Contacts of the helix formed by residues 98 - 106 (chain J) in PDB entry 6K71
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 LYS 98 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61J LYS 3.0 26.1 + - - -
62J ASP* 3.8 3.1 - - - +
96J CYS 3.9 3.8 + - - -
97J TRP* 1.3 110.4 - - + +
99J ALA* 1.3 60.4 + - - +
100J ALA* 3.1 5.8 - - + +
101J GLN* 3.0 58.4 + - + +
102J ILE* 3.7 3.1 + - - +
125J SER* 5.6 0.8 - - - -
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Residues in contact with ALA 99 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95J CYS* 4.6 13.9 - - - -
96J CYS 5.5 0.2 + - - -
97J TRP 3.7 1.2 - - - -
98J LYS* 1.3 72.4 - - - +
100J ALA* 1.3 50.8 + - - +
101J GLN 3.3 0.2 - - - -
102J ILE* 4.9 0.4 - - - +
103J LYS* 2.6 44.6 + - + +
124J THR* 4.1 32.5 - - + -
125J SER* 4.7 11.2 + - - +
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Residues in contact with ALA 100 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98J LYS* 3.0 3.3 + - + +
99J ALA* 1.3 77.4 - - - +
101J GLN* 1.3 59.1 + - + +
103J LYS* 3.5 9.1 - - - +
104J GLU* 2.9 31.0 + - - +
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Residues in contact with GLN 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62J ASP* 2.6 35.1 + - - +
63J GLN* 4.2 11.8 + - - +
64J PRO* 3.6 19.4 - - + +
67J LEU* 5.5 4.5 - - + -
97J TRP* 5.0 2.8 - - - +
98J LYS* 3.0 39.1 + - + +
100J ALA* 1.3 79.8 - - + +
102J ILE* 1.3 63.1 + - + +
104J GLU* 3.1 5.9 + - - +
105J HIS* 2.9 29.7 + - - +
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Residues in contact with ILE 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64J PRO* 4.3 15.7 - - + -
66J VAL* 4.4 10.8 - - + -
67J LEU* 3.7 26.5 - - + -
76J ILE* 5.4 1.8 - - + -
93J VAL* 6.3 1.3 - - + -
95J CYS* 3.7 33.2 - - + -
97J TRP* 4.1 13.2 - - + +
98J LYS 3.7 3.2 + - - +
99J ALA* 4.9 0.9 - - - +
101J GLN* 1.3 75.1 - - + +
103J LYS* 1.3 58.4 + - - +
105J HIS* 4.4 5.8 - - - +
106J LEU* 2.9 49.2 + - + +
122J ILE* 4.7 17.4 - - + +
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Residues in contact with LYS 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99J ALA* 2.6 25.6 + - + +
100J ALA* 3.5 9.6 - - - +
102J ILE* 1.3 77.6 - - - +
104J GLU* 1.3 63.9 + - + +
106J LEU* 3.3 4.6 + - - +
107J LEU* 3.2 49.7 + - + +
122J ILE* 6.5 0.4 - - - -
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Residues in contact with GLU 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J ALA 2.9 19.3 + - - +
101J GLN* 3.7 4.9 - - - +
103J LYS* 1.3 78.3 + - + +
105J HIS* 1.3 62.2 + - - +
107J LEU* 3.1 38.0 + - - +
108J LYS* 3.9 15.8 + - - +
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Residues in contact with HIS 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67J LEU* 3.8 25.5 - - + +
74J ALA* 3.4 27.4 - - + +
76J ILE* 3.5 27.8 - - + +
77J ASP* 4.0 10.3 + - - -
101J GLN 2.9 15.9 + - - +
102J ILE* 4.1 4.0 - - - +
104J GLU* 1.3 77.9 - - - +
106J LEU* 1.3 59.2 + - + +
107J LEU 3.2 2.4 + - - -
108J LYS* 3.8 11.2 + - - +
109J SER* 4.1 8.1 + - - -
328J THR* 6.5 0.9 - - + -
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Residues in contact with LEU 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J ILE* 3.7 30.5 - - + -
77J ASP* 5.9 0.4 - - - +
80J LEU* 5.4 3.1 - - + -
93J VAL* 6.2 4.3 - - + -
102J ILE* 2.9 37.2 + - + +
103J LYS* 3.5 6.5 - - - +
104J GLU 3.3 0.2 - - - -
105J HIS* 1.3 81.7 - - + +
107J LEU* 1.3 58.5 + - - +
108J LYS 3.5 1.1 - - - +
109J SER* 5.0 6.7 - - - +
111J TRP* 4.2 24.5 - - + +
112J CYS* 3.2 20.8 - - - +
120J VAL* 4.3 20.8 - - + +
122J ILE* 5.7 14.6 - - + -
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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