Contacts of the helix formed by residues 44 - 56 (chain C) in PDB entry 3RZW
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 44 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 4.3 8.1 - - + -
38C VAL* 4.4 7.4 - - + -
43C HIS* 1.3 67.8 - - - +
45C LYS* 1.3 65.1 + - - +
46C LYS 3.2 2.9 - - - -
47C LEU* 3.1 34.6 + - + +
48C LYS* 3.1 25.1 + - + +
71C ILE* 3.6 34.8 - - + -
72C ALA 4.0 2.5 - - - +
73C ASP 3.3 1.2 + - - -
75C HIS 2.8 21.5 + - - +
76C THR 4.1 9.2 - - - -
77C PRO* 4.1 21.8 - - + -
80C LEU* 3.8 20.4 - - + -
82C MET* 4.2 10.3 - - + -
88C ILE* 4.6 3.8 - - + -
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Residues in contact with LYS 45 (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 HIS* 3.2 8.0 - - + +
44C LEU* 1.3 74.0 - - - +
46C LYS* 1.3 57.9 + - - +
48C LYS* 3.2 5.4 + - - +
49C GLU* 2.8 67.4 + - + +
73C ASP* 3.1 57.4 + - + +
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Residues in contact with LYS 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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30B ASP* 5.0 10.9 + - - -
76B TYR* 3.4 16.8 - - - +
77B ASP* 3.5 39.9 - - - +
42C THR* 5.1 2.5 - - + -
43C HIS 3.9 9.5 + - - +
44C LEU 3.2 0.8 - - - -
45C LYS* 1.3 75.7 - - - +
47C LEU* 1.3 61.6 + - - +
49C GLU* 4.4 14.2 + - + +
50C SER* 2.8 44.8 + - - +
53C GLN* 5.8 3.8 - - - +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TYR* 3.5 14.6 + - - +
24C LEU* 4.0 8.1 - - + -
26C VAL* 4.0 17.7 - - + -
36C PHE* 3.6 42.2 - - + -
38C VAL* 3.8 15.7 - - + -
44C LEU* 3.1 19.6 + - + +
46C LYS* 1.3 79.1 - - - +
48C LYS* 1.3 70.6 + - + +
50C SER* 3.7 1.2 - - - -
51C TYR* 2.9 27.4 + - - +
64C PHE* 4.5 10.1 - - + -
88C ILE* 3.9 28.5 - - + -
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Residues in contact with LYS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 3.1 13.1 + - + +
45C LYS* 3.6 4.5 - - - +
47C LEU* 1.3 79.1 - - + +
49C GLU* 1.3 60.5 + - - +
51C TYR 3.4 0.9 + - - -
52C ALA* 3.0 30.3 + - - +
59C MET* 3.8 13.3 - - + +
64C PHE* 3.5 56.5 - - + -
71C ILE* 2.8 38.1 + - + +
72C ALA* 4.0 4.9 - - - +
73C ASP* 2.8 41.7 + - - +
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Residues in contact with GLU 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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45C LYS* 2.8 61.6 + - - +
46C LYS* 3.9 15.7 + - + +
48C LYS* 1.3 69.8 - - - +
50C SER* 1.3 65.1 + - - +
52C ALA* 3.4 5.8 + - - +
53C GLN* 3.0 39.7 + - - +
59C MET* 3.5 23.7 - - + +
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Residues in contact with SER 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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28B PHE* 3.5 30.2 - - - -
30B ASP* 4.5 2.8 + - - -
76B TYR* 3.7 16.0 + - - -
36C PHE* 3.8 10.1 - - - -
46C LYS* 2.8 37.0 + - - +
47C LEU 3.7 3.6 - - - -
49C GLU* 1.3 70.2 - - - +
51C TYR* 1.3 59.8 + - - +
53C GLN* 3.3 12.4 + - - +
54C ARG* 2.8 30.7 + - - +
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Residues in contact with TYR 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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28B PHE* 5.2 0.2 - - - -
26C VAL* 3.7 30.1 - - + -
28C GLY* 3.7 23.9 + - - -
30C ASP* 5.2 1.9 + - - -
32C SER* 4.3 8.4 + - - -
33C GLU 5.9 0.2 - - - -
34C ILE* 3.8 30.5 - - + -
36C PHE* 4.0 14.0 - + + -
47C LEU* 2.9 17.3 + - + +
48C LYS 3.6 4.7 - - - +
50C SER* 1.3 77.5 - - - +
52C ALA* 1.3 62.8 + - - +
54C ARG* 3.3 6.9 + - - +
55C GLN* 3.0 47.0 + - + +
62C LEU* 4.0 7.2 - - + -
64C PHE* 3.8 23.3 - + + -
90C VAL* 3.9 22.8 - - + +
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Residues in contact with ALA 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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48C LYS 3.0 18.1 + - - +
49C GLU* 3.8 6.1 - - - +
51C TYR* 1.3 77.3 - - - +
53C GLN* 1.3 62.8 + - - +
55C GLN* 3.2 4.6 + - - +
56C GLY 3.1 4.2 + - - -
57C VAL* 3.1 38.1 + - - +
59C MET* 4.2 22.9 - - + +
62C LEU* 4.2 21.8 - - + -
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Residues in contact with GLN 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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28B PHE* 5.7 3.4 - - + -
46C LYS* 5.8 3.4 - - - +
49C GLU* 3.0 39.7 + - - +
50C SER* 3.6 13.9 + - - +
52C ALA* 1.3 73.5 - - - +
54C ARG* 1.3 65.7 + - - +
56C GLY* 3.1 14.4 + - - +
57C VAL 4.8 2.5 - - - +
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Residues in contact with ARG 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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27B TRP 4.9 3.0 + - - -
28B PHE* 3.7 40.8 - - + +
29B ILE 3.3 25.7 + - - +
52B GLY* 3.8 6.5 + - - -
53B TYR* 3.7 34.5 - - - +
34C ILE* 3.8 27.3 - - + +
50C SER 2.8 18.1 + - - +
51C TYR 3.6 4.9 - - - +
53C GLN* 1.3 79.4 - - - +
55C GLN* 1.3 61.6 + - - +
56C GLY 3.4 0.2 + - - -
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Residues in contact with GLN 55 (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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30C ASP* 5.2 6.9 + - - -
32C SER* 5.2 6.4 + - - -
34C ILE* 3.7 23.9 - - - +
51C TYR* 3.0 45.6 + - + +
52C ALA* 3.2 8.7 + - - +
54C ARG* 1.3 79.1 - - - +
56C GLY* 1.3 59.9 + - - +
57C VAL* 3.7 20.2 + - + +
62C LEU* 5.1 1.8 - - + -
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Residues in contact with GLY 56 (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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52C ALA 3.1 0.2 + - - -
53C GLN* 3.1 17.8 + - - -
54C ARG 3.3 1.2 + - - -
55C GLN* 1.3 77.4 - - - +
57C VAL* 1.3 60.8 + - - +
58C PRO* 4.7 1.0 - - - +
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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