Contacts of the helix formed by residues 24 - 32 (chain F) in PDB entry 6C3P
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 24 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B PHE* 3.7 15.8 - - - -
15F TYR* 3.3 25.8 + - - +
16F ARG* 3.5 19.6 + - - +
17F VAL 3.7 10.8 + - - +
18F ASP* 4.0 5.1 + - - +
20F GLY 3.6 3.2 + - - +
21F VAL 3.0 13.3 + - - +
22F LEU 4.1 3.0 - - - +
23F ASN* 1.3 77.4 - - - +
25F GLY* 1.3 60.9 + - - +
26F CYS* 3.1 22.3 + - - +
27F PHE* 2.9 25.2 + - + +
28F VAL* 3.2 12.5 + - - +
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Residues in contact with GLY 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F ASN 3.3 7.0 + - - -
24F ASN* 1.3 70.5 + - - +
26F CYS* 1.3 66.8 + - - +
28F VAL* 3.2 12.5 - - - +
29F ASP* 2.9 26.7 + - - +
105F HIS* 5.8 2.0 - - - -
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Residues in contact with CYS 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B PHE* 3.9 11.9 - - + -
5F PHE* 3.3 16.1 - - + -
6F CYS* 2.0 51.8 - - - -
15F TYR* 5.1 8.7 - - - -
16F ARG* 5.1 0.9 - - - -
24F ASN* 3.1 19.6 + - - +
25F GLY* 1.3 75.9 - - - +
27F PHE* 1.3 58.8 + - - +
29F ASP* 3.4 3.3 + - - -
30F ALA* 2.9 26.0 + - - +
105F HIS* 4.9 7.1 - - - -
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Residues in contact with PHE 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 4.0 22.0 - - + -
95B PHE* 3.5 30.0 - + + -
96B ALA* 3.6 31.4 - - + -
18F ASP* 5.7 2.7 - - - +
21F VAL* 3.6 35.7 - - + +
22F LEU* 4.4 16.2 - - + -
24F ASN* 2.9 23.8 + - + +
26F CYS* 1.3 80.3 - - - +
28F VAL* 1.3 62.6 + - + +
30F ALA* 3.2 3.3 + - - +
31F LEU* 2.8 46.9 + - + +
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Residues in contact with VAL 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F LEU* 3.8 24.9 - - + +
24F ASN 3.2 6.3 + - - +
25F GLY* 3.2 21.8 - - - +
27F PHE* 1.3 80.0 - - + +
29F ASP* 1.3 60.7 + - + +
31F LEU* 3.2 10.8 + - + +
32F ASN* 2.5 41.0 + - - +
149F THR 5.8 0.7 - - - +
152F ILE* 4.4 22.7 - - + -
153F LYS* 4.7 23.8 - - + +
156F LYS* 5.2 6.5 - - + -
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Residues in contact with ASP 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F PHE* 4.0 1.5 - - + -
25F GLY 2.9 18.7 + - - +
26F CYS* 3.5 6.1 - - - +
28F VAL* 1.3 80.7 - - + +
30F ALA* 1.3 61.3 + - - +
32F ASN* 3.5 19.3 + - - +
33F VAL* 3.6 9.7 - - - +
105F HIS* 2.2 62.7 + - + +
106F LEU* 4.3 2.4 - - - +
109F PRO* 3.2 14.0 - - - +
153F LYS* 5.4 10.0 - - - +
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Residues in contact with ALA 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B MET* 5.6 0.9 - - - +
91B TRP* 4.1 22.5 - - + -
92B LEU* 4.8 8.7 - - + -
95B PHE* 5.1 6.1 - - + -
5F PHE* 3.5 28.6 - - + -
26F CYS 2.9 13.6 + - - +
27F PHE* 3.7 5.8 - - - +
29F ASP* 1.3 74.3 - - - +
31F LEU* 1.3 68.1 + - - +
33F VAL* 2.9 23.5 + - - +
34F VAL* 3.7 7.3 + - - +
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Residues in contact with LEU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU* 4.2 26.2 - - + +
22F LEU* 6.3 2.0 - - + -
27F PHE* 2.8 35.9 + - + +
28F VAL* 3.2 11.4 + - + +
30F ALA* 1.3 76.9 - - - +
32F ASN* 1.3 58.9 + - - +
33F VAL 3.0 5.4 + - - -
34F VAL* 3.2 23.6 + - + +
35F PRO* 3.2 10.0 - - - +
149F THR* 3.9 25.2 - - + +
152F ILE* 5.4 12.6 - - + -
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Residues in contact with ASN 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F VAL* 2.5 30.6 + - - +
29F ASP* 3.6 11.0 - - - +
30F ALA 3.1 0.6 - - - -
31F LEU* 1.3 75.2 - - - +
33F VAL* 1.3 60.7 + - - +
35F PRO* 3.9 5.1 - - - +
36F HIS* 3.7 22.9 + - - -
109F PRO* 4.6 9.0 - - + +
149F THR* 3.0 43.7 + - - +
150F LYS* 3.7 14.9 + - + +
153F LYS* 3.2 36.5 - - - +
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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