Contacts of the helix formed by residues 18 - 23 (chain C) in PDB entry 4GKH
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 ASN 18 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 6.2 0.2 - - - +
16C ASN 4.3 6.1 + - - -
17C SER* 1.3 79.0 + - - +
19C LEU* 1.3 65.3 + - - +
20C ASP* 3.4 20.9 + - - +
21C ALA* 3.7 9.4 + - - +
22C ASP* 3.2 16.5 - - - +
86C HIS* 3.6 9.1 + - - -
88C ILE* 3.7 21.5 - - - +
16D ASN 5.3 0.2 - - - +
17D SER 4.5 4.1 - - - +
18D ASN* 2.9 48.0 + - - +
19D LEU* 3.9 7.3 - - - +
86D HIS* 5.1 0.9 + - - -
88D ILE* 4.4 12.1 - - - +
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Residues in contact with LEU 19 (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 ASN* 1.3 76.2 + - - +
20C ASP* 1.3 54.9 + - - +
21C ALA 2.7 1.2 + - - -
22C ASP* 2.5 36.5 + - - +
23C LEU* 3.2 22.6 + - + +
54C LEU* 4.3 13.9 - - + -
86C HIS* 3.7 34.5 + - + +
88C ILE* 3.9 15.2 - - + +
95C TRP* 4.3 24.5 - - + -
97C LEU* 4.0 20.6 - - + -
15D LEU* 3.6 30.1 - - + -
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Residues in contact with ASP 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ASN* 3.4 23.7 + - - +
19C LEU* 1.3 75.3 + - - +
21C ALA* 1.3 59.7 + - - +
23C LEU* 3.5 1.6 + - - -
24C TYR* 3.2 39.7 + - + +
12D ARG* 3.3 30.2 + - - +
15D LEU* 3.3 17.9 - - - +
17D SER 5.0 6.8 - - - +
18D ASN* 4.8 5.3 + - - -
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Residues in contact with ALA 21 (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 SER* 5.9 4.0 - - - -
18C ASN 3.7 8.8 + - - +
19C LEU 2.7 5.3 + - - -
20C ASP* 1.3 75.6 + - - +
22C ASP* 1.3 62.3 + - - +
23C LEU 3.0 6.6 + - - -
24C TYR* 3.6 36.5 + - + +
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Residues in contact with ASP 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C SER* 4.8 8.0 - - - -
18C ASN 3.2 17.3 - - - +
19C LEU 2.5 19.9 + - - +
21C ALA* 1.3 74.4 - - - +
23C LEU* 1.3 61.9 + - + +
24C TYR 5.2 0.4 - - - -
26C TYR* 3.6 18.2 - - - -
52C LEU* 4.3 5.6 - - + +
85C LYS* 4.6 7.2 - - + +
86C HIS* 3.0 33.4 - - - +
97C LEU* 4.0 19.5 - - + +
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.2 42.1 + - + +
20C ASP* 3.5 3.3 + - - +
21C ALA 3.0 0.8 - - - -
22C ASP* 1.3 88.5 - - + +
24C TYR* 1.3 67.4 + - - +
25C GLY 3.3 3.1 + - - -
26C TYR* 3.4 20.6 + - - +
28C TRP* 3.8 34.0 + - + -
43C LEU* 3.7 24.9 - - + -
52C LEU* 5.2 0.2 - - + -
54C LEU* 4.9 2.2 - - + -
97C LEU* 4.0 21.3 - - + -
12D ARG* 3.7 24.9 + - + +
15D LEU* 4.7 5.8 - - + -
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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