Contacts of the strand formed by residues 130 - 135 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59F SER* 3.3 27.1 - - - +
60F ILE 4.9 0.9 - - - -
61F VAL* 3.5 28.9 - - + -
85F TYR* 3.8 28.7 - + - -
124F LEU* 3.5 33.0 - - + -
127F MET* 3.8 20.4 - - + -
128F ALA* 3.7 10.3 - - + -
129F PRO* 1.3 75.1 - - - +
131F ASP* 1.3 66.0 + - - +
132F MET 3.4 3.1 - - - +
148F TRP* 3.9 15.0 - + - -
152F TYR 2.9 15.3 + - - -
153F ILE* 3.4 16.8 - - + -
154F ARG* 3.0 25.6 + - - +
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Residues in contact with ASP 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F GLY 5.3 0.4 - - - -
57F ILE* 3.8 22.7 - - + +
58F HIS* 2.9 34.7 + - - +
59F SER* 2.9 28.8 + - - +
130F PHE* 1.3 73.9 - - - +
132F MET* 1.3 60.0 + - - +
153F ILE* 4.2 2.0 - - - -
154F ARG* 2.8 37.8 + - - +
157F GLY* 3.2 7.6 - - - -
158F LEU 2.9 21.9 + - - -
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Residues in contact with MET 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 4.8 10.3 - - + +
51F LEU* 5.6 2.0 - - + -
52F ILE* 3.9 26.2 - - + -
57F ILE* 3.9 24.5 - - + -
59F SER 3.2 3.7 + - - +
60F ILE* 3.3 13.1 - - + -
61F VAL 2.9 24.6 + - - -
74F MET* 4.1 24.5 - - - -
130F PHE* 3.4 3.6 + - - +
131F ASP* 1.3 81.2 - - - +
133F ILE* 1.3 67.3 + - - +
134F PHE* 4.3 8.1 - - + -
153F ILE* 3.7 9.7 - - - +
158F LEU* 3.2 26.2 - - + +
160F VAL* 3.9 25.4 - - + -
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Residues in contact with ILE 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F VAL* 3.2 18.2 - - + +
63F VAL* 4.3 14.1 - - + -
121F LEU* 4.8 1.3 - - + -
132F MET* 1.3 80.2 - - - +
134F PHE* 1.3 64.6 + - - +
135F ILE* 3.9 26.0 - - + -
145F TYR* 4.4 11.0 - - + +
148F TRP* 4.0 28.3 - - + -
149F ALA* 3.9 18.8 - - + -
153F ILE* 3.8 10.5 - - + +
158F LEU 3.0 8.8 + - - +
159F ILE* 3.9 25.6 - - + -
160F VAL* 2.9 27.2 + - - +
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Residues in contact with PHE 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40F LEU* 4.0 21.8 - - + -
48F LEU* 4.1 11.9 - - + -
60F ILE* 4.7 1.1 - - + +
61F VAL 2.9 11.8 + - - +
62F GLU* 3.3 30.1 - - + +
63F VAL* 2.8 26.7 + - - +
70F SER* 4.0 16.2 - - - -
74F MET* 4.0 15.3 - - + -
132F MET* 4.3 13.6 - - + +
133F ILE* 1.3 73.2 - - - +
135F ILE* 1.3 69.9 - - - +
136F ASP* 3.7 30.0 + - + -
160F VAL* 3.2 20.9 - - + -
162F ASP* 4.2 1.8 - - + -
211F MET* 3.9 23.8 - - + -
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Residues in contact with ILE 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F VAL* 4.2 6.3 - - + -
133F ILE* 3.9 32.5 - - + -
134F PHE* 1.3 74.3 - - - +
136F ASP* 1.3 62.7 + - - +
137F ALA 4.6 0.2 - - - +
142F TYR* 3.4 33.1 + - + -
145F TYR* 3.7 43.3 - - + -
146F LEU* 4.4 0.9 - - - +
159F ILE* 4.4 7.6 - - + -
160F VAL 2.7 13.7 + - - +
161F ALA* 3.2 4.0 - - + -
162F ASP 3.2 24.9 + - - -
190F 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