Contacts of the helix formed by residues 41 - 59 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ALA 3.4 10.0 + - - +
38A ALA 3.2 4.9 + - - +
39A LEU 3.0 0.4 - - - -
40A ASP* 1.3 80.9 - - + +
42A TRP* 1.3 59.1 + - - +
43A ALA* 3.3 3.1 - - - +
44A HIS* 3.0 16.2 + - - +
45A ALA* 2.8 27.7 + - + +
30C HIS 4.7 5.7 - - - +
48C ARG* 2.9 43.3 + - - -
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Residues in contact with TRP 42 (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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1A MSE 3.4 33.9 - - + -
3A LEU* 4.0 19.7 - - + -
35A LEU* 4.8 0.4 - - + -
38A ALA* 2.9 30.6 + - + +
39A LEU* 3.3 36.2 + - + +
40A ASP 3.6 0.2 - - - -
41A ASP* 1.3 76.6 - - - +
43A ALA* 1.3 68.1 + - - +
46A GLY* 2.8 37.8 + - - +
47A PRO* 3.5 1.7 - - + +
49A LEU* 4.3 9.6 - - + -
50A GLU* 5.5 3.7 + - - -
147A ASP* 3.9 14.6 + - - +
163A ARG* 3.4 38.4 - - - +
164A LEU* 4.3 11.4 - - + -
202A THR* 4.5 10.1 - - + -
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Residues in contact with ALA 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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41A ASP* 3.2 1.4 + - - +
42A TRP* 1.3 82.2 - - - +
44A HIS* 1.3 72.8 + - + +
47A PRO* 3.5 18.1 - - - +
147A ASP* 5.1 2.4 + - - +
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Residues in contact with HIS 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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41A ASP* 3.0 17.2 + - - +
42A TRP 2.8 0.8 + - - -
43A ALA* 1.3 91.5 - - + +
45A ALA* 1.3 63.0 + - - +
46A GLY 3.4 0.4 - - - -
47A PRO* 3.5 9.9 - - - +
48A ARG* 3.6 21.9 - - - +
44C HIS* 5.8 0.2 - - - -
48C ARG* 3.2 57.2 + - + +
51C ARG* 3.5 30.5 + - - -
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Residues in contact with ALA 45 (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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31A ILE* 4.1 24.6 - - + +
32A ALA* 5.1 0.2 - - + -
38A ALA* 3.7 30.5 - - + +
41A ASP* 2.8 25.3 + - + +
44A HIS* 1.3 73.3 - - - +
46A GLY* 1.3 65.2 + - - +
48A ARG* 3.0 7.3 + - - +
49A LEU* 2.9 26.7 + - + +
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Residues in contact with GLY 46 (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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1A MSE 4.0 0.5 - - - +
42A TRP* 2.8 51.0 + - - +
45A ALA* 1.3 72.4 - - - +
47A PRO* 1.3 67.0 - - - +
49A LEU* 3.0 7.1 + - - +
50A GLU* 2.9 31.2 + - - +
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Residues in contact with PRO 47 (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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42A TRP* 3.5 3.8 - - + +
43A ALA* 3.5 25.8 - - - +
44A HIS* 3.5 9.0 - - - +
46A GLY* 1.3 89.4 - - - +
48A ARG* 1.3 60.1 + - + +
50A GLU* 3.4 19.7 + - + +
51A ARG* 3.2 34.4 + - - +
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Residues in contact with ARG 48 (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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30A HIS* 4.0 25.8 + - - +
31A ILE* 3.5 38.1 + - + +
44A HIS* 3.6 18.4 - - - +
45A ALA* 3.0 8.3 + - - +
47A PRO* 1.3 74.8 - - + +
49A LEU* 1.3 64.2 - - - +
51A ARG* 3.4 29.0 + - - +
52A VAL* 3.3 23.6 + - - +
41C ASP* 2.9 39.0 + - - -
44C HIS* 3.3 42.0 + - + +
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Residues in contact with LEU 49 (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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1A MSE 3.5 20.1 - - + +
3A LEU* 4.2 21.5 - - + -
15A LEU* 4.3 6.3 - - + -
17A VAL* 4.2 12.5 - - + +
28A VAL* 3.7 31.9 - - + -
31A ILE* 3.8 20.0 - - + -
38A ALA* 3.9 27.4 - - + -
42A TRP* 4.3 6.3 - - + -
45A ALA* 2.9 20.5 + - + +
46A GLY 3.0 4.7 + - - +
48A ARG* 1.3 73.2 - - - +
50A GLU* 1.3 60.1 + - - +
52A VAL* 3.1 7.9 + - - +
53A ALA* 2.8 27.9 + - - +
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Residues in contact with GLU 50 (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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-2A PHE* 4.0 9.7 - - + -
0A GLY 6.3 0.7 - - - -
1A MSE 3.8 23.4 - - + +
