Contacts of the helix formed by residues 80 - 87 (chain K) in PDB entry 4QOC
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 ASP 80 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60K TYR* 2.4 32.7 + - - -
64K LYS* 4.6 7.6 - - - +
66K LEU* 3.8 36.6 - - + +
77K CYS* 3.5 8.0 + - + +
78K SER 4.8 1.4 - - - +
79K ASN* 1.3 87.5 + - - +
81K LEU* 1.3 60.7 + - - +
82K LEU* 3.0 5.8 - - + +
83K GLY* 2.7 24.6 + - - -
84K ASP* 3.2 13.6 + - - +
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Residues in contact with LEU 81 (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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33K LEU* 4.7 19.3 - - + +
36K LYS* 5.9 7.6 - - + +
37K LEU* 4.5 23.1 - - + +
60K TYR* 4.1 12.1 - - + +
80K ASP* 1.3 75.5 + - - +
82K LEU* 1.3 50.6 + - - +
84K ASP* 2.6 41.6 + - + +
85K LEU* 2.8 50.6 + - + +
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Residues in contact with LEU 82 (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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37K LEU* 4.7 7.0 - - + -
57K LEU* 3.9 28.5 - - + -
60K TYR* 3.9 16.6 + - + -
61K ILE* 3.5 33.2 - - + -
66K LEU* 3.9 17.7 - - + -
75K VAL* 4.5 2.7 - - + -
77K CYS* 4.1 17.9 - - + -
80K ASP* 3.0 2.2 + - + +
81K LEU* 1.3 79.8 - - - +
83K GLY* 1.3 55.9 + - - +
85K LEU* 3.2 9.0 + - + +
86K PHE* 2.9 51.1 + - + +
91K PHE* 4.4 8.5 - - + -
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Residues in contact with GLY 83 (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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77K CYS* 2.9 29.8 + - - +
78K SER* 5.1 1.1 - - - -
80K ASP 2.7 12.4 + - - -
82K LEU* 1.3 75.7 - - - +
84K ASP* 1.3 61.6 + - - -
86K PHE* 4.7 0.4 - - - -
87K GLY* 3.0 19.8 + - - -
88K VAL 3.4 21.3 + - - +
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Residues in contact with ASP 84 (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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78K SER 5.5 2.9 - - - +
79K ASN 5.6 0.2 - - - +
80K ASP 3.2 5.6 + - - +
81K LEU* 2.6 44.9 + - + +
83K GLY* 1.3 73.6 - - - +
85K LEU* 1.3 60.0 + - + +
87K GLY* 3.7 7.1 + - - -
105K ARG* 5.3 1.7 + - - -
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Residues in contact with LEU 85 (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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33K LEU* 4.6 12.6 - - + +
34K LEU* 4.2 29.6 - - + +
37K LEU* 3.7 28.5 - - + -
81K LEU* 2.8 57.7 + - + +
82K LEU* 3.6 11.9 - - + +
84K ASP* 1.3 79.8 - - + +
86K PHE* 1.3 69.0 + - + +
87K GLY 3.6 0.2 + - - -
105K ARG* 3.8 11.3 + - - +
106K ASN* 3.1 37.9 + - - +
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Residues in contact with PHE 86 (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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34K LEU* 6.0 1.6 - - + -
57K LEU* 4.0 11.2 - - + -
77K CYS* 5.5 0.2 - - - -
82K LEU* 2.9 39.4 + - + +
85K LEU* 1.3 84.0 - - + +
87K GLY* 1.3 62.5 + - - +
88K VAL* 3.8 11.0 - - + +
91K PHE* 3.6 24.0 - + + -
99K ILE* 5.0 0.7 - - + -
102K MET* 3.5 60.1 - - + +
103K ILE* 4.0 25.4 - - + -
105K ARG* 3.6 18.4 + - - +
106K ASN* 4.2 5.4 - - - -
201K 35T 3.6 30.3 - - + -
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Residues in contact with GLY 87 (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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83K GLY 3.0 10.7 + - - -
84K ASP 3.7 4.9 + - - -
85K LEU 3.3 2.8 + - - -
86K PHE* 1.3 79.0 - - - +
88K VAL* 1.3 66.7 + - - +
105K ARG* 3.6 19.6 + - - -
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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