Contacts of the helix formed by residues 100 - 109 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96E PHE* 5.9 0.7 - - - +
97E GLU* 3.0 48.9 + - + +
98E GLU 3.3 0.6 - - - -
99E ALA* 1.3 77.4 - - - +
101E LEU* 1.3 62.6 + - - +
102E PRO* 3.3 4.3 - - - +
103E GLY* 3.1 14.2 + - - -
104E LEU* 3.1 17.6 + - - +
135E GLU* 4.9 0.2 + - - -
195I THR* 3.7 13.5 + - - +
231I THR 3.4 20.4 + - - -
232I ALA* 3.2 26.0 - - - +
233I ASP* 4.1 3.1 - - - -
236I GLU* 6.6 0.2 - - + -
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Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E ALA 4.0 1.6 - - - -
100E ASN* 1.3 73.1 - - - +
102E PRO* 1.3 67.9 - - + +
104E LEU* 3.0 28.1 + - + +
105E LEU* 2.8 49.0 + - + +
128E PHE* 4.4 3.6 - - + -
136E PHE* 4.1 32.5 - - + -
261E TRP* 4.1 17.9 - - + -
304E LEU* 4.2 24.0 - - + +
308E ILE* 4.1 24.5 - - + -
233I ASP* 4.5 4.0 + - - +
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Residues in contact with PRO 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ASN* 3.3 9.4 - - - +
101E LEU* 1.3 97.5 - - + +
103E GLY* 1.3 56.2 + - - +
105E LEU* 3.4 5.3 + - + -
106E ALA* 3.0 27.4 + - - +
261E TRP* 3.8 25.4 - - + +
262E GLY* 4.9 0.7 - - - -
231I THR* 4.0 12.2 - - + +
232I ALA 3.7 25.4 - - - +
233I ASP* 4.0 12.1 - - - +
258I ILE* 3.7 27.8 - - + +
259I THR* 6.0 0.9 - - - +
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Residues in contact with GLY 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96E PHE* 5.0 4.1 - - - -
100E ASN* 3.1 19.6 + - - -
102E PRO* 1.3 73.1 - - - +
104E LEU* 1.3 65.4 + - - +
106E ALA* 3.4 14.4 + - - +
107E SER* 3.5 12.0 + - - -
193I ASN* 4.6 8.2 - - - +
195I THR* 3.9 25.4 - - - -
231I THR* 4.5 3.3 - - - +
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Residues in contact with LEU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ILE* 4.0 12.3 - - + -
96E PHE* 3.5 55.0 - - + +
100E ASN 3.1 11.1 + - - +
101E LEU* 3.0 20.7 + - + +
103E GLY* 1.3 73.5 - - - +
105E LEU* 1.3 61.9 + - + +
107E SER* 3.0 5.7 + - - -
108E ILE* 2.8 36.2 + - + +
126E LEU* 4.3 6.1 - - + -
128E PHE* 3.1 41.5 - - + -
132E LEU* 4.6 6.5 - - + -
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E LEU* 2.8 36.3 + - + +
102E PRO* 3.7 5.8 - - + +
104E LEU* 1.3 73.2 - - + +
106E ALA* 1.3 61.0 + - - +
108E ILE* 4.3 15.7 - - + -
109E ALA* 2.7 42.5 + - + +
123E LEU* 5.8 1.6 - - + -
126E LEU* 4.6 8.1 - - + -
261E TRP* 3.5 52.0 - - + +
300E VAL* 5.7 2.0 - - + -
304E LEU* 4.0 19.3 - - + -
258I ILE* 3.7 5.4 - - + -
284I MET* 4.1 12.8 - - + -
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Residues in contact with ALA 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E PRO 3.0 12.0 + - - +
103E GLY* 3.5 11.9 - - - +
104E LEU 3.2 0.4 - - - -
105E LEU* 1.3 76.2 - - - +
107E SER* 1.3 59.4 + - - +
110E GLY* 3.4 18.0 - - - -
111E ASN 4.5 0.9 + - - -
192I GLU* 3.5 32.3 - - + +
193I ASN* 4.3 2.5 - - - -
255I ASP* 3.4 25.1 - - - +
258I ILE* 3.1 18.6 - - + +
283I ALA* 4.8 0.7 - - - -
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Residues in contact with SER 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E GLU 4.7 0.9 - - - +
50E SER* 2.4 57.0 + - - +
51E SER* 4.4 0.9 - - - -
91E TYR* 5.2 0.2 - - - -
96E PHE* 4.0 22.3 - - - -
103E GLY 3.5 5.3 + - - -
104E LEU 3.0 7.9 + - - -
106E ALA* 1.3 82.5 - - - +
108E ILE* 1.3 61.4 + - - +
109E ALA 3.3 0.8 + - - -
110E GLY* 4.3 3.1 + - - -
112E ILE* 4.4 2.3 - - - +
165I LYS* 6.2 0.4 - - - +
192I GLU* 5.8 0.2 - - - -
193I ASN* 3.4 29.3 + - - +
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Residues in contact with ILE 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ILE* 5.6 0.9 - - + -
27E ALA* 3.6 20.0 - - + -
29E PHE* 3.4 22.1 - - + -
50E SER* 4.7 0.4 - - - +
91E TYR* 2.5 62.6 - - + +
96E PHE* 5.1 4.5 - - + -
104E LEU* 2.8 24.3 + - + +
105E LEU* 4.3 7.0 - - + -
107E SER* 1.3 77.4 - - - +
109E ALA* 1.3 66.8 + - + +
110E GLY 3.9 0.2 - - - -
112E ILE* 3.5 5.8 - - - +
123E LEU* 4.1 7.6 - - + +
126E LEU* 4.1 31.0 - - + -
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Residues in contact with ALA 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E LEU* 2.7 20.6 + - + +
108E ILE* 1.3 85.1 - - + +
110E GLY* 1.3 56.9 + - - +
112E ILE* 4.3 1.3 - - - -
113E PHE* 3.3 26.1 - - + -
123E LEU* 4.1 17.0 - - + -
296E ILE* 4.3 3.8 - - + -
284I MET* 3.1 40.4 - - + +
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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