Contacts of the helix formed by residues 41 - 59 (chain B) in PDB entry 3LZK
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 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B ALA 3.4 11.1 + - - +
38B ALA 3.1 5.7 + - - -
39B LEU 3.1 0.4 - - - -
40B ASP* 1.3 78.1 - - + +
42B TRP* 1.3 64.9 + - - +
43B ALA* 3.3 3.3 + - - +
44B HIS* 3.0 22.6 + - - +
45B ALA* 3.0 13.4 + - + +
30D HIS 4.9 4.3 - - - +
48D ARG* 2.8 43.5 + - - -
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Residues in contact with TRP 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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1B MSE 3.7 32.5 - - + -
3B LEU* 3.9 22.0 - - + -
35B LEU* 4.8 0.7 - - + -
38B ALA* 2.9 33.4 + - + +
39B LEU* 3.4 32.0 + - + +
40B ASP 3.6 0.6 + - - -
41B ASP* 1.3 76.4 - - - +
43B ALA* 1.3 61.7 + - - +
44B HIS 3.0 0.2 - - - -
45B ALA 3.8 0.2 - - - -
46B GLY* 2.8 40.5 + - - +
47B PRO* 3.6 2.5 - - + +
49B LEU* 4.3 10.1 - - + -
50B GLU* 5.9 1.9 + - - -
147B ASP* 4.1 13.0 - - - +
163B ARG* 3.4 40.4 - - + +
164B LEU* 4.3 11.9 - - + -
202B THR* 4.7 8.7 - - + -
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Residues in contact with ALA 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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41B ASP* 3.1 1.4 + - - +
42B TRP* 1.3 81.9 - - - +
44B HIS* 1.3 75.1 + - + +
47B PRO* 3.7 15.7 - - - +
147B ASP* 5.2 1.8 + - - +
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Residues in contact with HIS 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASP* 3.0 21.7 + - - +
43B ALA* 1.3 92.7 - - + +
45B ALA* 1.3 62.6 + - - +
46B GLY 3.5 0.7 - - - -
47B PRO* 3.5 8.4 - - - +
48B ARG* 3.3 25.2 - - - +
51B ARG* 5.4 0.2 + - - -
44D HIS* 5.6 1.0 - - + -
48D ARG* 3.1 48.9 + - + +
51D ARG* 3.4 31.1 + - - -
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Residues in contact with ALA 45 (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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31B ILE* 4.1 23.3 - - + +
32B ALA* 5.2 1.8 - - + -
37B ALA 5.2 0.2 - - - +
38B ALA* 3.8 31.4 - - + +
41B ASP* 3.0 20.1 + - + +
44B HIS* 1.3 77.1 - - - +
46B GLY* 1.3 66.2 + - - +
48B ARG* 3.0 6.1 + - - +
49B LEU* 2.9 26.9 + - + +
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Residues in contact with GLY 46 (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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1B MSE 3.7 1.0 - - - +
42B TRP* 2.8 51.5 + - - +
45B ALA* 1.3 71.8 - - - +
47B PRO* 1.3 60.7 - - - +
49B LEU* 3.2 7.1 + - - +
50B GLU* 2.9 35.9 + - - +
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Residues in contact with PRO 47 (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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42B TRP* 3.6 10.3 - - + +
43B ALA* 3.7 13.0 - - - +
44B HIS 3.5 13.5 - - - +
46B GLY* 1.3 90.8 - - - +
48B ARG* 1.3 59.3 - - - +
50B GLU* 3.4 17.3 + - + +
51B ARG* 3.3 41.4 + - - +
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Residues in contact with ARG 48 (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 HIS* 4.1 22.2 + - - +
31B ILE* 3.7 40.3 + - + +
44B HIS* 3.3 21.3 - - - +
45B ALA* 3.0 7.2 + - - +
47B PRO* 1.3 76.2 - - - +
49B LEU* 1.3 63.0 + - - +
51B ARG* 3.3 38.2 + - - +
52B VAL* 3.3 15.6 + - - +
41D ASP* 2.8 41.2 + - - -
44D HIS* 3.3 41.6 + - + +
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Residues in contact with LEU 49 (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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1B MSE 3.6 17.6 - - - +
3B LEU* 4.3 22.0 - - + -
15B LEU* 4.3 7.2 - - + -
17B VAL* 4.1 14.5 - - + +
28B VAL* 3.7 32.5 - - + -
31B ILE* 4.1 15.7 - - + -
38B ALA* 4.0 26.7 - - + -
42B TRP* 4.3 9.6 - - + -
45B ALA* 2.9 19.5 + - + +
46B GLY 3.5 6.7 - - - +
48B ARG* 1.3 74.9 - - - +
50B GLU* 1.3 64.4 + - - +
52B VAL* 3.1 9.0 + - - +
53B ALA* 3.0 18.7 + - - +
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Residues in contact with GLU 50 (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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-1B GLN 5.6 2.3 + - - -
0B GLY* 5.6 7.0 + - - +
1B MSE 3.8 25.4 - - + +
42B TRP* 5.9 1.7 + - - -
46B GLY 2.9 22.2 + - - +
47B PRO* 3.6 18.4 - - + +
48B ARG 3.2 0.4 - - - -
