Contacts of the helix formed by residues 111 - 115 (chain O) in PDB entry 1KYO
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 ALA 111 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109O ARG 3.8 1.8 + - - -
110O VAL* 1.3 74.6 - - - +
112O TRP* 1.3 62.2 + - - +
113O ARG* 3.4 29.2 - - + +
114O THR* 2.5 36.5 + - + +
115O LEU* 3.8 2.8 - - - +
152O SER 4.4 0.7 - - - +
153O ASP 3.2 15.5 - - - +
154O TYR* 3.5 31.6 - - + +
155O ILE* 5.0 0.2 - - - -
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Residues in contact with TRP 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94O TYR* 3.5 28.7 - + - -
98O ARG* 3.9 7.9 - - - -
110O VAL 3.9 0.6 + - - -
111O ALA* 1.3 69.4 - - - +
113O ARG* 1.3 53.2 + - - +
114O THR 2.7 13.7 + - - -
115O LEU* 3.0 26.3 + - + +
125O VAL* 3.5 32.3 - - + +
128O MET* 3.7 24.7 - - + -
129O ALA* 4.0 17.1 - - + +
132O PHE* 3.9 20.2 - + - -
134O TYR* 2.8 25.2 + - - -
150O LYS 3.8 10.5 - - - -
151O LEU* 3.5 14.1 - - + +
153O ASP 2.8 31.3 + - - -
154O TYR 3.6 4.4 + - - -
155O ILE* 3.7 23.8 - - + -
156O PRO* 3.6 21.8 - - + -
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Residues in contact with ARG 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70N ARG 5.1 1.8 + - - -
71N ASP* 3.3 24.2 + - - -
111O ALA* 3.7 22.3 - - + +
112O TRP* 1.3 70.8 - - - +
114O THR* 1.3 75.4 + - - +
115O LEU 3.3 0.9 + - - -
116O VAL* 3.5 29.8 + - + +
151O LEU* 2.9 36.1 + - + +
152O SER* 4.5 12.9 + - - +
154O TYR* 4.1 8.9 + - - -
86P ALA* 3.5 34.7 + - - +
87P ASP* 3.7 21.3 + - - +
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Residues in contact with THR 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110O VAL* 3.2 20.7 - - + +
111O ALA* 2.5 29.4 + - + +
112O TRP 2.7 5.7 + - - -
113O ARG* 1.3 94.5 - - - +
115O LEU* 1.3 59.6 + - - +
116O VAL 4.6 0.7 - - - -
118O VAL* 3.1 15.5 - - - +
257O TRP* 3.0 27.8 - - - -
261O PRO* 6.2 2.5 - - + -
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Residues in contact with LEU 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94O TYR* 4.5 14.1 - - + -
110O VAL* 4.6 2.2 - - + -
111O ALA 3.8 3.1 - - - +
112O TRP* 3.0 38.4 + - + +
114O THR* 1.3 86.6 - - - +
116O VAL* 1.3 56.6 + - - +
117O GLY 3.1 0.7 + - - -
118O VAL* 2.8 26.9 + - - -
119O SER* 2.9 32.2 + - - +
120O HIS* 3.3 12.3 + - + +
125O VAL* 3.9 15.7 - - + -
128O MET* 5.3 2.5 - - + -
155O ILE* 4.5 10.1 - - + -
254O PHE* 4.1 16.2 - - + -
257O TRP* 3.8 22.9 - - + -
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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