Contacts of the helix formed by residues 108 - 115 (chain X) in PDB entry 1YKX
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 TRP 108 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28X TRP* 3.9 21.8 - + - -
31X ALA* 5.1 3.4 - - + -
35X GLU* 3.8 25.1 - - + +
56X LEU* 2.8 43.5 + - + +
58X ILE* 4.9 1.1 - - + +
95X ALA* 3.8 31.2 - - + -
98X ILE* 3.7 34.3 - - + -
99X VAL* 4.3 9.4 - - + -
104X GLY 4.4 1.6 - - - -
105X MET* 3.0 43.8 + - + +
106X ASN 3.9 1.6 - - - -
107X ALA* 1.3 78.9 - - + +
109X VAL* 1.3 65.9 + - - +
110X ALA 3.2 0.9 - - - -
111X TRP* 3.0 22.1 + - + +
112X ARG* 3.1 14.2 + - - +
1903X EOH 3.7 18.9 - - + +
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Residues in contact with VAL 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X GLU* 3.9 8.7 + - - +
106X ASN 4.3 0.6 + - - -
107X ALA 3.6 4.8 + - - -
108X TRP* 1.3 71.5 - - - +
110X ALA* 1.3 70.8 + - + +
112X ARG* 3.2 24.9 + - - +
113X ASN* 3.0 48.0 + - - +
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Residues in contact with ALA 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X ALA* 4.9 1.1 - - - +
34X PHE* 4.0 26.2 - - + +
35X GLU* 3.1 29.8 + - + +
108X TRP 3.2 1.0 - - - -
109X VAL* 1.3 84.3 - - + +
111X TRP* 1.3 56.9 + - - +
113X ASN* 4.6 1.6 - - - +
114X ARG* 2.8 42.5 + - - +
115X CYS* 3.8 2.6 + - - -
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Residues in contact with TRP 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23X TYR* 3.9 25.6 - + - -
27X ASN* 3.0 41.3 + - - +
31X ALA* 4.2 9.9 - - + +
105X MET* 3.3 50.2 - - + +
106X ASN* 3.5 25.6 - - - -
108X TRP* 3.0 22.5 + - + +
110X ALA* 1.3 80.0 - - - +
112X ARG* 1.3 69.4 + - + +
115X CYS* 2.9 33.6 + - + +
116X LYS* 2.8 65.4 + - + -
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Residues in contact with ARG 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X ASN* 2.9 63.0 + - - +
108X TRP 3.1 5.6 + - - +
109X VAL* 3.2 29.0 + - - +
111X TRP* 1.3 85.6 - - + +
113X ASN* 1.3 76.5 + - - +
116X LYS* 3.5 24.7 + - + +
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Residues in contact with ASN 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X VAL* 3.0 39.8 + - - +
110X ALA* 5.0 1.3 - - - +
112X ARG* 1.3 94.0 + - - +
114X ARG* 1.3 71.1 + - + +
115X CYS 3.9 0.2 - - - -
116X LYS 5.8 0.7 - - - -
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Residues in contact with ARG 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X CYS* 4.1 1.7 - - - -
34X PHE* 3.3 67.9 + - + +
110X ALA* 2.8 26.0 + - - +
113X ASN* 1.3 88.0 - - + +
115X CYS* 1.3 62.1 + - - +
116X LYS 5.2 0.2 - - - -
118X THR* 3.8 15.2 + - - +
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Residues in contact with CYS 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30X CYS* 2.0 63.3 - - + -
31X ALA* 3.7 3.6 - - - -
34X PHE* 3.8 6.1 - - - -
110X ALA 4.3 0.9 - - - -
111X TRP* 2.9 35.4 + - + +
113X ASN 3.9 0.2 - - - -
114X ARG* 1.3 80.2 - - - +
116X LYS* 1.3 70.5 + - - +
117X GLY 3.2 0.7 + - - -
118X THR* 2.6 26.1 + - - -
120X VAL* 3.6 11.2 - - + +
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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