Contacts of the helix formed by residues 110 - 115 (chain I) in PDB entry 3KDO
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 GLY 110 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283E ALA* 3.9 6.1 - - - -
284E MET* 3.4 25.3 + - - -
286E ALA* 5.4 1.4 - - - +
105I LEU 3.5 2.5 + - - -
106I ALA 3.4 17.6 + - - -
107I SER 4.2 1.6 + - - -
109I ALA* 1.3 76.8 - - - +
111I ASN* 1.3 66.2 + - - -
112I ILE* 3.2 6.6 + - - +
113I PHE* 3.3 18.4 + - - +
114I GLY 4.7 0.2 + - - -
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Residues in contact with ASN 111 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E LYS* 4.2 2.2 - - - +
192E GLU* 2.4 40.7 + - - +
281E HIS* 3.2 20.8 - - - -
283E ALA* 3.9 6.7 - - - +
284E MET 5.0 0.7 - - - +
285E HIS* 5.9 3.6 - - - -
286E ALA* 6.4 0.2 - - - -
322E LYS* 6.4 0.2 - - - -
323E LEU* 4.3 13.1 - - + +
600E CAP 3.4 37.8 + - - +
49I GLU* 5.5 9.4 - - + +
106I ALA 4.5 2.4 + - - -
107I SER 5.7 0.6 + - - -
110I GLY* 1.3 70.8 - - - -
112I ILE* 1.3 52.6 + - + +
113I PHE 2.7 0.4 + - - -
114I GLY* 2.6 32.6 + - - -
115I MET* 3.7 6.1 + - + +
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Residues in contact with ILE 112 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I PHE* 3.6 26.5 - - + -
46I VAL* 3.6 30.1 - - + +
49I GLU* 3.7 20.4 - - + +
50I SER* 3.9 10.8 - - - +
107I SER 4.3 4.0 - - - +
108I ILE* 3.6 30.7 - - - +
109I ALA* 4.1 1.3 - - - +
110I GLY 4.1 12.1 - - - +
111I ASN* 1.3 76.6 - - - +
113I PHE* 1.3 66.9 + - + +
114I GLY 3.3 0.9 + - - -
115I MET* 3.3 31.5 + - + +
118I VAL* 4.1 3.8 - - - +
121I LEU* 3.4 19.2 - - + +
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Residues in contact with PHE 113 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284E MET* 4.6 1.6 - - - -
286E ALA* 3.5 21.9 - - + +
287E ALA* 3.8 18.2 - - + +
290E ARG* 2.9 18.8 + - - -
29I PHE* 5.1 2.7 - + - -
108I ILE 5.1 0.9 - - - -
109I ALA* 3.5 35.0 - - + -
110I GLY 3.3 18.5 + - - +
111I ASN 2.7 3.8 + - - -
112I ILE* 1.3 76.1 - - + +
114I GLY* 1.3 56.9 + - - +
115I MET 3.6 0.4 - - - -
118I VAL* 4.9 0.6 - - - +
121I LEU* 3.2 34.8 - - + -
123I LEU* 4.1 14.4 - - + -
294I HIS* 3.2 19.9 - + - -
295I GLY* 3.1 32.3 - - - -
296I ILE* 3.6 18.4 - - + -
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Residues in contact with GLY 114 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285E HIS* 5.6 2.7 - - - -
286E ALA* 3.6 16.1 - - - +
290E ARG* 3.7 5.8 - - - -
323E LEU* 3.3 14.8 - - - -
324E GLU* 2.9 29.4 + - - +
111I ASN 2.6 16.8 + - - -
113I PHE* 1.3 72.9 - - - +
115I MET* 1.3 64.6 + - - +
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Residues in contact with MET 115 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290E ARG* 3.0 20.8 + - - -
322E LYS* 3.7 6.1 - - + +
323E LEU* 3.5 17.2 - - + +
45I ALA* 3.8 29.8 - - + +
46I VAL* 3.3 36.8 - - + +
49I GLU* 3.9 17.3 - - + -
111I ASN* 4.2 1.8 - - + +
112I ILE* 3.3 28.5 + - - +
113I PHE 3.6 1.8 - - - -
114I GLY* 1.3 76.0 - - - +
116I LYS* 1.3 65.0 + - - +
117I ARG* 4.1 9.6 - - + +
118I VAL* 3.2 19.9 - - + +
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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