Contacts of the strand formed by residues 229 - 232 (chain G) in PDB entry 5M64
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 LEU 229 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134G GLU* 2.7 21.9 + - - +
135G GLY* 3.1 29.1 + - - +
137G ILE* 4.2 19.5 - - + -
145G ILE* 5.8 3.8 - - + -
147G LEU* 4.2 20.2 - - + -
166G TRP* 6.3 2.2 - - + -
217G TRP* 6.1 1.6 - - + -
225G ILE* 3.6 29.2 - - + -
226G ASP 3.3 22.4 - - - +
227G GLY 3.2 11.9 - - - +
228G LYS* 1.3 75.9 - - - +
230G ARG* 1.3 69.1 + - - +
231G PHE* 4.4 1.0 - - + +
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Residues in contact with ARG 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G ASN 3.6 21.1 + - - -
33G GLY* 3.9 22.8 - - - -
34G THR* 3.5 17.1 - - - +
132G VAL* 4.7 7.6 - - + -
133G LEU 4.1 1.9 + - - -
134G GLU* 2.3 32.1 + - - +
228G LYS* 3.4 30.0 + - - +
229G LEU* 1.3 80.4 - - - +
231G PHE* 1.3 65.3 + - - +
249G LEU* 4.9 5.0 - - - +
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Residues in contact with PHE 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132G VAL* 3.3 9.8 - - - +
133G LEU* 2.7 62.0 + - + +
134G GLU 4.6 6.1 - - - +
135G GLY* 4.9 0.4 - - - +
145G ILE* 5.9 0.4 - - + -
147G LEU* 3.6 35.9 - - + -
155G ALA* 4.9 10.5 - - + -
156G SER 5.4 0.2 - - - -
157G ILE* 3.6 20.4 - - + -
229G LEU* 4.4 4.5 - - + +
230G ARG* 1.3 78.9 - - - +
232G THR* 1.3 78.3 + - - +
233G VAL* 5.3 0.2 - - - -
245G VAL* 5.4 2.7 - - + -
246G ASP 4.8 1.1 - - - -
247G GLY* 3.5 26.7 - - - -
248G THR 3.6 14.1 - - - -
249G LEU* 3.7 24.5 - - + -
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Residues in contact with THR 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G GLY 6.0 0.7 - - - -
131G ASP 3.4 13.2 - - - +
132G VAL* 4.9 7.2 - - + -
133G LEU* 3.5 4.3 - - - -
231G PHE* 1.3 106.5 - - - +
233G VAL* 1.3 61.7 + - - +
247G GLY* 3.2 5.9 - - - -
248G THR* 2.4 44.9 + - - +
249G LEU* 5.1 5.3 - - + +
250G ILE 5.1 1.1 + - - +
251G SER* 5.5 11.0 - - - -
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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