Contacts of the helix formed by residues 100 - 109 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C PHE* 6.1 0.2 - - - +
97C GLU* 2.8 50.8 + - + +
98C GLU 3.3 0.8 - - - -
99C ALA* 1.3 78.1 - - - +
101C LEU* 1.3 63.0 + - - +
102C PRO* 3.5 3.8 - - - +
103C GLY* 3.0 17.6 + - - -
104C LEU* 3.1 19.3 + - - +
195F THR* 3.8 10.1 + - - +
231F THR 3.4 19.8 + - - -
232F ALA* 3.3 27.0 - - - +
233F ASP* 4.2 3.4 - - - -
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C ALA 4.0 1.2 - - - -
100C ASN* 1.3 69.4 - - - +
102C PRO* 1.3 77.3 - - + +
104C LEU* 3.0 18.3 + - + +
105C LEU* 2.8 41.9 + - + +
128C PHE* 4.5 7.4 - - + -
136C PHE* 4.3 23.7 - - + -
261C TRP* 4.0 27.1 - - + -
304C LEU* 4.1 26.2 - - + -
308C ILE* 4.0 22.4 - - + -
233F ASP* 4.4 4.9 + - - +
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Residues in contact with PRO 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ASN* 3.5 8.3 - - - +
101C LEU* 1.3 97.0 - - + +
103C GLY* 1.3 56.0 + - - +
105C LEU* 3.3 6.7 + - + +
106C ALA* 3.0 27.5 + - - +
261C TRP* 3.9 26.5 - - + +
262C GLY* 4.6 1.6 - - - +
231F THR* 4.0 16.1 - - + +
232F ALA* 3.8 22.7 - - - +
233F ASP* 3.9 13.5 - - - +
258F ILE* 3.8 27.3 - - + +
259F THR* 6.0 0.4 - - - -
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Residues in contact with GLY 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C PHE* 4.9 3.6 - - - -
100C ASN* 3.0 20.3 + - - -
101C LEU 3.1 0.2 - - - -
102C PRO* 1.3 75.5 - - - +
104C LEU* 1.3 61.6 + - - +
106C ALA* 3.4 18.2 + - - +
107C SER* 3.6 8.0 + - - -
193F ASN* 4.5 8.0 - - - +
195F THR* 3.9 24.5 - - - -
231F THR* 4.5 3.8 - - - +
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 3.9 23.8 - - + -
96C PHE* 4.2 28.6 - - + +
100C ASN 3.1 11.3 + - - +
101C LEU* 3.0 15.5 + - + +
103C GLY* 1.3 72.6 - - - +
105C LEU* 1.3 76.6 + - + +
107C SER* 3.1 14.2 + - - -
108C ILE* 3.2 20.2 + - + +
126C LEU* 4.1 26.5 - - + -
128C PHE* 3.7 29.4 - - + -
132C LEU* 3.9 8.1 - - + -
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Residues in contact with LEU 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C LEU* 2.8 33.2 + - + +
102C PRO* 3.7 5.4 - - + +
104C LEU* 1.3 83.0 - - + +
106C ALA* 1.3 61.0 + - - +
108C ILE* 4.5 1.3 - - + +
109C ALA* 2.8 48.8 + - + +
123C LEU* 5.7 1.8 - - + -
126C LEU* 4.6 7.4 - - + -
261C TRP* 3.6 51.1 - - + +
296C ILE* 6.2 0.7 - - + -
300C VAL* 5.5 2.9 - - + -
304C LEU* 4.0 20.2 - - + -
258F ILE* 4.0 5.3 - - + +
284F MET* 4.1 12.8 - - + -
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C PRO 3.0 12.3 + - - +
103C GLY* 3.5 13.5 - - - +
104C LEU 3.2 0.4 - - - -
105C LEU* 1.3 75.4 - - - +
107C SER* 1.3 60.0 + - - +
110C GLY* 3.5 16.5 - - - -
111C ASN 4.6 0.7 + - - -
192F GLU* 3.4 45.0 - - + +
193F ASN* 4.1 3.3 - - - +
255F ASP* 3.5 13.0 - - - +
258F ILE* 3.4 14.8 - - + +
283F ALA* 4.9 0.4 - - - -
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Residues in contact with SER 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLU 4.6 1.7 - - - +
50C SER* 3.1 36.2 + - - +
51C SER* 5.0 0.5 - - - -
96C PHE* 3.7 18.3 - - - -
103C GLY 3.6 2.4 + - - -
104C LEU 3.1 11.3 + - - -
106C ALA* 1.3 83.3 - - - +
108C ILE* 1.3 72.9 + - - +
109C ALA 3.4 0.6 + - - -
110C GLY* 4.1 3.5 + - - -
111C ASN 5.6 0.3 + - - -
112C ILE* 4.5 3.1 - - - +
165F LYS* 6.5 0.2 - - - +
193F ASN* 3.0 34.9 + - - +
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Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 5.5 2.5 - - + -
27C ALA* 3.8 11.0 - - + -
29C PHE* 3.4 8.1 - - + -
50C SER* 4.4 3.6 - - - -
91C TYR* 3.6 50.5 - - + -
96C PHE* 3.8 11.9 - - + -
104C LEU* 3.2 16.5 + - + +
105C LEU* 5.3 1.1 - - + -
107C SER* 1.3 91.1 - - - +
109C ALA* 1.3 59.6 + - + +
110C GLY 3.7 0.4 - - - -
112C ILE* 3.2 17.5 - - - +
113C PHE* 4.9 0.3 - - - -
123C LEU* 3.8 33.3 - - + +
126C LEU* 4.0 16.2 - - + -
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LEU* 2.8 24.9 + - + +
108C ILE* 1.3 78.9 - - - +
110C GLY* 1.3 60.2 + - - +
112C ILE* 4.4 0.4 - - - -
113C PHE* 3.5 22.3 - - + -
123C LEU* 4.4 11.7 - - + -
296C ILE* 4.0 9.6 - - + -
284F MET* 3.1 44.0 - - + +
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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