Contacts of the strand formed by residues 130 - 135 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A SER* 3.3 24.9 - - - +
60A ILE 5.0 1.1 - - - -
61A VAL* 3.5 28.3 - - + -
85A TYR* 3.9 16.8 - + - -
124A LEU* 3.5 32.8 - - + -
127A MET* 3.8 19.1 - - + -
128A ALA* 3.7 10.3 - - + -
129A PRO* 1.3 75.6 - - - +
131A ASP* 1.3 65.5 + - - +
132A MET 3.4 3.1 - - - +
148A TRP* 3.9 15.7 - + - -
152A TYR 2.9 16.4 + - - -
153A ILE* 3.4 17.5 - - + -
154A ARG* 2.9 26.5 + - - +
308A IOD 3.9 22.0 - - + -
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Residues in contact with ASP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLY 5.3 0.4 - - - -
57A ILE* 3.8 22.8 - - + +
58A HIS* 2.9 32.1 + - - +
59A SER* 2.9 28.2 + - - +
129A PRO 5.6 0.2 - - - +
130A PHE* 1.3 74.4 - - - +
132A MET* 1.3 59.0 + - - +
153A ILE* 4.2 2.0 - - - -
154A ARG* 2.8 38.4 + - - +
157A GLY* 3.2 6.8 - - - -
158A LEU 2.9 21.8 + - - -
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Residues in contact with MET 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.8 9.6 - - + +
51A LEU* 5.7 2.2 - - + -
52A ILE* 3.9 26.2 - - + -
57A ILE* 3.9 22.9 - - + -
59A SER 3.2 4.5 + - - +
60A ILE* 3.4 12.2 - - + -
61A VAL 2.9 24.1 + - - -
74A MET* 4.1 25.6 - - - -
130A PHE* 3.4 3.6 + - - +
131A ASP* 1.3 80.8 - - - +
133A ILE* 1.3 67.8 + - - +
134A PHE* 4.3 7.2 - - + -
153A ILE* 3.7 10.4 - - - +
158A LEU* 3.2 28.0 - - + +
160A VAL* 3.9 24.9 - - + -
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Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.2 16.8 - - + +
63A VAL* 4.3 14.8 - - + -
121A LEU* 4.8 1.6 - - + -
132A MET* 1.3 80.7 - - - +
134A PHE* 1.3 63.4 + - - +
135A ILE* 3.8 26.2 - - + -
145A TYR* 4.4 10.5 - - + +
148A TRP* 4.0 27.6 - - + -
149A ALA* 4.0 19.3 - - + -
153A ILE* 3.7 10.0 - - + +
158A LEU 3.0 9.2 + - - +
159A ILE* 3.9 24.9 - - + -
160A VAL* 2.9 27.0 + - - +
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Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.0 22.4 - - + -
48A LEU* 4.1 9.2 - - + -
60A ILE* 4.8 0.7 - - + -
61A VAL 2.9 12.0 + - - +
62A GLU* 3.3 30.1 - - + +
63A VAL* 2.9 26.2 + - - +
70A SER* 3.9 15.9 - - - -
74A MET* 4.0 25.8 - - + -
132A MET* 4.3 6.9 - - + +
133A ILE* 1.3 72.5 - - - +
135A ILE* 1.3 69.0 + - - +
136A ASP* 3.8 29.4 - - + -
160A VAL* 3.2 20.9 - - + -
162A ASP* 4.2 2.2 - - + -
211A MET* 3.9 24.9 - - + -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL* 4.2 6.5 - - + -
133A ILE* 3.8 31.6 - - + -
134A PHE* 1.3 73.5 - - - +
136A ASP* 1.3 64.5 + - - +
137A ALA 4.6 0.7 - - - +
142A TYR* 3.4 34.1 + - + -
145A TYR* 3.8 38.1 - - + -
146A LEU* 4.4 4.9 - - - +
159A ILE* 4.4 7.6 - - + -
160A VAL 2.8 14.1 + - - +
161A ALA* 3.2 4.6 - - + -
162A ASP 3.2 24.8 + - - -
190A PHE* 4.0 26.0 - - + -
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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