Contacts of the strand formed by residues 129 - 134 (chain D) in PDB entry 3CME
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 ASP 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23380 G 2.7 67.4 + - + +
23470 C 4.8 5.2 - - - +
22D VAL 3.7 1.2 - - - +
23D VAL* 3.3 5.5 - - - +
24D HIS* 3.0 52.3 + - - +
26D GLY 4.7 1.4 + - - -
105D SER* 4.6 4.5 - - - +
106D PHE 3.8 0.4 - - - -
107D GLY 4.7 0.9 - - - -
128D LEU* 1.3 81.3 + - - +
130D VAL* 1.3 63.6 + - - +
131D THR* 4.1 3.1 - - - +
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Residues in contact with VAL 130 (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 VAL* 3.9 15.0 - - + -
22D VAL 3.7 2.0 - - - -
23D VAL* 3.9 4.3 - - + -
83D PHE* 3.6 37.5 - - + -
84D LEU* 4.4 1.6 - - + -
87D ALA* 5.5 0.2 - - + -
105D SER* 2.8 13.8 + - - -
106D PHE* 2.9 69.5 + - + +
107D GLY* 5.8 0.4 - - - -
128D LEU* 3.8 18.2 - - + -
129D ASP* 1.3 77.7 - - - +
131D THR* 1.3 61.2 + - - +
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Residues in contact with THR 131 (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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23370 G 3.8 9.8 + - + +
23470 C 4.0 8.0 + - - -
23480 C 3.6 46.0 + - - +
20D LYS 3.9 0.3 - - - +
21D VAL* 3.1 9.2 - - - +
22D VAL* 2.8 44.8 + - - -
103D ASN* 5.7 2.7 - - + -
104D PHE 4.2 3.8 - - - +
105D SER* 3.1 25.1 + - - +
129D ASP* 4.9 3.1 - - - +
130D VAL* 1.3 75.7 + - - +
132D VAL* 1.3 66.2 + - - +
133D ASN 4.1 0.2 - - - -
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Residues in contact with VAL 132 (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 ILE* 3.8 32.1 - - + -
20D LYS 3.8 2.2 - - - +
21D VAL* 4.4 2.7 - - + +
84D LEU* 3.8 26.0 - - + -
103D ASN* 3.4 15.0 + - - +
104D PHE* 2.9 70.8 + - + +
106D PHE* 4.2 6.7 - - + -
130D VAL* 4.7 0.2 - - + -
131D THR* 1.3 79.8 - - - +
133D ASN* 1.3 62.1 + - - +
134D LEU* 3.6 11.0 + - + +
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Residues in contact with ASN 133 (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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23480 C 4.2 4.7 - - - +
23490 G 3.7 21.8 + - - +
18D ILE* 3.5 3.5 - - - +
19D GLU* 2.6 58.5 + - - +
20D LYS* 2.8 43.9 + - + +
101D THR* 6.1 1.0 - - - +
103D ASN* 2.5 35.9 + - - +
131D THR 4.1 1.0 - - - -
132D VAL* 1.3 70.9 - - - +
134D LEU* 1.3 59.7 + - - +
135D VAL* 5.8 1.5 - - - +
139D TYR* 5.2 5.0 + - - -
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Residues in contact with LEU 134 (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 PRO* 5.4 0.7 - - + -
17D ARG 3.2 20.9 - - - +
18D ILE* 3.3 25.8 - - + -
101D THR* 4.8 4.9 - - - +
102D GLY 3.5 15.9 - - - +
103D ASN* 2.8 15.0 + - - +
104D PHE* 4.0 6.7 - - + -
132D VAL* 4.0 13.0 - - + +
133D ASN* 1.3 76.7 + - - +
135D VAL* 1.3 64.5 + - - +
157D LEU* 3.2 31.0 - - + +
162D ALA* 4.0 7.9 - - + +
165D PHE* 3.9 16.2 - - + -
166D ILE* 3.7 33.7 - - + -
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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