Contacts of the strand formed by residues 130 - 135 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C SER* 3.3 25.4 - - - +
61C VAL* 3.6 30.5 - - + -
85C TYR* 3.8 29.2 - + - -
124C LEU* 3.4 36.6 - - + -
127C MET* 3.7 20.6 - - + -
128C ALA* 3.7 10.5 - - + -
129C PRO* 1.3 76.8 - - - +
131C ASP* 1.3 64.9 + - - +
132C MET 3.4 3.6 - - - +
148C TRP* 3.9 14.4 - + - -
152C TYR 2.9 15.9 + - - -
153C ILE* 3.4 18.4 - - + -
154C ARG* 3.0 25.7 + - - +
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Residues in contact with ASP 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C GLY 5.3 0.4 - - - -
57C ILE* 3.8 23.4 - - + +
58C HIS* 2.9 32.6 + - - +
59C SER* 2.9 29.0 + - - +
129C PRO 5.5 0.3 - - - +
130C PHE* 1.3 73.6 - - - +
132C MET* 1.3 60.3 + - - +
153C ILE* 4.2 2.0 - - - -
154C ARG* 2.8 34.8 + - - +
157C GLY* 3.2 7.1 - - - -
158C LEU 2.9 22.0 + - - -
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Residues in contact with MET 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 4.8 10.1 - - + +
51C LEU* 5.6 2.2 - - + -
52C ILE* 3.9 26.0 - - + -
57C ILE* 3.9 21.8 - - + -
59C SER 3.2 3.9 + - - +
60C ILE* 3.4 13.8 - - + -
61C VAL* 2.9 24.6 + - - -
74C MET* 4.1 24.5 - - - -
130C PHE* 3.4 3.8 - - - +
131C ASP* 1.3 81.5 - - - +
133C ILE* 1.3 68.1 + - - +
134C PHE* 4.3 8.3 - - + -
153C ILE* 3.7 10.0 - - - +
158C LEU* 3.2 28.3 - - + +
160C VAL* 3.9 25.1 - - + -
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Residues in contact with ILE 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 3.2 17.9 - - + +
63C VAL* 4.3 14.4 - - + -
121C LEU* 4.8 2.0 - - + -
132C MET* 1.3 77.6 - - - +
134C PHE* 1.3 63.8 + - - +
135C ILE* 3.9 25.6 - - + -
145C TYR* 4.4 11.9 - - + +
148C TRP* 4.0 26.9 - - + -
149C ALA* 4.0 15.3 - - + -
153C ILE* 3.8 10.2 - - + +
158C LEU 3.0 7.8 + - - +
159C ILE* 3.9 30.1 - - + -
160C VAL* 2.9 29.3 + - - +
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Residues in contact with PHE 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C LEU* 4.0 21.5 - - + -
48C LEU* 4.1 11.7 - - + -
60C ILE* 4.7 1.5 - - + +
61C VAL 2.8 10.5 + - - +
62C GLU* 3.3 29.0 - - + +
63C VAL* 2.9 26.5 + - - +
70C SER* 4.0 15.3 - - - -
74C MET* 4.0 22.7 - - + -
132C MET* 4.3 6.6 - - + +
133C ILE* 1.3 74.0 - - - +
135C ILE* 1.3 70.2 + - - +
136C ASP* 3.8 28.7 + - + -
160C VAL* 3.3 19.3 - - + -
162C ASP* 4.4 1.8 - - + -
211C MET* 3.9 25.4 - - + -
301C SAH 4.1 1.6 - - - -
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Residues in contact with ILE 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C VAL* 4.2 7.0 - - + -
133C ILE* 3.9 32.1 - - + -
134C PHE* 1.3 75.0 - - - +
136C ASP* 1.3 63.7 + - - +
137C ALA 4.5 1.6 - - - +
142C TYR* 3.5 37.4 + - + -
145C TYR* 3.8 38.4 - - + -
146C LEU* 4.6 1.3 - - - +
159C ILE* 4.4 7.9 - - + -
160C VAL 2.7 14.1 + - - +
161C ALA* 3.2 4.5 - - + -
162C ASP 3.2 24.4 + - - -
190C PHE* 4.1 25.4 - - + -
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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