Contacts of the helix formed by residues 72 - 81 (chain K) in PDB entry 6T9L
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 SER 72 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68K CYS 4.2 2.5 - - - -
69K TRP* 3.4 15.2 + - - +
70K ASN 3.6 0.4 - - - -
71K HIS* 1.3 79.3 - - - +
73K HIS* 1.3 59.0 + - - +
74K PHE 3.4 2.2 - - - -
75K LEU* 3.2 36.9 - - - +
76K SER* 2.9 25.5 + - - -
79K LYS* 4.8 5.0 + - - +
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Residues in contact with HIS 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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46K CYS* 3.3 10.0 - - - -
48K THR* 3.6 32.7 + - + +
49K CYS* 3.4 32.5 - - + -
65K PHE* 3.7 12.5 - - - -
67K GLY* 3.9 3.4 - - - -
68K CYS* 3.1 19.9 + - - +
71K HIS* 3.6 28.9 + + + +
72K SER* 1.3 78.1 - - - +
74K PHE* 1.3 58.7 + - - +
76K SER* 2.5 20.7 + - - -
77K HIS 3.5 5.2 + - - -
501K ZN 2.7 19.8 - - - -
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Residues in contact with PHE 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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58K PHE* 3.1 43.5 - - + -
59K MET 3.6 7.9 - - - -
60K CYS* 3.6 29.4 - - + -
65K PHE* 3.6 29.2 - + - -
67K GLY* 3.4 28.9 - - - +
68K CYS 3.4 6.9 + - - +
73K HIS* 1.3 77.6 - - - +
75K LEU* 1.3 63.6 + - - +
77K HIS* 3.2 16.2 + + - +
78K SER 3.6 2.1 + - - -
83K HIS 4.3 11.2 - - - +
85K PHE 4.7 1.3 - - - -
86K GLY* 3.8 15.3 - - - -
97K PHE* 3.3 31.1 - + + -
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Residues in contact with LEU 75 (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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68K CYS 4.9 0.4 + - - -
69K TRP* 6.2 4.0 - - + -
72K SER* 3.2 31.4 + - - +
73K HIS 3.4 0.4 - - - -
74K PHE* 1.3 76.8 - - - +
76K SER* 1.3 60.4 + - - +
78K SER* 2.5 24.2 + - - +
79K LYS* 3.1 38.5 + - + +
97K PHE* 3.6 44.4 - - + -
100K GLU* 4.6 11.7 - - - +
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Residues in contact with SER 76 (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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48K THR* 5.6 0.7 + - - -
72K SER* 2.9 19.4 + - - -
73K HIS* 2.5 29.3 + - - -
75K LEU* 1.3 72.9 - - - +
77K HIS* 1.3 60.0 + - - +
79K LYS* 4.1 11.4 - - - -
80K GLN* 2.9 51.4 + - - +
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Residues in contact with HIS 77 (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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60K CYS* 3.5 9.9 - - - -
63K CYS* 4.0 4.7 - - - -
65K PHE* 3.3 52.3 - + + -
73K HIS 3.5 0.8 + - - -
74K PHE* 3.2 18.3 + + + +
75K LEU 3.2 0.6 - - - -
76K SER* 1.3 81.8 + - - +
78K SER* 1.3 55.0 + - - +
80K GLN* 5.3 0.2 - - - -
81K ILE* 3.0 50.4 + - + +
82K GLY 3.2 4.7 + - - -
83K HIS* 3.5 30.9 + + + -
502K ZN 3.0 25.7 - - - -
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Residues in contact with SER 78 (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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74K PHE 3.6 1.4 + - - -
75K LEU* 2.5 27.0 + - - +
77K HIS* 1.3 78.4 - - - +
79K LYS* 1.3 62.3 + - - +
80K GLN 3.2 0.4 - - - -
82K GLY* 3.1 19.9 + - - -
83K HIS 3.3 33.8 + - - +
84K ILE* 3.7 18.9 - - - +
97K PHE* 3.2 18.3 - - - +
98K LYS* 5.4 4.3 + - - -
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Residues in contact with LYS 79 (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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72K SER* 4.8 3.9 + - - +
75K LEU* 3.1 48.9 + - + +
76K SER* 3.2 11.8 + - - +
78K SER* 1.3 78.4 - - - +
80K GLN* 1.3 62.2 + - + +
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Residues in contact with GLN 80 (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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76K SER* 2.9 31.6 + - - +
77K HIS* 5.3 0.2 - - - -
79K LYS* 1.3 84.4 - - + +
81K ILE* 1.3 75.3 + - + +
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Residues in contact with ILE 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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77K HIS* 3.0 45.6 + - + +
80K GLN* 1.3 96.3 - - + +
82K GLY* 1.3 61.2 + - - +
83K HIS* 3.4 29.3 + - + +
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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