Contacts of the strand formed by residues 130 - 135 (chain D) in PDB entry 4OA5
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 PHE 130 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D SER* 3.3 18.8 - - - +
61D VAL* 3.6 23.8 - - + -
85D TYR* 3.5 35.7 - + - -
124D LEU* 3.5 38.1 - - + -
127D MET* 3.8 21.5 - - + -
128D ALA* 3.7 10.1 - - + -
129D PRO* 1.3 75.7 - - - +
131D ASP* 1.3 66.3 + - - +
132D MET 3.4 3.1 - - - +
148D TRP* 3.9 19.3 - + - -
152D TYR 2.9 13.9 + - - -
153D ILE* 3.4 16.9 - - + -
154D ARG* 3.0 26.1 + - - +
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Residues in contact with ASP 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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56D GLY 5.4 0.9 - - - -
57D ILE* 3.8 22.6 - - + +
58D HIS* 2.9 31.8 + - - +
59D SER* 2.9 29.7 + - - +
130D PHE* 1.3 74.9 - - - +
132D MET* 1.3 59.6 + - - +
153D ILE* 4.1 2.7 - - - -
154D ARG* 2.8 38.6 + - - +
157D GLY* 3.2 6.1 - - - -
158D LEU 2.9 22.1 + - - -
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Residues in contact with MET 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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48D LEU* 4.8 9.9 - - + +
51D LEU* 5.6 2.2 - - + -
52D ILE* 3.9 25.6 - - + -
57D ILE* 3.9 24.0 - - + -
59D SER 3.2 3.5 + - - +
60D ILE* 3.3 13.3 - - + -
61D VAL 2.9 24.4 + - - -
74D MET* 4.1 24.9 - - - -
130D PHE* 3.4 2.8 + - - +
131D ASP* 1.3 80.6 - - - +
133D ILE* 1.3 68.1 - - - +
134D PHE* 4.3 8.3 - - + -
153D ILE* 3.7 10.5 - - - +
158D LEU* 3.2 26.5 - - + +
160D VAL* 3.9 24.9 - - + -
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Residues in contact with ILE 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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61D VAL* 3.2 17.0 - - + +
63D VAL* 4.3 14.4 - - + -
121D LEU* 4.8 1.8 - - + -
132D MET* 1.3 82.3 - - - +
134D PHE* 1.3 64.9 + - - +
135D ILE* 3.8 26.2 - - + -
145D TYR* 4.4 11.2 - - + +
148D TRP* 4.0 28.0 - - + -
149D ALA* 4.0 18.4 - - + -
153D ILE* 3.8 10.2 - - + +
158D LEU 3.0 9.3 + - - +
159D ILE* 3.9 24.5 - - + -
160D VAL* 2.9 27.0 + - - +
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Residues in contact with PHE 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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40D LEU* 4.0 21.8 - - + -
48D LEU* 4.1 11.9 - - + -
60D ILE* 4.7 1.3 - - + +
61D VAL 2.8 10.9 + - - +
62D GLU* 3.3 31.0 - - + -
63D VAL 2.9 26.2 + - - -
70D SER* 4.0 15.7 - - - -
74D MET* 4.0 22.4 - - + -
132D MET* 4.3 6.7 - - + +
133D ILE* 1.3 74.3 - - - +
135D ILE* 1.3 71.2 + - - +
136D ASP* 3.8 30.2 + - + -
160D VAL* 3.3 19.5 - - + -
162D ASP* 4.2 2.0 - - + -
211D MET* 3.9 24.2 - - - -
301D SAH 4.1 0.9 - - - -
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Residues in contact with ILE 135 (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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63D VAL* 4.2 6.7 - - + -
133D ILE* 3.8 31.0 - - + -
134D PHE* 1.3 74.9 - - - +
136D ASP* 1.3 63.7 + - - +
137D ALA 4.5 0.7 - - - +
142D TYR* 3.4 32.6 + - + -
145D TYR* 3.7 44.0 - - + -
146D LEU* 4.4 1.1 - - - +
159D ILE* 4.4 8.1 - - + -
160D VAL 2.8 13.5 + - - +
161D ALA* 3.2 5.3 - - + -
162D ASP 3.2 24.6 + - - -
190D PHE* 4.0 25.6 - - + -
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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