Contacts of the helix formed by residues 43 - 52 (chain C) in PDB entry 4WCX
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 THR 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C LYS* 4.2 9.4 - - - +
42C ILE* 1.3 76.0 - - - +
44C PRO* 1.3 75.8 - - + +
45C GLU* 3.5 9.0 + - - +
46C GLU* 2.9 40.8 + - - +
47C ALA* 2.9 21.2 + - - +
250C LEU* 5.5 0.4 - - - -
254C ASN* 5.1 2.9 - - - +
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Residues in contact with PRO 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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17C ASP* 4.2 2.5 - - - -
42C ILE 4.5 1.3 - - - +
43C THR* 1.3 88.6 - - + +
45C GLU* 1.3 60.9 + - - +
47C ALA* 3.3 10.7 + - + +
48C ALA* 3.0 21.3 + - - +
247C VAL* 3.8 15.1 - - + +
250C LEU* 3.8 10.8 - - + -
251C TYR* 3.5 63.0 - - + +
254C ASN* 3.5 22.9 - - - +
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Residues in contact with GLU 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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17C ASP* 3.5 40.4 + - + +
20C LYS* 3.0 39.7 + - + +
43C THR* 3.2 8.7 + - - +
44C PRO* 1.3 79.0 - - - +
46C GLU* 1.3 65.5 + - + +
48C ALA* 3.2 16.6 + - - +
49C VAL* 3.4 13.0 + - + +
251C TYR* 4.3 4.1 + - - +
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Residues in contact with GLU 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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32C ILE* 3.6 38.8 - - + +
35C LYS* 2.7 45.6 + - - +
42C ILE* 3.4 7.1 - - + +
43C THR* 2.9 35.6 + - - +
45C GLU* 1.3 75.9 - - + +
47C ALA* 1.3 65.4 + - - +
49C VAL* 3.1 19.4 + - - +
50C LEU* 3.3 8.0 + - - +
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Residues in contact with ALA 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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42C ILE* 3.9 14.5 - - + +
43C THR 2.9 10.5 + - - +
44C PRO 3.5 9.0 - - - +
46C GLU* 1.3 76.2 - - - +
48C ALA* 1.3 58.7 + - - +
50C LEU* 3.1 5.5 + - - +
51C LEU* 2.9 35.8 + - + +
247C VAL* 5.1 1.1 - - + -
250C LEU* 3.6 30.7 - - + -
298C VAL* 3.6 15.6 - - + +
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Residues in contact with ALA 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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17C ASP* 3.7 29.4 - - + +
18C LEU* 4.3 7.9 - - + +
21C ALA* 3.2 13.7 - - + +
44C PRO 3.0 12.5 + - - +
45C GLU 3.4 10.5 - - - +
46C GLU 3.1 0.6 - - - -
47C ALA* 1.3 77.4 - - - +
49C VAL* 1.3 62.4 + - - +
51C LEU* 3.3 6.5 + - - +
52C ASN* 3.2 17.7 + - - +
243C LYS* 5.9 0.3 - - - +
247C VAL* 3.8 20.6 - - + +
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Residues in contact with VAL 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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20C LYS 5.3 0.9 - - - +
21C ALA* 3.8 16.0 - - - +
24C ALA* 3.8 30.5 - - + -
25C THR 5.0 0.2 - - - +
28C ASP* 4.7 2.7 - - + -
29C ALA* 4.1 24.5 - - + +
32C ILE* 3.7 24.2 - - + -
45C GLU* 3.4 15.2 + - + +
46C GLU* 3.1 8.2 + - - +
48C ALA* 1.3 77.0 - - - +
50C LEU* 1.3 62.0 + - - +
52C ASN* 3.3 13.0 + - - +
53C VAL* 3.6 11.3 + - + +
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Residues in contact with LEU 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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29C ALA* 3.9 21.5 - - + +
32C ILE* 3.9 14.8 - - + -
33C ILE* 3.9 26.7 - - + -
42C ILE* 3.8 20.2 - - + -
46C GLU 3.3 9.6 + - - +
47C ALA 3.1 6.5 + - - +
49C VAL* 1.3 71.5 - - + +
51C LEU* 1.3 65.4 + - - +
52C ASN 3.0 2.2 - - - -
53C VAL* 3.1 22.0 + - - +
62C MET* 3.9 13.1 - - + +
294C LYS* 3.7 8.7 - - - +
298C VAL* 3.8 17.3 - - + -
301C MET* 3.8 33.2 - - + -
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Residues in contact with LEU 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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18C LEU* 6.2 0.2 - - + -
47C ALA* 2.9 22.2 + - + +
48C ALA* 3.3 5.1 + - - +
50C LEU* 1.3 76.4 - - - +
52C ASN* 1.3 57.3 + - - +
53C VAL 3.3 0.2 - - - -
242C TYR* 3.7 17.9 + - + -
243C LYS* 3.3 36.6 - - + +
246C THR* 3.9 18.4 - - + -
247C VAL* 3.7 28.9 - - + -
294C LYS* 2.9 28.4 + - + -
295C LEU* 4.0 30.5 - - + +
298C VAL* 4.1 14.6 - - + -
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Residues in contact with ASN 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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18C LEU 5.1 0.9 - - - +
21C ALA* 3.8 16.5 + - + +
22C LYS* 3.8 37.0 + - - +
48C ALA 3.2 14.5 + - - +
49C VAL 3.7 6.5 - - - +
50C LEU 3.0 1.4 - - - -
51C LEU* 1.3 79.1 - - - +
53C VAL* 1.3 62.6 + - - +
54C GLU* 3.4 13.1 + - - +
243C LYS* 3.2 25.2 + - + +
294C LYS* 4.4 1.1 - - - -
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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