Contacts of the helix formed by residues 33 - 45 (chain O) in PDB entry 5L4K
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 LEU 33 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28O LEU* 3.0 35.8 + - + +
31O LYS* 3.9 32.3 - - + +
32O LYS* 1.3 77.8 - - - +
34O TRP* 1.3 55.7 + - - +
35O HIS 3.1 3.1 - - - -
36O GLN* 2.7 44.6 + - + +
37O LEU* 3.2 9.9 + - - +
15W TYR* 4.1 14.6 - - + +
18W ASN* 3.6 20.9 - - - +
20W ASP* 4.2 14.1 - - + +
148W VAL* 5.2 11.4 - - + -
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Residues in contact with TRP 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O LYS* 3.2 48.8 - - + +
33O LEU* 1.3 72.5 - - - +
35O HIS* 1.3 52.5 + - - +
37O LEU* 3.2 11.2 + - + +
38O THR* 2.6 38.9 + - - -
69O HIS* 4.7 4.3 - + - -
70O ARG* 2.9 88.0 - - + +
71O VAL* 4.9 0.3 - - - +
17W ARG* 2.8 41.5 - - + +
18W ASN* 3.1 4.6 + - - -
19W GLY* 3.8 18.8 - - - -
23W PRO 5.2 0.9 - - - -
24W THR* 4.7 15.5 - - + -
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Residues in contact with HIS 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O LEU 2.9 1.0 + - - -
34O TRP* 1.3 78.1 - - - +
36O GLN* 1.3 68.1 + - - +
38O THR* 3.8 6.1 + - - -
39O LEU* 3.2 41.9 + - + +
14W GLU* 3.4 56.8 + - + +
15W TYR* 3.5 46.0 - + + -
17W ARG* 5.5 2.0 - - - +
18W ASN* 3.3 5.7 + - - +
83W LYS* 4.5 10.8 + - + +
115W SER* 4.0 11.5 + - - -
116W PRO* 5.2 2.1 - - + +
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Residues in contact with GLN 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O LEU* 3.8 27.3 - - + +
33O LEU* 2.7 35.4 + - + +
35O HIS* 1.3 80.2 + - + +
37O LEU* 1.3 59.0 + - - +
39O LEU* 3.4 13.9 + - - +
40O GLN* 3.0 29.8 + - - +
15W TYR* 3.9 22.1 - - + -
116W PRO* 5.1 6.9 - - - +
148W VAL* 3.7 28.4 - - + +
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Residues in contact with LEU 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25O LEU* 3.8 41.5 - - + +
28O LEU* 3.9 32.5 - - + +
29O TYR* 4.1 6.5 - - + -
33O LEU 3.2 4.2 + - - +
34O TRP* 3.5 15.9 - - + +
36O GLN* 1.3 74.5 - - - +
38O THR* 1.3 59.9 + - - +
40O GLN* 3.0 3.1 + - - +
41O VAL* 2.8 38.6 + - + +
63O PHE* 4.5 3.8 - - + -
67O PHE* 3.7 28.7 - - + -
70O ARG* 3.6 27.4 - - - +
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Residues in contact with THR 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34O TRP 2.6 24.3 + - - -
35O HIS* 4.0 9.9 - - - -
36O GLN 3.3 0.2 - - - -
37O LEU* 1.3 76.5 - - - +
39O LEU* 1.3 63.6 + - + +
41O VAL* 4.1 7.2 - - - +
42O LEU* 3.7 20.8 + - - +
70O ARG 4.1 2.1 + - - -
71O VAL* 3.2 38.8 - - + +
72O ASN* 4.6 7.4 - - - +
75O SER* 3.7 30.1 - - - +
76O LEU 5.5 0.2 - - - +
79O ILE* 4.9 3.9 - - + +
14W GLU* 5.3 5.8 - - - +
17W ARG* 4.7 2.8 + - - -
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Residues in contact with LEU 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O HIS* 3.2 43.7 - - + +
36O GLN* 3.4 16.5 + - - +
