Contacts of the strand formed by residues 122 - 128 (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 THR 122 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D LEU* 3.9 6.7 - - - +
17D LEU* 3.4 17.7 - - + +
19D ILE* 4.2 14.9 - - + +
49D PHE* 4.3 10.7 - - - -
95D PHE* 4.0 27.4 - - + -
120D THR 3.7 9.6 - - - +
121D GLY* 1.3 84.0 - - - +
123D CYS* 1.3 56.7 + - - +
136D ALA* 3.6 2.8 - - - +
137D ASN* 2.6 58.6 + - - +
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Residues in contact with CYS 123 (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* 4.2 6.9 - - + +
17D LEU 3.1 4.7 + - - +
18D ASP* 3.4 21.0 - - - +
19D ILE* 2.9 27.8 + - - +
49D PHE* 4.3 2.7 - - - -
122D THR* 1.3 75.1 - - - +
124D ALA* 1.3 64.0 + - - +
125D ALA* 4.0 0.4 - - - -
134D LEU* 4.0 20.9 - - - -
135D ILE 3.4 11.2 - - - -
136D ALA* 4.0 8.3 - - - +
500D 5I5 3.7 39.9 - - - +
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Residues in contact with ALA 124 (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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19D ILE* 3.3 4.9 - - + -
48D LEU* 4.0 4.9 - - + -
49D PHE* 3.4 24.1 - - + -
52D LEU* 4.0 21.5 - - + -
123D CYS* 1.3 73.9 - - - +
125D ALA* 1.3 60.6 + - - +
126D CYS* 3.6 3.1 - - - -
133D SER 3.1 2.4 - - - +
134D LEU* 3.1 27.7 - - - +
135D ILE* 2.8 28.5 + - + +
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Residues in contact with ALA 125 (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* 5.5 7.4 - - + -
19D ILE 2.8 11.0 + - - +
20D SER* 3.4 22.1 - - - -
21D ALA 3.3 21.1 + - - +
52D LEU* 5.6 1.3 - - - +
123D CYS* 3.9 1.2 + - - +
124D ALA* 1.3 70.3 - - - +
126D CYS* 1.3 61.3 + - - +
127D ILE* 3.3 8.8 + - + +
132D ARG* 4.2 18.8 - - + +
133D SER 3.5 3.4 - - - -
134D LEU* 3.6 20.6 - - + -
332D ARG* 5.6 1.1 - - - +
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Residues in contact with CYS 126 (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 4.0 3.8 - - - -
23D VAL* 4.2 9.6 - - + -
27D PHE* 3.7 26.9 - - - -
28D LEU* 4.1 16.1 - - + +
33D LEU* 5.2 0.7 - - - -
35D PRO 4.6 1.2 - - - +
48D LEU* 4.7 1.6 - - - -
52D LEU* 4.3 10.1 - - - -
124D ALA* 4.2 10.3 - - - -
125D ALA* 1.3 71.7 - - - +
127D ILE* 1.3 59.6 - - - +
128D THR* 4.1 0.9 + - - +
132D ARG* 3.7 1.3 + - - -
133D SER* 2.7 47.4 + - - +
135D ILE* 3.6 24.9 - - - -
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Residues in contact with ILE 127 (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* 4.2 16.4 - - - +
21D ALA* 3.1 22.3 + - - +
22D VAL* 3.3 17.4 - - + +
23D VAL* 2.8 28.4 + - - +
125D ALA 3.5 10.5 - - - +
126D CYS* 1.3 70.1 - - - +
128D THR* 1.3 67.3 + - - +
129D GLY 3.6 16.2 - - - +
131D ASN 3.3 17.3 - - - +
132D ARG* 3.3 33.9 - - + +
334D THR* 3.7 22.0 - - + +
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Residues in contact with THR 128 (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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22D VAL* 4.9 1.1 - - - -
23D VAL* 3.6 34.5 - - + +
24D ASP* 4.1 7.4 - - - +
25D LYS* 4.6 1.3 - - - +
28D LEU* 3.7 27.2 - - + +
35D PRO* 4.2 5.5 + - - +
126D CYS 4.1 0.6 + - - -
127D ILE* 1.3 81.2 - - - +
129D GLY* 1.3 55.0 + - - +
130D ASP 3.1 0.7 + - - -
131D ASN* 2.7 55.6 + - - +
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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