6 - - + -
42D GLY 2.9 20.5 + - - +
43D PRO 3.9 2.5 - - - +
45D ASP* 1.3 70.6 - - - +
47D LEU* 1.3 59.4 + - - +
49D SER* 3.3 2.8 + - - -
50D ILE* 2.9 53.4 + - - +
72D CYS* 4.1 4.5 - - - -
80D PHE* 4.4 1.8 - - + -
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Residues in contact with LEU 47 (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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43D PRO 2.9 22.7 + - - +
44D LYS* 4.0 5.2 - - + +
46D CYS* 1.3 71.2 - - - +
48D ARG* 1.4 60.6 + - + +
50D ILE* 3.3 3.3 + - + +
51D MET* 2.9 46.8 + - + +
69D LEU* 3.7 29.8 - - + -
80D PHE* 3.9 13.1 - - + -
83D GLU* 3.3 39.9 - - + +
84D VAL* 3.8 13.9 - - + -
86D SER* 5.2 0.4 - - - +
89D PHE* 3.9 13.9 - - + +
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Residues in contact with ARG 48 (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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7D ASN* 4.4 7.0 - - - +
44D LYS* 3.0 53.9 + - + +
45D ASP* 3.7 5.8 - - - +
47D LEU* 1.4 77.0 - - + +
49D SER* 1.4 60.7 + - - +
51D MET* 3.6 5.5 + - - +
52D ARG* 3.3 29.9 + - - +
88D ASP* 3.1 29.9 + - - +
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Residues in contact with SER 49 (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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7D ASN* 3.7 7.5 - - - +
9D PHE* 3.9 10.8 - - - -
10D ASP* 2.9 43.3 + - - +
13D VAL* 3.4 15.6 - - - +
45D ASP 3.0 17.3 + - - -
46D CYS 3.5 5.2 - - - -
48D ARG* 1.4 73.5 - - - +
50D ILE* 1.4 64.0 + - - +
52D ARG* 3.6 11.9 + - - +
53D ARG* 3.7 16.5 + - - +
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Residues in contact with ILE 50 (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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13D VAL* 4.3 8.1 - - + -
46D CYS* 2.9 42.5 + - - +
47D LEU* 3.7 4.0 - - - +
49D SER* 1.4 72.5 - - - +
51D MET* 1.3 60.5 + - - +
53D ARG* 2.9 23.2 + - - +
54D VAL* 2.9 23.9 + - + +
65D ALA* 3.5 25.1 - - + +
68D LEU* 4.0 28.3 - - + +
69D LEU* 3.9 18.8 - - + -
72D CYS* 3.7 20.4 - - - -
80D PHE* 4.3 10.3 - - + -
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Residues in contact with MET 51 (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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47D LEU* 2.9 39.8 + - + +
48D ARG* 4.1 5.8 - - - +
49D SER 3.6 0.2 - - - -
50D ILE* 1.3 70.8 - - - +
52D ARG* 1.3 59.4 + - - +
54D VAL* 3.4 31.1 + - + +
55D ASN* 2.8 32.7 + - - -
69D LEU* 4.1 12.6 - - + -
89D PHE* 3.7 33.2 - - + -
92D GLU* 3.7 46.2 - - + +
93D VAL* 4.9 3.8 - - + +
96D VAL* 4.9 1.8 - - + -
108D LEU* 5.1 4.3 - - + -
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Residues in contact with ARG 52 (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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91B SER* 3.2 31.9 + - - -
92B GLU* 3.4 23.6 + - - -
95B ASN* 3.2 50.9 - - - +
10D ASP* 6.0 2.2 - - - +
48D ARG* 3.3 16.6 + - - +
49D SER* 3.8 10.8 - - - +
50D ILE 3.1 1.0 + - - -
51D MET* 1.3 75.5 - - - +
53D ARG* 1.3 62.1 + - + +
55D ASN* 3.3 16.9 + - - +
56D HIS* 3.5 10.0 + - - +
92D GLU* 5.6 1.8 - - - +
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Residues in contact with ARG 53 (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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99B LYS* 3.2 35.7 - - - +
13D VAL* 3.8 13.2 - - + -
14D GLU* 3.6 37.9 + - - +
17D THR* 2.8 45.6 + - - +
18D SER* 4.6 2.4 - - - +
19D GLU* 5.3 0.6 + - - +
49D SER 3.7 13.0 + - - +
50D ILE 2.9 9.0 + - - +
52D ARG* 1.3 72.7 - - + +
54D VAL* 1.3 63.7 + - - +
55D ASN 3.2 1.6 - - - -
56D HIS* 3.3 27.9 + - - +
61D VAL* 3.3 18.4 - - + +
62D ALA* 3.6 13.0 + - - -
65D ALA* 3.9 14.6 - - + -
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Residues in contact with VAL 54 (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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50D ILE* 2.9 32.8 + - + +
51D MET* 3.6 26.7 - - + +
52D ARG 3.3 0.2 - - - -
53D ARG* 1.3 76.5 - - - +
55D ASN* 1.3 58.7 + - - +
56D HIS 3.3 2.3 + - - +
62D ALA* 3.6 18.7 - - - +
65D ALA* 3.7 18.8 - - + -
66D LEU* 4.2 31.0 - - + +
96D VAL* 3.9 30.6 - - + +
104D VAL* 4.5 6.1 - - + +
108D LEU* 5.5 1.3 - - + -
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Residues in contact with ASN 55 (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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51D MET 2.8 21.9 + - - +
52D ARG* 3.5 13.7 - - - +
53D ARG 3.2 0.4 - - - -
54D VAL* 1.3 75.5 - - - +
56D HIS* 1.4 63.8 + - - +
57D LYS* 3.7 1.0 + - - -
92D GLU* 3.1 25.9 + - - +
95D ASN* 2.7 27.1 + - - +
96D VAL* 3.5 27.7 - - - +
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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