37O LEU 3.1 0.6 - - - -
38O THR* 1.3 82.8 - - + +
40O GLN* 1.3 61.9 + - - +
42O LEU* 3.9 4.0 + - - +
43O ASP* 3.6 19.6 + - - +
75O SER* 5.7 2.9 - - - +
14W GLU* 4.0 11.4 - - - +
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Residues in contact with GLN 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O VAL* 4.3 17.3 - - + +
24O ARG* 3.5 40.3 + - - +
25O LEU* 4.3 17.9 - - + -
28O LEU* 5.1 4.7 - - + -
36O GLN 3.0 18.7 + - - +
37O LEU* 3.0 4.0 + - - +
39O LEU* 1.3 79.1 - - - +
41O VAL* 1.3 59.9 + - - +
43O ASP* 3.3 26.1 + - - +
44O PHE* 2.9 31.5 + - - +
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Residues in contact with VAL 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25O LEU* 3.8 28.3 - - + -
37O LEU* 2.8 30.9 + - + +
38O THR* 4.1 5.2 - - - +
40O GLN* 1.3 69.7 - - - +
42O LEU* 1.3 63.1 + - - +
43O ASP 3.3 0.2 - - - -
44O PHE* 3.7 10.1 - - + -
45O VAL* 3.0 36.7 + - + +
63O PHE* 5.1 4.7 - - + -
64O ILE* 4.7 13.5 - - + -
67O PHE* 4.0 28.9 - - + -
79O ILE* 3.6 24.6 - - + +
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Residues in contact with LEU 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O THR 3.7 15.3 + - - +
39O LEU* 4.3 4.7 - - - +
40O GLN 3.4 0.4 - - - -
41O VAL* 1.3 81.1 - - - +
43O ASP* 1.3 58.6 + - - +
45O VAL* 4.3 0.7 - - - -
46O GLN* 3.3 26.8 + - - +
75O SER* 4.3 14.8 - - - +
78O GLU* 3.6 43.5 - - + +
79O ILE* 3.8 18.2 - - + +
82O HIS* 3.5 29.4 + - + +
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Residues in contact with ASP 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39O LEU 3.6 15.0 + - - +
40O GLN* 3.3 26.9 + - - +
41O VAL 3.3 0.2 - - - -
42O LEU* 1.3 75.4 - - - +
44O PHE* 1.3 61.8 + - - +
45O VAL 3.5 0.4 - - - -
46O GLN* 3.4 8.5 + - - +
47O ASP* 3.0 39.7 + - - +
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Residues in contact with PHE 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O LEU* 6.0 0.7 - - + -
18O GLN* 2.9 29.8 - - + -
21O VAL* 3.9 15.3 - - + -
22O TRP* 3.3 41.3 - + - -
25O LEU* 3.7 28.9 - - + -
40O GLN* 2.9 20.7 + - - +
41O VAL* 3.5 10.5 + - + -
42O LEU 3.5 0.2 - - - -
43O ASP* 1.3 75.2 - - - +
45O VAL* 1.3 68.2 + - + +
46O GLN 3.1 1.7 + - - -
47O ASP* 3.6 13.0 + - - +
51O ALA* 3.1 43.2 - - + +
59O LEU* 3.9 20.2 - - + -
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Residues in contact with VAL 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O VAL* 3.0 23.0 + - + +
42O LEU* 4.7 0.7 - - - +
44O PHE* 1.3 81.9 - - + +
46O GLN* 1.3 59.5 + - - +
47O ASP 3.6 5.2 + - - +
51O ALA* 4.7 5.1 - - - -
52O GLN* 4.2 11.3 + - - +
59O LEU* 5.6 10.3 - - + -
60O TYR* 6.4 0.4 - - + -
64O ILE* 4.2 14.4 - - + -
79O ILE* 4.1 23.6 - - + +
82O HIS* 3.5 37.7 - - + -
83O VAL* 4.9 6.1 - - + +
85O ARG* 3.5 9.3 + - - +
86O GLN* 5.4 9.3 + - - +
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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