Contacts of the strand formed by residues 232 - 236 (chain A) in PDB entry 4M83
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 LYS 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A ALA* 5.2 0.2 - - - -
231A GLU* 1.3 97.8 + - + +
233A VAL* 1.3 62.8 + - - +
261A GLY 3.0 4.9 + - - +
262A TRP* 3.2 49.5 - - + +
263A HIS 2.9 24.5 + - - +
300A ASP* 3.3 19.5 + - + +
364A VAL* 4.5 26.2 + - + +
365A ASP* 6.1 1.9 - - - +
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Residues in contact with VAL 233 (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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224A TRP* 4.0 24.2 - - + -
226A ARG* 3.6 44.0 - - + +
227A PRO* 4.7 0.4 - - + -
230A ALA* 3.9 15.0 - - + -
232A LYS* 1.3 74.4 - - - +
234A VAL* 1.3 64.3 + - - +
235A LEU 4.9 0.2 - - - +
262A TRP* 5.0 0.7 - - - -
263A HIS* 3.3 14.4 - - + +
265A VAL* 4.3 11.0 - - + -
295A ILE* 5.0 2.5 - - + -
299A ALA* 3.8 18.5 - - + -
300A ASP* 2.8 34.4 + - - +
301A LEU* 3.2 7.3 + - - +
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Residues in contact with VAL 234 (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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232A LYS 3.9 0.2 + - - -
233A VAL* 1.3 76.3 - - - +
235A LEU* 1.3 63.9 + - - +
256A PHE* 4.0 21.1 - - + -
262A TRP* 3.9 27.1 - - + -
263A HIS 2.9 16.5 + - - +
264A LEU* 3.4 21.1 - - + +
265A VAL* 2.9 26.5 + - - +
301A LEU* 3.4 22.2 - - + +
303A VAL* 3.9 28.5 - - + -
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Residues in contact with LEU 235 (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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233A VAL 4.2 0.2 - - - -
234A VAL* 1.3 73.0 - - - +
236A VAL* 1.3 61.8 + - - +
237A SER* 3.5 31.4 - - - +
265A VAL* 3.4 34.1 - - + +
267A GLN* 5.5 0.7 - - + -
290A VAL* 4.5 4.9 - - + -
292A GLN* 3.9 22.7 - - + +
295A ILE* 4.0 28.3 - - + -
296A LEU* 3.9 22.7 - - + -
299A ALA* 4.7 2.8 - - + +
301A LEU 3.0 11.0 + - - +
302A PHE* 3.4 9.1 - - + -
303A VAL* 2.8 31.7 + - - +
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Residues in contact with VAL 236 (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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234A VAL* 4.1 1.1 + - + -
235A LEU* 1.3 74.2 - - - +
237A SER* 1.3 64.6 + - - +
238A LEU* 4.6 4.9 - - + -
248A PHE* 4.4 9.4 - - + -
249A TYR* 4.2 21.5 - - + -
252A CYS* 3.8 24.5 - - + -
256A PHE* 5.2 1.1 - - + -
264A LEU* 3.9 12.6 - - + -
265A VAL 3.0 9.2 + - - +
266A LEU* 3.6 26.5 - - + -
267A GLN* 3.3 22.3 + - - +
303A VAL* 3.5 31.4 - - + +
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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