Contacts of the helix formed by residues 42 - 54 (chain C) in PDB entry 3U8Z
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 LYS 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C LYS 4.6 3.4 - - - +
41C TRP* 1.3 77.1 - - - +
43C GLY* 1.3 66.2 + - - +
44C LYS* 3.2 3.1 - - + +
45C ASP* 2.8 30.1 + - - +
46C LEU 3.4 4.7 + - - -
77C MET 3.4 11.0 - - - +
78C ASP* 3.3 34.8 + - - +
79C LYS 3.4 11.4 - - - +
80C LYS* 3.9 14.4 - - + +
81C VAL* 3.7 6.5 - - - +
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Residues in contact with GLY 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LYS* 1.3 72.8 - - - +
44C LYS* 1.3 51.1 + - - +
46C LEU* 3.5 2.3 + - - +
47C PHE* 2.8 36.4 + - - +
75C LEU* 3.9 11.0 - - - +
76C LYS 3.5 18.2 - - - -
77C MET* 3.4 10.2 + - - +
79C LYS 3.0 12.7 + - - -
81C VAL* 3.7 14.5 - - - +
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Residues in contact with LYS 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLU* 4.0 19.4 + - - +
42C LYS* 3.2 2.4 - - + -
43C GLY* 1.3 76.8 - - - +
45C ASP* 1.4 57.2 + - - +
47C PHE* 5.6 1.2 - - + -
48C ASP* 2.9 57.5 + - - +
77C MET* 3.0 41.6 + - + +
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Residues in contact with ASP 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LYS 4.9 0.2 - - - +
41C TRP* 3.5 41.6 + - + -
42C LYS* 2.8 36.6 + - - +
44C LYS* 1.4 75.0 - - - +
46C LEU* 1.3 64.2 - - - +
48C ASP* 3.6 3.2 + - - +
49C LEU* 3.2 23.9 + - - +
52C ARG* 5.8 0.2 + - - -
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C VAL* 4.0 21.3 - - + -
26C ILE* 4.3 14.1 - - + -
35C PHE* 4.7 12.3 - - + -
37C CYS* 4.4 17.3 - - + -
41C TRP* 4.1 6.3 - - + -
42C LYS 3.4 2.6 + - - +
43C GLY 3.8 5.6 - - - +
45C ASP* 1.3 78.9 - - - +
47C PHE* 1.4 61.7 + - - +
49C LEU* 3.3 10.8 + - + +
50C VAL* 3.2 29.6 + - + +
64C LEU* 4.0 14.8 - - + -
75C LEU* 4.3 0.7 - - + -
81C VAL* 4.0 28.5 - - + -
94C PHE* 3.9 31.4 - - + -
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Residues in contact with PHE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C GLY 2.8 22.2 + - - +
44C LYS* 3.9 2.5 - - + +
45C ASP 3.4 0.2 - - - -
46C LEU* 1.4 71.9 - - - +
48C ASP* 1.3 71.5 + - - +
50C VAL* 3.2 6.9 + - - +
51C CYS* 3.1 47.7 + - - -
59C THR* 3.4 34.8 - - - -
62C PHE* 3.5 24.2 - - + -
63C GLY* 3.8 6.3 - - - -
64C LEU* 4.0 22.4 - - + +
77C MET* 3.7 25.4 - - + -
96C PHE* 3.6 26.2 - + - -
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Residues in contact with ASP 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ARG* 3.5 27.7 + - + +
44C LYS* 2.9 53.1 + - - +
45C ASP* 4.3 3.6 - - - +
47C PHE* 1.3 86.3 - - - +
49C LEU* 1.3 60.2 + - - +
51C CYS* 3.8 5.4 - - - +
52C ARG* 2.9 44.0 + - - +
59C THR* 5.1 2.6 + - - +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 5.5 5.4 - - + +
35C PHE* 3.6 39.0 - - + -
36C ASN 4.8 4.5 - - - +
41C TRP* 3.6 32.5 - - + -
45C ASP 3.2 14.4 + - - +
46C LEU* 3.4 12.8 - - + +
47C PHE 3.3 0.2 - - - -
48C ASP* 1.3 74.5 - - - +
50C VAL* 1.4 54.3 + - - +
52C ARG* 3.6 25.4 + - + +
53C THR* 2.6 40.7 + - - +
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 3.8 26.2 - - + -
33C MET* 3.6 24.7 - - + -
35C PHE* 3.8 27.8 - - + -
46C LEU* 3.2 17.8 + - + +
47C PHE* 3.6 6.7 - - - +
49C LEU* 1.4 75.1 - - - +
51C CYS* 1.3 62.2 + - - +
53C THR* 3.2 5.4 + - - -
54C LEU* 3.2 24.3 + - + +
64C LEU* 4.6 4.9 - - + -
96C PHE* 3.7 29.4 - - + -
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Residues in contact with CYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ARG* 4.0 4.9 - - - -
47C PHE* 3.1 48.0 + - - +
48C ASP* 3.8 7.2 - - - +
50C VAL* 1.3 75.9 - - - +
52C ARG* 1.4 54.2 + - - +
54C LEU* 3.2 3.9 + - - -
55C GLY 3.0 8.0 + - - -
56C LEU* 2.8 61.6 + - + +
59C THR* 3.6 23.6 - - + -
96C PHE* 4.0 5.4 - - - -
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Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 5.7 0.2 - - - +
116A HIS* 3.4 45.1 - - + +
148A ALA 4.7 11.1 + - - -
149A LYS* 4.3 17.7 + - - +
151A GLY* 5.6 4.6 - - - +
198A ARG* 4.2 32.9 - - - +
201A ASP* 4.2 19.5 - - - -
204A GLU* 5.0 1.1 - - - +
41C TRP* 6.2 1.2 - - - -
45C ASP 5.8 0.4 + - - -
48C ASP* 2.9 32.6 + - - +
49C LEU* 3.8 28.7 - - + +
51C CYS* 1.4 74.6 - - - +
53C THR* 1.4 61.7 + - - +
55C GLY* 3.2 11.8 + - - -
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Residues in contact with THR 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 3.7 39.3 + - + +
31A ALA* 4.6 0.9 - - + -
33A MET* 3.9 23.6 - - + -
54A LEU* 3.7 9.9 - - - +
113A ILE* 3.3 17.8 - - - +
33C MET* 4.0 6.1 - - - -
35C PHE* 3.2 29.4 - - + -
49C LEU* 2.6 22.7 + - - +
50C VAL 3.2 10.5 + - - -
52C ARG* 1.4 75.2 - - - +
54C LEU* 1.3 56.7 + - + +
55C GLY 3.4 0.2 - - - -
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Residues in contact with LEU 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A THR* 3.7 26.7 - - + +
54A LEU* 3.4 31.7 - - + +
113A ILE* 4.3 1.1 - - - -
28C THR* 4.8 6.3 - - + -
33C MET* 3.9 31.0 - - + -
50C VAL* 3.2 17.9 + - + +
51C CYS* 3.2 5.8 + - - +
53C THR* 1.3 78.6 - - - +
55C GLY* 1.3 63.2 + - - +
56C LEU* 3.2 5.3 + - + -
96C PHE* 4.0 30.3 - - + -
113C ILE* 3.5 24.3 - - + +
117C LEU* 4.4 12.1 - - + -
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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