Contacts of the helix formed by residues 22 - 29 (chain C) in PDB entry 3CJS
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 PRO 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C LEU* 4.0 24.2 - - + -
11C GLN 5.4 3.6 - - - +
12C LEU* 4.2 20.6 - - + -
20C ALA 4.3 0.2 - - - +
21C PRO* 1.3 84.9 - - + +
23C VAL* 1.3 65.7 + - + +
24C GLY 3.6 0.2 - - - -
25C PRO* 3.4 5.7 - - + +
26C ALA* 3.0 26.5 + - + +
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Residues in contact with VAL 23 (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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10C LEU* 4.3 9.0 - - + -
12C LEU* 3.8 38.4 - - + -
17C ALA* 4.7 5.2 - - + -
18C THR 3.3 27.4 - - - +
20C ALA 3.0 7.0 + - - +
22C PRO* 1.3 77.4 - - + +
24C GLY* 1.3 64.3 + - - +
26C ALA 3.3 0.5 + - - -
27C LEU* 3.0 28.4 + - + +
34C ILE* 4.2 9.0 - - + -
37C PHE* 3.9 17.9 - - + -
38C VAL* 3.8 18.6 - - + -
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Residues in contact with GLY 24 (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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19C PRO 3.0 26.1 + - - -
23C VAL* 1.3 74.0 - - - +
25C PRO* 1.3 63.5 - - - +
28C GLY* 2.8 30.0 + - - -
34C ILE* 3.5 22.0 - - - +
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Residues in contact with PRO 25 (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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21C PRO* 3.9 27.8 - - + -
22C PRO* 3.4 16.2 - - + +
24C GLY* 1.3 88.1 - - - +
26C ALA* 1.3 61.6 + - - +
28C GLY* 5.0 0.2 - - - -
29C GLN* 3.1 31.2 + - - +
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Residues in contact with ALA 26 (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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8C VAL* 3.7 30.2 - - + +
10C LEU* 3.9 12.8 - - + -
22C PRO* 3.0 21.5 + - + +
23C VAL 3.9 2.0 - - - +
25C PRO* 1.3 77.0 - - - +
27C LEU* 1.3 63.7 + - + +
29C GLN* 2.9 29.4 - - - +
30C HIS* 3.5 8.7 + - - -
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Residues in contact with LEU 27 (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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8C VAL* 5.1 1.8 - - + -
10C LEU* 4.3 5.6 - - + -
23C VAL* 3.0 22.3 + - + +
26C ALA* 1.3 83.9 - - + +
28C GLY* 1.3 64.8 + - - +
29C GLN 3.2 1.8 - - - -
30C HIS* 3.1 9.7 + - - +
32C ALA* 3.1 47.2 + - + +
33C ASN 5.0 0.9 - - - +
34C ILE* 4.0 14.6 - - + -
37C PHE* 3.9 38.4 - - + -
57C ILE* 4.0 41.1 - - + -
59C ILE* 4.5 4.9 - - + -
65C PHE* 4.9 4.0 - - + -
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Residues in contact with GLY 28 (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 GLY 2.8 18.8 + - - -
25C PRO* 5.4 0.2 - - - -
27C LEU* 1.3 73.5 - - - +
29C GLN* 1.3 61.9 + - - +
30C HIS 3.0 5.2 - - - -
31C GLY* 3.0 15.7 + - - -
32C ALA 4.4 4.9 - - - -
34C ILE* 4.2 12.5 - - - +
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Residues in contact with GLN 29 (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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8C VAL* 4.4 3.6 - - - +
25C PRO* 3.1 16.2 + - - +
26C ALA* 2.9 27.2 - - - +
28C GLY* 1.3 75.6 - - - +
30C HIS* 1.3 93.6 + - + +
31C GLY 3.5 0.2 - - - -
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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