Contacts of the strand formed by residues 130 - 135 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E SER* 3.3 26.5 - - - +
61E VAL* 3.6 28.5 - - + -
85E TYR* 3.8 29.4 - + - -
124E LEU* 3.4 36.8 - - + -
127E MET* 3.7 22.0 - - + -
128E ALA* 3.7 11.2 - - + -
129E PRO* 1.3 76.2 - - - +
131E ASP* 1.3 66.1 + - - +
132E MET 3.4 3.4 - - - +
148E TRP* 3.9 13.9 - + - -
152E TYR 2.9 15.7 + - - -
153E ILE* 3.4 17.3 - - + -
154E ARG* 3.0 25.3 + - - +
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Residues in contact with ASP 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D THR* 4.9 9.4 - - - +
56E GLY 4.8 1.1 - - - +
57E ILE* 3.8 22.7 - - + +
58E HIS* 2.8 34.6 + - - +
59E SER* 2.9 29.1 + - - +
130E PHE* 1.3 74.9 - - - +
132E MET* 1.3 59.5 + - - +
153E ILE* 4.1 2.2 - - - -
154E ARG* 2.8 33.9 + - - +
157E GLY* 3.1 7.3 - - - -
158E LEU 2.9 22.0 + - - -
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Residues in contact with MET 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E LEU* 4.8 10.1 - - + +
51E LEU* 5.7 2.0 - - + -
52E ILE* 3.9 25.6 - - + -
57E ILE* 3.9 22.2 - - + -
59E SER 3.2 3.9 + - - +
60E ILE* 3.3 12.7 - - + -
61E VAL* 2.9 25.0 + - - +
74E MET* 4.1 24.9 - - - -
130E PHE* 3.4 3.4 - - - +
131E ASP* 1.3 81.2 - - - +
133E ILE* 1.3 68.2 + - - +
134E PHE* 4.3 7.9 - - + -
153E ILE* 3.7 9.9 - - - +
158E LEU* 3.2 28.7 - - + +
160E VAL* 3.9 25.1 - - + -
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Residues in contact with ILE 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E VAL* 3.2 16.8 - - + +
63E VAL* 4.3 14.1 - - + -
121E LEU* 4.8 1.6 - - + -
132E MET* 1.3 80.5 - - - +
134E PHE* 1.3 64.8 + - - +
135E ILE* 3.9 26.0 - - + -
145E TYR* 4.4 11.4 - - + +
148E TRP* 4.1 27.1 - - + -
149E ALA* 4.0 15.3 - - + -
153E ILE* 3.8 10.7 - - + +
158E LEU 3.0 8.0 + - - +
159E ILE* 3.9 28.9 - - + -
160E VAL* 2.9 26.7 + - - +
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Residues in contact with PHE 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU* 4.0 22.0 - - + -
48E LEU* 4.1 9.9 - - + -
60E ILE* 4.8 0.7 - - + -
61E VAL 2.8 11.7 + - - +
62E GLU* 3.3 29.4 - - + -
63E VAL* 2.9 25.8 + - - +
70E SER* 3.9 16.8 - - - -
74E MET* 4.0 26.7 - - + -
132E MET* 4.3 7.3 - - + +
133E ILE* 1.3 72.6 - - - +
135E ILE* 1.3 70.8 + - - +
136E ASP* 3.8 27.1 + - + -
160E VAL* 3.2 19.3 - - + -
162E ASP* 4.3 1.8 - - + -
211E MET* 3.9 24.2 - - + -
301E SAH 4.1 1.1 - - - -
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Residues in contact with ILE 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E VAL* 4.2 6.3 - - + -
133E ILE* 3.9 32.5 - - + -
134E PHE* 1.3 74.0 - - - +
136E ASP* 1.3 65.0 + - - +
137E ALA 4.5 1.3 - - - +
142E TYR* 3.4 36.0 + - + -
145E TYR* 3.8 39.5 - - + -
146E LEU* 4.5 0.9 - - - +
159E ILE* 4.4 8.3 - - + -
160E VAL 2.7 13.9 + - - +
161E ALA* 3.2 4.6 - - + -
162E ASP 3.2 24.8 + - - -
190E PHE* 4.1 25.1 - - + -
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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