49B LEU* 1.3 76.4 - - - +
51B ARG* 1.3 58.1 + - + +
53B ALA* 3.2 5.6 + - - +
54B GLU* 2.9 29.9 + - - +
202B THR* 6.4 0.7 - - - -
204B GLU* 5.3 5.2 - - - +
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Residues in contact with ARG 51 (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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47B PRO* 3.3 28.8 + - - +
48B ARG* 3.5 32.1 - - - +
49B LEU 3.2 0.6 - - - -
50B GLU* 1.3 78.9 - - + +
52B VAL* 1.3 56.1 + - + +
54B GLU* 3.4 17.5 + - - +
55B GLY* 3.0 23.2 + - - -
44D HIS* 3.3 31.5 + - - -
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Residues in contact with VAL 52 (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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17B VAL* 3.6 27.8 - - + -
26B SER* 4.9 1.3 - - - -
28B VAL* 3.9 21.3 - - + -
30B HIS* 4.8 8.1 - - + +
31B ILE* 4.0 13.0 - - + -
48B ARG 3.3 11.6 + - - +
49B LEU* 3.1 9.9 + - - +
51B ARG* 1.3 76.0 - - + +
53B ALA* 1.3 60.9 + - - +
55B GLY* 3.1 2.8 + - - -
56B ILE* 2.9 35.2 + - + +
61B GLN* 4.2 27.3 - - + +
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Residues in contact with ALA 53 (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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0B GLY 4.3 7.0 - - - +
1B MSE 3.4 33.4 - - + -
17B VAL* 3.8 17.5 - - + -
18B VAL 5.8 0.7 - - - +
20B LYS* 4.1 12.9 + - - +
49B LEU 3.0 9.2 + - - +
50B GLU* 3.2 8.9 + - - +
52B VAL* 1.3 75.5 - - - +
54B GLU* 1.3 63.4 + - - +
56B ILE* 3.2 6.7 + - - +
57B GLU* 3.0 22.7 + - - +
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Residues in contact with GLU 54 (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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-1B GLN* 4.3 20.5 + - - +
20B LYS* 5.8 0.4 - - - +
50B GLU 2.9 12.3 + - - +
51B ARG* 3.5 22.5 - - - +
52B VAL 3.2 0.2 - - - -
53B ALA* 1.3 77.6 - - - +
55B GLY* 1.3 60.6 + - - +
57B GLU* 3.3 8.3 + - + +
58B THR* 3.1 36.8 + - + +
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Residues in contact with GLY 55 (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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51B ARG 3.0 14.1 + - - -
52B VAL* 3.1 3.5 + - - -
54B GLU* 1.3 75.2 - - - +
56B ILE* 1.3 59.1 + - - +
58B THR* 3.8 7.9 - - - -
59B GLY 3.0 23.9 + - - -
60B ALA* 3.1 14.9 + - - -
61B GLN* 3.1 18.4 + - - -
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Residues in contact with ILE 56 (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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17B VAL* 3.5 46.4 - - + +
18B VAL 4.5 0.9 - - - +
19B SER* 3.8 32.8 - - - +
20B LYS* 6.4 0.2 - - - +
24B ARG* 2.7 32.8 + - + +
25B CYS* 4.5 1.6 - - - -
26B SER* 4.0 16.6 - - - +
52B VAL* 2.9 15.6 + - + +
53B ALA* 3.2 8.2 + - - +
55B GLY* 1.3 76.2 - - - +
57B GLU* 1.3 59.7 + - - +
59B GLY* 3.5 5.0 + - - -
61B GLN* 3.8 21.8 - - + -
63B THR* 3.9 17.7 - - + +
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Residues in contact with GLU 57 (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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-1B GLN* 6.1 1.1 - - - +
19B SER* 6.4 0.2 - - - -
20B LYS* 3.7 28.4 + - - +
24B ARG* 4.9 4.4 + - - +
53B ALA 3.0 12.4 + - - +
54B GLU* 3.3 15.0 - - + +
55B GLY 3.2 0.4 - - - -
56B ILE* 1.3 81.2 - - - +
58B THR* 1.3 64.8 + - + +
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Residues in contact with THR 58 (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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54B GLU* 3.1 23.1 + - + +
55B GLY* 3.3 9.5 + - - -
56B ILE 3.4 0.2 - - - -
57B GLU* 1.3 83.6 - - + +
59B GLY* 1.3 58.9 + - - +
60B ALA* 3.3 17.3 + - - +
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Residues in contact with GLY 59 (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 ARG* 5.0 5.4 - - - -
55B GLY 3.0 5.9 + - - -
56B ILE 3.5 7.2 + - - -
57B GLU 3.4 3.0 - - - -
58B THR* 1.3 78.5 - - - +
60B ALA* 1.3 64.5 + - - +
61B GLN 3.3 10.2 - - - +
62B PRO* 5.5 0.2 - - - +
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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
------------------------------------------------------------
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