Contacts of the helix formed by residues 42 - 51 (chain C) in PDB entry 4DQ0
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 GLY 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39C CYS* 2.7 30.0 + - - -
40C GLY 3.1 1.8 + - - -
41C ASN* 1.3 72.7 - - - +
43C ARG* 1.3 64.9 + - - +
44C ASN 3.2 3.3 + - - -
45C SER* 3.2 6.2 + - - -
46C LEU* 3.0 33.1 + - - +
68C VAL* 4.0 15.5 - - - -
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Residues in contact with ARG 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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9C PHE* 5.1 6.1 - - - +
15C LEU* 4.8 10.3 - - + -
16C THR* 3.2 34.8 - - - +
17C ARG 3.0 29.1 + - - +
18C THR* 4.5 5.7 + - - +
19C HIS* 3.8 27.3 - - - +
39C CYS 5.1 3.4 - - - +
41C ASN* 3.0 18.7 + - - +
42C GLY* 1.3 78.2 - - - +
44C ASN* 1.3 85.0 + - - +
46C LEU* 3.7 3.0 + - - +
47C TYR* 3.3 20.4 + - - +
102C THR* 4.4 9.3 + - - -
103C VAL* 4.4 7.3 - - - +
201C NHE 2.7 45.2 + - - -
183D ASN* 4.8 0.2 - - - +
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Residues in contact with ASN 44 (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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18C THR* 3.7 7.6 - - - +
19C HIS* 3.1 33.5 + - - +
22C VAL* 3.8 18.0 - - + +
36C ASP* 3.7 14.4 + - - +
39C CYS* 5.4 3.2 + - - +
42C GLY 3.2 0.4 - - - -
43C ARG* 1.3 90.5 - - - +
45C SER* 1.3 60.6 + - - +
47C TYR* 3.3 7.6 + - - +
48C LEU* 2.9 34.4 + - - +
100C LEU* 4.1 13.8 - - + +
102C THR* 3.5 24.5 + - - +
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Residues in contact with SER 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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36C ASP* 2.8 29.1 + - - +
39C CYS* 3.7 0.5 - - - +
42C GLY* 3.2 13.8 + - - -
44C ASN* 1.3 79.0 - - - +
46C LEU* 1.3 57.7 + - - +
48C LEU* 3.5 2.9 + - - -
49C ALA* 2.9 31.5 + - - +
55C VAL* 3.4 17.5 - - - +
57C ALA* 3.2 32.0 - - - +
68C VAL* 5.6 0.9 - - - -
80C LEU* 3.9 7.7 - - - +
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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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9C PHE* 3.4 22.8 - - + -
15C LEU* 3.7 28.0 - - + -
41C ASN 4.7 2.5 - - - +
42C GLY* 3.0 22.9 + - - +
43C ARG* 4.1 2.0 - - - +
45C SER* 1.3 73.1 - - - +
47C TYR* 1.3 67.3 + - - +
49C ALA* 3.9 3.0 - - - +
50C ALA* 2.9 27.5 + - - +
68C VAL* 4.5 11.0 - - + -
71C ILE* 3.8 35.9 - - + -
72C LYS 4.6 2.5 - - - +
77C LEU* 3.8 15.8 - - + +
80C LEU* 3.5 25.8 - - + -
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Residues in contact with TYR 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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2C ILE* 3.7 28.3 - - + +
4C ARG 3.3 22.0 - - - -
5C ASP* 3.8 7.2 - - - -
6C GLU* 3.7 18.1 + - - +
9C PHE* 3.7 13.9 - + + -
18C THR* 3.5 29.2 - - + +
22C VAL* 4.3 4.0 - - + -
23C LEU* 3.5 27.2 - - + +
26C VAL* 4.5 20.5 - - + +
43C ARG 3.3 13.1 + - - +
44C ASN 3.3 8.5 + - - +
46C LEU* 1.3 78.8 - - - +
48C LEU* 1.3 74.1 + - + +
50C ALA* 3.3 0.9 + - - +
51C ASN* 2.8 40.9 + - + +
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Residues in contact with LEU 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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22C VAL* 4.2 9.9 - - + -
26C VAL* 3.5 32.1 - - + -
34C THR* 4.2 11.4 - - + -
36C ASP* 5.7 0.4 - - + +
44C ASN 2.9 22.1 + - - +
45C SER* 5.0 2.0 - - - +
47C TYR* 1.3 88.8 - - + +
49C ALA* 1.3 61.4 + - - +
51C ASN* 3.3 5.0 + - - -
53C TYR* 2.8 60.2 + - + -
55C VAL* 3.9 7.4 - - + -
98C PHE* 4.3 8.7 - - + -
100C LEU* 4.0 33.9 - - + -
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Residues in contact with ALA 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 SER 2.9 20.4 + - - +
46C LEU 3.9 2.2 - - - +
48C LEU* 1.3 73.7 - - - +
50C ALA* 1.3 66.7 + - - +
51C ASN 3.2 0.7 + - - -
52C GLY* 3.3 4.5 + - - -
53C TYR 3.6 11.2 - - - +
55C VAL* 3.6 6.9 - - + +
77C LEU* 4.5 11.2 - - + +
79C ASN* 2.9 33.0 + - - +
80C LEU* 3.9 26.2 - - + -
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Residues in contact with ALA 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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3C ILE* 3.9 18.4 - - - +
4C ARG* 3.5 30.5 - - + +
9C PHE* 3.8 13.5 - - + -
46C LEU 2.9 17.9 + - - +
47C TYR 3.8 3.6 - - - +
49C ALA* 1.3 78.2 - - - +
51C ASN* 1.3 59.9 + - - +
52C GLY 3.4 2.5 + - - -
77C LEU* 4.0 17.2 - - + +
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Residues in contact with ASN 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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1C MET 4.6 6.9 - - - +
2C ILE* 3.9 16.8 - - + +
3C ILE* 2.5 44.4 + - - +
4C ARG* 2.8 31.7 + - - +
31C PRO* 3.9 8.5 - - - +
47C TYR* 2.8 44.1 + - + +
48C LEU* 3.3 6.3 + - - +
49C ALA 3.1 1.0 - - - -
50C ALA* 1.3 77.6 - - - +
52C GLY* 1.3 57.1 + - - +
53C TYR* 3.6 16.6 - - + -
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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