Contacts of the helix formed by residues 114 - 118 (chain K) in PDB entry 2J28
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 114 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93K GLN* 4.6 19.8 + - + +
94K PRO* 3.4 41.0 + - + +
96K GLY 4.4 12.5 + - - -
97K THR 5.0 3.9 + - - -
112K PHE 2.4 21.9 + - - +
113K MET* 1.3 70.2 - - - +
115K ILE* 1.3 62.0 + - - +
117K SER* 3.1 15.6 + - - -
118K LEU* 3.5 27.4 - - + +
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Residues in contact with ILE 115 (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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61K VAL* 3.8 13.0 - - + -
63K VAL* 3.3 31.4 - - + -
85K VAL* 3.6 23.3 - - + -
87K LEU* 6.5 0.2 - - + -
94K PRO* 4.6 8.3 - - + +
99K ILE* 3.4 22.3 - - + +
103K VAL* 4.5 8.9 - - + +
107K LEU* 3.5 29.6 - - + +
112K PHE* 3.5 28.6 + - + -
113K MET 3.0 2.1 - - - +
114K LYS* 1.3 82.6 - - - +
116K ILE* 1.3 64.6 + - + +
117K SER 3.2 4.3 + - - -
118K LEU* 3.6 17.7 + - - +
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Residues in contact with ILE 116 (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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103K VAL* 3.9 18.7 - - + +
104K THR 3.7 21.3 - - - +
107K LEU* 3.6 21.3 - - + +
108K ARG* 3.5 36.6 - - + +
113K MET* 3.1 45.5 + - + +
115K ILE* 1.3 75.3 - - + +
117K SER* 1.3 56.5 + - - +
118K LEU 3.4 5.3 + - - +
122K VAL 4.4 12.4 - - - +
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Residues in contact with SER 117 (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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113K MET 2.9 17.3 + - - -
114K LYS* 3.1 10.2 + - - -
115K ILE 3.2 0.8 - - - -
116K ILE* 1.3 77.5 - - - +
118K LEU* 1.3 73.7 + - - +
120K PRO* 5.8 0.2 - - - -
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Residues in contact with LEU 118 (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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94K PRO* 6.2 0.4 - - + -
96K GLY 5.4 1.8 - - - +
97K THR 4.1 19.3 - - - +
98K ARG* 4.9 6.1 - - + -
99K ILE* 3.7 42.1 - - + +
103K VAL* 5.0 6.8 - - - +
114K LYS* 3.5 30.1 - - + +
115K ILE 3.6 9.5 + - - +
116K ILE 3.4 3.8 + - - +
117K SER* 1.3 92.6 - - - +
119K ALA* 1.3 73.7 + - - +
120K PRO* 3.2 8.3 - - - +
121K GLU 4.5 1.9 + - - -
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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