Contacts of the helix formed by residues 117 - 122 (chain K) in PDB entry 1Y69
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 GLU 117 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24470 G 5.2 1.9 + - - -
58K HIS* 4.8 12.7 - - + +
113K GLU 3.8 16.2 + - - +
115K ALA 3.1 0.6 - - - -
116K LYS* 1.3 76.7 - - - +
118K ALA* 1.3 67.6 + - - +
119K PHE 3.4 0.7 - - - -
120K ARG* 2.6 40.5 + - - +
121K LEU* 3.0 47.8 + - + +
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Residues in contact with ALA 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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54K VAL* 5.3 1.0 - - - +
55K MET* 4.4 16.8 - - + +
58K HIS* 3.8 22.0 + - + -
59K PHE* 4.1 13.5 - - + -
114K GLN 3.3 23.8 - - - +
115K ALA* 3.2 7.2 + - - +
117K GLU* 1.3 79.8 - - - +
119K PHE* 1.3 68.0 + - + +
120K ARG 3.4 0.2 + - - -
121K LEU* 3.7 5.0 + - - +
122K ALA* 3.7 18.9 + - - +
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Residues in contact with PHE 119 (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 TYR* 4.0 11.9 - - + -
34K GLY* 3.0 35.7 - - - -
35K LEU* 3.4 28.3 - - + +
55K MET* 6.0 4.7 - - - -
105K PHE* 3.8 15.3 - - + -
106K GLU* 4.2 0.2 - - - -
107K VAL* 3.4 35.4 - - + -
115K ALA* 2.6 39.2 + - + +
118K ALA* 1.3 77.9 - - + +
120K ARG* 1.3 63.3 + - - +
122K ALA* 3.4 19.9 - - - +
123K GLY* 4.3 2.6 + - - -
130K THR* 5.3 2.8 + - - -
132K MET* 3.6 29.8 - - + -
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Residues in contact with ARG 120 (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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10420 G 5.7 4.5 + - - +
24470 G 5.1 7.4 + - - -
116K LYS 3.1 23.8 + - - +
117K GLU* 2.6 45.0 + - - +
118K ALA 3.2 0.2 - - - -
119K PHE* 1.3 79.7 - - - +
121K LEU* 1.3 66.7 + - + +
123K GLY* 3.9 4.9 + - - -
124K HIS* 2.9 27.9 + - + +
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Residues in contact with LEU 121 (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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24460 C 3.7 12.7 + - - +
24470 G 4.1 39.7 - - - +
54K VAL* 4.4 17.3 - - + +
58K HIS* 5.0 20.0 - - + +
117K GLU* 3.0 46.3 + - + +
118K ALA* 4.1 5.2 - - - +
120K ARG* 1.3 80.5 - - + +
122K ALA* 1.3 58.0 + - - +
123K GLY 2.9 1.7 + - - -
124K HIS* 2.8 27.4 + - + -
125K LYS* 3.1 5.7 + - - -
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Residues in contact with ALA 122 (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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35K LEU* 4.9 6.9 - - - +
51K CYS* 4.0 25.6 - - + -
54K VAL* 4.0 17.2 - - + +
55K MET* 4.4 14.6 - - + -
105K PHE* 5.3 4.8 - - + -
118K ALA 3.7 11.1 + - - +
119K PHE* 3.4 13.2 - - - +
120K ARG 3.4 0.4 - - - -
121K LEU* 1.3 73.6 - - - +
123K GLY* 1.3 57.1 + - - +
125K LYS* 3.5 13.7 - - - +
126K LEU* 4.0 8.7 - - - +
130K THR* 5.6 0.2 + - - -
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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