Contacts of the helix formed by residues 110 - 115 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B LEU 3.4 2.9 + - - -
106B ALA 3.7 17.7 + - - -
107B SER 4.2 3.2 + - - -
108B ILE 3.9 0.4 - - - -
109B ALA* 1.3 77.4 - - - +
111B ASN* 1.3 65.1 + - - +
112B ILE* 3.1 6.2 + - - +
113B PHE* 3.5 20.3 + - - +
283G ALA* 4.0 7.4 - - - -
284G MET* 3.5 22.3 + - - -
286G ALA* 5.3 1.2 - - - +
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Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLU* 5.3 13.3 + - + +
106B ALA 4.7 1.8 + - - -
107B SER 5.6 0.6 + - - -
110B GLY* 1.3 71.8 - - - -
112B ILE* 1.3 63.4 + - - +
113B PHE 3.1 0.4 - - - -
114B GLY* 2.9 18.7 + - - -
115B MET* 3.8 4.7 + - + -
165G LYS* 4.5 1.0 - - - +
192G GLU* 3.0 33.9 + - - +
281G HIS* 3.2 21.4 - - - -
283G ALA* 3.9 6.6 - - - +
284G MET 5.1 0.2 - - - +
285G HIS* 6.0 2.0 - - - -
286G ALA* 6.3 0.4 - - - -
322G LYS* 6.3 0.7 - - - -
323G LEU* 3.9 19.8 - - + +
600G CAP 3.1 42.4 + - - +
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 3.6 36.8 - - + -
46B VAL* 3.6 25.8 - - + +
49B GLU* 4.1 15.5 - - + +
50B SER* 3.9 15.5 - - - +
107B SER 4.5 1.1 - - - +
108B ILE 3.7 17.9 - - - +
109B ALA* 4.5 0.7 - - - -
110B GLY 4.3 10.8 - - - +
111B ASN* 1.3 77.4 - - - +
113B PHE* 1.3 68.7 + - + +
114B GLY 3.2 1.2 + - - -
115B MET* 3.2 43.8 + - + +
118B VAL* 4.1 4.0 - - - +
121B LEU* 3.5 17.2 - - + +
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Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 5.1 1.6 - + - -
108B ILE 5.1 1.1 - - - -
109B ALA* 3.3 36.3 - - + -
110B GLY 3.5 19.0 + - - +
111B ASN 3.0 1.0 + - - -
112B ILE* 1.3 81.0 - - + +
114B GLY* 1.3 56.6 - - - +
115B MET 3.5 0.2 - - - -
118B VAL* 4.8 0.8 - - - +
121B LEU* 3.4 35.0 - - + -
123B LEU* 4.3 11.4 - - + -
294B HIS* 3.3 19.3 - + + -
295B GLY* 3.3 23.3 - - - -
296B ILE* 3.6 25.6 - - + -
284G MET 4.5 2.5 - - - -
286G ALA* 3.4 19.2 - - + +
287G ALA* 3.7 20.9 - - + +
290G ARG* 2.9 21.1 + - - -
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Residues in contact with GLY 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASN 2.9 9.9 + - - -
113B PHE* 1.3 79.7 - - - +
115B MET* 1.3 59.6 + - - +
285G HIS* 5.7 2.2 - - - -
286G ALA* 3.4 15.2 - - - +
290G ARG* 3.5 7.2 - - - -
323G LEU* 3.3 12.4 - - - -
324G GLU* 2.7 36.6 + - - +
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Residues in contact with MET 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B TYR* 5.8 0.4 - - - -
45B ALA* 3.8 26.7 - - + +
46B VAL* 3.5 33.2 - - + +
49B GLU* 3.8 22.0 - - + -
111B ASN 4.1 0.7 - - - +
112B ILE* 3.2 38.1 + - + +
113B PHE 3.5 0.4 - - - -
114B GLY* 1.3 76.5 - - - +
116B LYS* 1.3 63.6 + - - +
117B ARG* 3.0 12.8 - - + +
118B VAL* 3.1 18.4 - - + +
121B LEU* 4.7 0.7 - - + -
290G ARG* 3.0 16.9 + - - -
322G LYS* 4.1 3.8 - - + +
323G LEU* 3.5 20.2 - - + -
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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