Contacts of the helix formed by residues 100 - 109 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A THR* 3.6 14.3 - - - +
231A THR 3.3 21.4 + - - -
232A ALA* 3.3 19.4 - - + +
233A ASP* 4.1 4.0 - - - -
96H PHE* 6.1 0.5 - - - +
97H GLU* 3.3 46.2 + - + +
98H GLU 3.3 0.8 + - - -
99H ALA* 1.3 78.1 - - - +
101H LEU* 1.3 62.6 + - - +
102H PRO* 3.1 10.4 - - - +
103H GLY* 2.9 14.8 + - - -
104H LEU* 3.0 17.9 + - - +
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Residues in contact with LEU 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ASP* 4.5 3.6 + - - +
99H ALA 4.0 1.0 - - - -
100H ASN* 1.3 72.1 - - - +
102H PRO* 1.3 68.8 - - + +
104H LEU* 2.8 28.2 + - + +
105H LEU* 2.8 41.5 + - + +
128H PHE* 4.3 15.7 - - + -
136H PHE* 4.1 32.4 - - + -
261H TRP* 4.1 26.5 - - + -
304H LEU* 4.2 21.5 - - + -
308H ILE* 4.1 13.2 - - + -
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Residues in contact with PRO 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A THR* 4.0 15.6 - - + +
232A ALA 3.7 21.3 - - - +
233A ASP* 3.8 13.2 - - - +
258A ILE* 3.6 30.6 - - + +
259A THR* 6.0 0.9 - - - -
100H ASN* 3.1 12.1 - - - +
101H LEU* 1.3 96.7 - - + +
103H GLY* 1.3 59.3 + - - +
105H LEU* 3.5 4.8 + - + -
106H ALA* 3.2 21.3 + - - +
261H TRP* 3.9 26.0 - - + +
262H GLY* 5.3 1.1 - - - +
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Residues in contact with GLY 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ASN 4.5 7.6 - - - +
195A THR* 3.8 25.4 - - - -
231A THR* 4.4 3.8 - - - +
96H PHE* 5.0 3.7 - - - -
100H ASN* 2.9 19.2 + - - +
102H PRO* 1.3 74.4 - - - +
104H LEU* 1.3 64.5 + - - +
106H ALA* 3.5 17.0 + - - +
107H SER* 3.7 8.8 + - - -
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Residues in contact with LEU 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ILE* 4.9 4.9 - - + -
96H PHE* 4.4 31.5 - - + +
100H ASN 3.0 10.4 + - - +
101H LEU* 2.8 15.6 + - + +
103H GLY* 1.3 74.9 - - - +
105H LEU* 1.3 70.1 + - + +
107H SER* 3.0 19.2 + - - -
108H ILE* 3.1 33.7 + - + +
126H LEU* 4.1 17.7 - - + -
128H PHE* 3.4 33.2 - - + -
132H LEU* 3.9 14.4 - - + -
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ILE* 3.8 4.5 - - + -
284A MET* 4.0 15.7 - - + -
101H LEU* 2.8 35.0 + - + +
102H PRO* 3.9 5.4 - - + +
104H LEU* 1.3 84.4 - - + +
106H ALA* 1.3 57.4 + - - +
108H ILE* 4.6 1.8 - - + +
109H ALA* 2.9 42.7 + - + +
123H LEU* 5.9 2.5 - - + -
126H LEU* 4.7 7.2 - - + -
261H TRP* 3.5 51.8 - - + +
296H ILE* 6.5 0.2 - - + -
300H VAL* 5.7 2.0 - - + -
304H LEU* 3.9 20.4 - - + -
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Residues in contact with ALA 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLU* 3.2 45.0 - - + +
193A ASN* 4.3 3.7 - - - +
255A ASP* 3.5 13.7 - - - +
258A ILE* 3.3 16.1 - - + +
283A ALA* 4.9 0.2 - - - -
102H PRO 3.2 9.0 + - - +
103H GLY* 3.6 13.2 - - - +
104H LEU 3.1 0.4 - - - -
105H LEU* 1.3 76.0 - - - +
107H SER* 1.3 61.0 + - - +
110H GLY* 3.7 16.0 - - - -
111H ASN 4.7 0.9 + - - -
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Residues in contact with SER 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LYS* 6.4 0.4 - - - +
193A ASN* 3.0 33.6 + - - +
49H GLU 4.9 0.3 - - - +
50H SER* 3.0 39.7 + - - +
51H SER* 5.1 0.3 - - - -
96H PHE* 3.8 25.1 - - - -
103H GLY 3.7 4.6 + - - -
104H LEU 3.0 9.9 + - - -
106H ALA* 1.3 80.3 - - - +
108H ILE* 1.3 62.0 + - - +
109H ALA 3.2 4.9 + - - -
110H GLY 4.0 4.0 + - - -
111H ASN 5.6 0.5 + - - -
112H ILE* 4.7 2.1 - - - +
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Residues in contact with ILE 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H ILE* 3.6 20.2 - - + -
27H ALA* 3.4 25.4 - - + -
29H PHE* 3.3 23.0 - - + -
50H SER* 4.4 5.6 - - - -
91H TYR* 4.0 30.3 - - + +
96H PHE* 4.5 4.5 - - + -
104H LEU* 3.1 28.1 + - + +
105H LEU* 5.3 1.1 - - + -
107H SER* 1.3 78.8 - - - +
109H ALA* 1.3 61.0 + - + +
110H GLY 3.9 0.2 - - - -
112H ILE* 3.5 5.8 - - - +
123H LEU* 3.9 12.2 - - + +
126H LEU* 3.6 26.2 - - + -
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Residues in contact with ALA 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A MET* 3.1 41.0 - - + +
105H LEU* 2.9 21.5 + - + +
108H ILE* 1.3 82.3 - - - +
110H GLY* 1.3 60.9 + - - +
112H ILE* 4.3 1.6 - - - -
113H PHE* 3.6 22.8 - - + -
123H LEU* 4.1 15.5 - - + -
296H ILE* 4.3 5.6 - - + -
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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