42A TRP* 5.5 3.5 + - - -
46A GLY* 2.9 22.5 + - - +
47A PRO* 3.5 21.4 - - - +
48A ARG 3.3 0.4 - - - -
49A LEU* 1.3 77.2 - - - +
51A ARG* 1.3 56.6 + - - +
53A ALA* 3.2 6.3 + - - +
54A GLU* 2.9 28.3 + - - +
202A THR* 6.2 0.7 - - + -
204A GLU* 4.7 11.1 - - - +
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Residues in contact with ARG 51 (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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47A PRO* 3.2 23.3 + - - +
48A ARG* 3.7 33.5 - - - +
49A LEU 3.3 0.4 - - - -
50A GLU* 1.3 78.0 - - - +
52A VAL* 1.3 58.2 + - + +
54A GLU* 3.3 16.6 + - - +
55A GLY* 3.0 24.9 + - - -
44C HIS* 3.4 31.7 + - - -
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Residues in contact with VAL 52 (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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17A VAL* 3.9 25.6 - - + -
26A SER* 4.6 2.2 - - - -
28A VAL* 3.9 20.9 - - + -
30A HIS* 4.9 8.5 - - + +
31A ILE* 4.1 11.9 - - + -
48A ARG 3.3 12.5 + - - +
49A LEU* 3.1 9.3 + - - +
51A ARG* 1.3 74.5 - - + +
53A ALA* 1.3 65.8 + - - +
55A GLY* 3.0 2.9 + - - -
56A ILE* 2.9 25.2 + - + +
61A GLN* 4.2 32.1 - - + +
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Residues in contact with ALA 53 (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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-2A PHE* 3.8 12.8 - - + -
0A GLY 4.4 0.2 - - - +
1A MSE 3.5 33.9 - - + -
17A VAL* 3.8 17.0 - - + +
18A VAL 5.8 1.1 - - - +
20A LYS* 5.9 3.2 - - + +
49A LEU 2.8 12.4 + - - +
50A GLU 3.4 9.0 - - - +
52A VAL* 1.3 76.5 - - - +
54A GLU* 1.3 61.5 + - - +
56A ILE* 3.3 6.1 + - - +
57A GLU* 3.1 21.5 + - - +
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Residues in contact with GLU 54 (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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-2A PHE* 3.7 45.5 - - + +
50A GLU 2.9 12.1 + - - +
51A ARG* 3.6 21.2 - - - +
52A VAL 3.2 0.2 - - - -
53A ALA* 1.3 76.6 - - - +
55A GLY* 1.3 57.8 + - - +
57A GLU* 3.2 3.1 + - - +
58A THR* 3.0 43.6 + - + +
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Residues in contact with GLY 55 (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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51A ARG 3.0 15.5 + - - -
52A VAL* 3.5 3.6 - - - -
54A GLU* 1.3 74.5 - - - +
56A ILE* 1.3 59.7 + - - +
58A THR* 3.8 7.4 - - - -
59A GLY* 2.9 23.2 + - - -
60A ALA* 3.0 15.7 + - - -
61A GLN* 3.1 18.5 + - - -
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Residues in contact with ILE 56 (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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17A VAL* 3.4 48.5 - - + +
18A VAL 4.6 3.4 - - - +
19A SER* 3.7 31.9 - - - +
24A ARG* 4.9 3.6 - - + -
25A CYS 4.6 0.9 - - - -
26A SER* 4.1 11.9 - - - +
52A VAL* 2.9 14.7 + - + +
53A ALA* 3.3 7.8 + - - +
55A GLY* 1.3 72.4 - - - +
57A GLU* 1.3 67.6 + - - +
59A GLY* 3.3 10.2 + - - -
61A GLN* 3.6 16.1 - - + +
63A THR* 3.8 26.2 - - + +
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Residues in contact with GLU 57 (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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-2A PHE* 3.6 32.2 - - + -
20A LYS* 4.7 19.4 + - + +
53A ALA 3.1 12.9 + - - +
54A GLU 3.2 8.2 + - - +
56A ILE* 1.3 81.9 - - - +
58A THR* 1.3 66.2 + - - +
59A GLY 3.6 0.2 + - - -
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Residues in contact with THR 58 (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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54A GLU* 3.0 27.3 + - + +
55A GLY* 3.4 6.1 + - - -
57A GLU* 1.3 85.1 - - - +
59A GLY* 1.3 61.8 + - - +
60A ALA* 3.4 20.3 + - - +
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Residues in contact with GLY 59 (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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55A GLY 2.9 7.2 + - - -
56A ILE 3.3 10.8 + - - -
57A GLU 3.3 0.6 + - - -
58A THR* 1.3 78.4 - - - +
60A ALA* 1.3 61.4 + - - +
61A GLN 3.2 9.9 + - - +
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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