Contacts of the helix formed by residues 100 - 109 (chain F) 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 ASN 100 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195C THR* 3.6 11.9 + - - +
231C THR 3.3 20.6 + - - -
232C ALA* 3.3 25.9 - - - +
233C ASP* 4.2 3.6 - - - -
96F PHE* 5.9 0.5 - - - +
97F GLU* 3.0 49.6 + - + +
98F GLU 3.3 0.4 - - - -
99F ALA* 1.3 78.3 - - - +
101F LEU* 1.3 63.3 + - - +
102F PRO* 3.3 4.0 - - - +
103F GLY* 2.9 16.0 + - - -
104F LEU* 3.0 21.3 + - - +
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Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C ASP* 4.5 4.3 + - - +
99F ALA 4.0 1.8 - - - -
100F ASN* 1.3 69.7 - - - +
102F PRO* 1.3 66.2 - - + +
104F LEU* 2.9 13.2 + - + +
105F LEU* 2.7 54.8 + - + +
128F PHE* 4.3 14.6 - - + -
136F PHE* 4.2 28.4 - - + -
261F TRP* 4.0 28.3 - - + -
304F LEU* 4.1 27.6 - - + -
308F ILE* 4.1 17.5 - - + -
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Residues in contact with PRO 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C THR* 4.0 15.8 - - + +
232C ALA 3.7 23.3 - - - +
233C ASP* 3.9 13.2 - - - +
258C ILE* 3.7 26.5 - - + +
259C THR* 6.1 0.4 - - - -
100F ASN* 3.3 9.6 - - - +
101F LEU* 1.3 96.2 - - + +
103F GLY* 1.3 61.8 + - - +
105F LEU* 3.3 6.7 + - + +
106F ALA* 3.0 22.7 + - - +
261F TRP* 3.8 25.8 - - + +
262F GLY* 4.7 1.6 - - - -
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Residues in contact with GLY 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ASN* 4.7 6.2 - - - +
195C THR* 4.0 21.3 - - - -
231C THR* 4.4 3.0 - - - +
96F PHE* 4.9 3.3 - - - -
100F ASN* 2.9 25.0 + - - -
102F PRO* 1.3 75.7 - - - +
104F LEU* 1.3 61.8 + - - +
106F ALA* 3.3 19.4 + - - +
107F SER* 3.6 8.7 + - - -
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Residues in contact with LEU 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ILE* 3.9 23.1 - - + -
96F PHE* 4.1 31.1 - - + +
100F ASN 3.0 11.3 + - - +
101F LEU* 2.9 15.3 + - + +
103F GLY* 1.3 73.5 - - - +
105F LEU* 1.3 69.5 + - + +
107F SER* 3.0 13.7 + - - -
108F ILE* 3.1 36.2 + - + +
126F LEU* 4.6 11.7 - - + -
128F PHE* 3.8 29.4 - - + -
132F LEU* 4.0 7.0 - - + -
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Residues in contact with LEU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C ILE* 4.0 5.8 - - + -
284C MET* 4.1 11.9 - - + -
101F LEU* 2.7 39.2 + - + +
102F PRO* 3.7 5.2 - - + +
104F LEU* 1.3 73.3 - - + +
106F ALA* 1.3 57.6 + - - +
108F ILE* 3.8 19.1 - - + -
109F ALA* 2.9 41.3 + - + +
123F LEU* 5.7 0.7 - - + -
126F LEU* 4.6 4.5 - - + -
261F TRP* 3.4 53.2 - - + +
296F ILE* 6.2 0.7 - - + -
300F VAL* 5.5 2.0 - - + -
304F LEU* 3.9 21.3 - - + -
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Residues in contact with ALA 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLU* 3.5 37.9 - - + +
193C ASN* 4.1 7.5 - - - +
255C ASP* 3.5 13.2 - - - +
258C ILE* 3.3 17.0 - - + +
283C ALA* 5.0 0.2 - - - -
102F PRO 3.0 9.8 + - - +
103F GLY* 3.3 14.6 - - - +
104F LEU 3.1 0.2 - - - -
105F LEU* 1.3 76.3 - - - +
107F SER* 1.3 59.8 + - - +
110F GLY* 3.5 17.5 - - - -
111F ASN 4.6 0.5 + - - -
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Residues in contact with SER 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ASN* 3.1 34.6 + - - +
49F GLU 4.7 1.1 - - - +
50F SER* 3.0 41.8 + - - +
51F SER* 5.3 0.2 - - - -
96F PHE* 3.6 25.6 - - - -
103F GLY 3.6 4.0 + - - -
104F LEU 3.0 9.6 + - - -
106F ALA* 1.3 80.7 - - - +
108F ILE* 1.3 62.2 + - - +
109F ALA 3.3 1.1 + - - -
110F GLY* 4.1 3.8 + - - -
111F ASN 5.6 0.3 + - - -
112F ILE* 4.6 3.1 - - - +
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Residues in contact with ILE 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F ILE* 5.8 1.6 - - + -
27F ALA* 4.3 8.7 - - + -
29F PHE* 3.3 13.5 - - + -
50F SER* 4.4 4.3 - - - -
91F TYR* 3.6 44.4 - - + +
96F PHE* 4.7 4.0 - - + -
104F LEU* 3.1 35.0 - - + +
105F LEU* 3.8 9.0 - - + -
107F SER* 1.3 79.9 - - - +
109F ALA* 1.3 74.9 + - + +
110F GLY 3.8 0.4 - - - -
112F ILE* 3.3 17.6 - - - +
113F PHE* 4.9 0.2 - - - -
123F LEU* 4.0 7.4 - - + +
126F LEU* 3.8 33.2 - - + -
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Residues in contact with ALA 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C MET* 3.1 43.1 - - + +
105F LEU* 2.9 18.5 + - + +
108F ILE* 1.3 92.8 - - + +
110F GLY* 1.3 57.8 + - - +
112F ILE* 4.4 0.7 - - - -
113F PHE* 3.5 23.2 - - + -
123F LEU* 4.1 11.9 - - + -
296F ILE* 4.1 5.2 - - + -
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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