Contacts of the helix formed by residues 69 - 74 (chain K) in PDB entry 6AHU
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 LEU 69 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150C LEU* 3.8 36.6 - - + -
207C TRP* 4.1 3.8 - - + +
208C LEU* 4.0 19.7 - - + -
22K HIS* 3.4 33.0 - - + +
25K LEU* 3.8 40.1 - - + +
35K ALA* 6.0 0.4 - - - +
68K LEU* 1.3 88.5 - - + +
70K VAL* 1.3 65.1 + - - +
71K PRO* 3.5 2.2 - - - -
72K GLY* 3.1 16.4 + - - +
73K LEU* 3.7 18.1 + - + +
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Residues in contact with VAL 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K LEU* 4.6 10.5 - - + -
32K GLN* 3.3 49.8 - - + +
35K ALA* 5.1 5.4 - - + -
36K ARG* 5.3 8.5 - - + +
67K SER* 3.8 22.7 - - - -
68K LEU 5.0 0.2 - - - +
69K LEU* 1.3 77.8 - - - +
71K PRO* 1.4 68.4 - - + +
72K GLY 3.2 0.2 + - - -
73K LEU* 5.2 2.2 - - - -
74K THR* 3.1 28.6 + - + -
75K CYS* 3.4 20.6 + - - -
92K CYS* 5.8 1.6 - - + -
94K THR* 5.7 1.1 - - - +
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Residues in contact with PRO 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C LEU* 4.4 1.9 - - - +
60K THR* 4.6 5.2 - - - +
62K CYS* 4.3 11.7 - - + -
67K SER* 3.6 29.8 - - - +
68K LEU 4.6 0.7 - - - +
69K LEU 3.8 2.5 - - - +
70K VAL* 1.4 86.5 - - + +
72K GLY* 1.3 59.7 + - - +
73K LEU 3.4 0.6 + - - -
75K CYS* 3.7 29.0 - - + +
77K GLN* 3.4 38.1 + - + +
90K GLN* 5.7 1.8 - - + -
91K THR 4.9 3.8 - - - +
92K CYS* 4.2 19.1 - - + +
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Residues in contact with GLY 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C HIS* 5.8 0.4 - - - -
147C LEU* 3.4 25.7 - - - +
150C LEU* 3.7 29.7 - - - +
151C SER* 4.8 7.1 + - - -
69K LEU 3.1 11.1 + - - -
71K PRO* 1.3 80.4 - - - +
73K LEU* 1.3 59.9 + - - +
77K GLN* 4.3 4.0 - - - +
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Residues in contact with LEU 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLU* 5.3 12.6 - - - +
150C LEU* 4.7 17.3 - - + +
151C SER* 5.1 11.0 + - - +
208C LEU* 5.0 8.5 - - + -
25K LEU* 5.4 12.1 - - + +
29K PRO* 5.3 12.6 - - + -
32K GLN* 5.5 3.8 - - - +
69K LEU* 3.8 41.5 - - + +
70K VAL* 3.6 2.0 + - - +
72K GLY* 1.3 77.2 - - - +
74K THR* 1.3 84.6 + - - +
75K CYS 5.1 1.1 - - - -
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Residues in contact with THR 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C GLU* 4.5 13.3 - - - +
32K GLN* 4.0 14.3 + - - +
70K VAL* 3.1 19.5 + - + -
73K LEU* 1.3 96.4 + - - +
75K CYS* 1.3 75.8 + - - +
93K LEU* 4.8 11.6 - - + +
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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