Contacts of the strand formed by residues 17 - 22 (chain D) in PDB entry 2I6A
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 LEU 17 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 1.3 73.5 - - - +
18D ASP* 1.3 69.7 + - - +
19D ILE* 3.5 2.8 + - + +
60D TYR* 3.8 19.1 - - + -
61D HIS 3.0 33.9 - - - +
62D ALA* 3.8 7.4 - - - +
95D PHE* 3.1 53.8 - - + +
98D ILE* 4.1 25.8 - - + -
99D LEU* 4.1 8.4 - - + +
121D GLY 3.2 13.0 + - - +
122D THR* 3.4 13.1 - - + +
123D CYS 3.1 17.7 + - - -
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Residues in contact with ASP 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.9 0.7 + - - +
17D LEU* 1.3 73.9 - - - +
19D ILE* 1.3 62.3 + - - +
20D SER* 3.9 3.1 - - - +
59D GLU 3.5 0.7 - - - +
60D TYR* 3.3 7.4 - - - -
61D HIS* 2.8 34.5 + - - +
63D GLY* 3.7 7.7 - - - -
123D CYS* 3.4 17.2 - - - +
125D ALA* 5.5 5.4 - - + -
134D LEU* 6.5 0.7 - - - -
332D ARG* 2.7 46.5 + - - +
500D 5I5 2.7 41.6 + - - -
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Residues in contact with ILE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 4.0 8.7 - - + +
18D ASP* 1.3 75.3 - - - +
20D SER* 1.3 60.3 + - - +
49D PHE* 5.0 13.0 - - + +
52D LEU* 3.9 16.0 - - + +
53D VAL* 4.4 13.5 - - + -
58D VAL* 3.0 29.6 - - + -
59D GLU 3.3 4.5 - - - -
60D TYR* 3.8 28.7 - - + -
95D PHE* 4.7 7.4 - - + -
122D THR* 4.2 25.6 - - + +
123D CYS 2.9 8.8 + - - +
124D ALA* 3.3 6.2 - - + +
125D ALA 2.8 23.1 + - - +
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Residues in contact with SER 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ASP 5.3 0.4 - - - -
19D ILE* 1.3 75.3 - - - +
21D ALA* 1.3 68.5 + - - +
52D LEU* 5.5 0.7 - - - -
57D LYS 4.1 0.5 - - - +
58D VAL* 3.0 2.1 - - - +
59D GLU* 2.8 45.1 + - - +
61D HIS* 5.0 5.9 - - - -
125D ALA* 3.4 26.7 - - - -
127D ILE* 4.2 11.9 - - - +
132D ARG* 4.9 6.3 + - - -
332D ARG* 5.0 9.7 + - - -
333D ARG 5.5 2.9 + - - -
334D THR* 5.1 3.8 + - - +
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Residues in contact with ALA 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D SER* 1.3 83.1 + - - +
22D VAL* 1.3 62.9 + - - +
23D VAL* 3.5 4.9 + - - +
52D LEU* 4.4 11.0 - - + +
56D PHE* 4.0 17.3 - - + -
57D LYS 3.7 21.1 - - - +
58D VAL* 3.7 13.7 - - + -
125D ALA 3.3 5.4 + - - +
126D CYS* 4.0 0.2 - - - -
127D ILE* 3.1 29.7 + - - +
334D THR* 6.3 1.8 - - - -
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Residues in contact with VAL 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ALA* 1.3 72.8 - - - +
23D VAL* 1.3 67.0 + - - +
56D PHE* 3.2 20.4 - - - +
57D LYS 5.0 2.0 + - - -
127D ILE* 3.3 28.5 - - + +
128D THR* 4.9 0.4 - - - -
129D GLY 4.8 9.6 - - - +
334D THR* 4.3 24.2 - - + +
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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