Contacts of the strand formed by residues 234 - 237 (chain B) in PDB entry 3DM6
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 234 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B ASN* 1.3 70.1 - - - +
235B ARG* 1.3 57.9 + - - +
236B LEU* 3.7 38.8 - - + -
283B ILE* 4.9 16.6 - - + -
285B LEU* 4.7 11.7 - - + -
300B ILE* 5.7 2.2 - - + -
323B ALA 3.1 6.1 + - - -
324B ILE* 3.3 24.4 - - + +
325B SER 3.2 21.1 + - - -
331B THR* 4.1 10.1 - - + -
332B VAL 3.4 14.6 - - - +
333B MET* 4.7 0.9 - - - -
334B GLY 4.5 1.6 - - - +
336B VAL* 3.5 24.7 - - + +
337B ILE* 4.2 27.4 - - + -
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Residues in contact with ARG 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B THR* 4.1 13.7 - - - +
231B THR* 3.7 15.0 - - + -
233B ASN* 3.9 13.7 - - + +
234B LEU* 1.3 74.4 - - - +
236B LEU* 1.3 58.5 + - - +
325B SER* 3.4 10.3 + - - +
326B GLN 3.0 24.3 + - - -
327B SER* 3.6 31.1 + - - +
328B SER 4.9 0.6 - - - +
329B THR* 3.9 5.7 + - - -
331B THR* 3.2 8.7 - - - +
332B VAL* 2.8 45.4 + - + +
1000B 757 3.1 47.3 + - - +
1138B IPA 3.9 23.2 - - - +
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ILE* 5.9 0.9 - - + -
206B VAL* 6.2 3.6 - - + -
234B LEU* 3.7 32.8 - - + -
235B ARG* 1.3 74.6 - - - +
237B PRO* 1.3 69.7 - - + +
240B VAL* 4.2 16.2 - - + -
241B PHE* 3.8 20.3 - - + +
244B ALA* 3.9 24.9 - - + -
283B ILE* 6.3 1.3 - - + -
285B LEU* 5.3 9.2 - - + -
324B ILE* 3.6 25.6 - - + -
325B SER 2.8 9.8 + - - +
326B GLN* 3.5 2.1 - - - -
327B SER* 2.8 25.1 + - - -
331B THR* 3.9 15.3 - - + +
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Residues in contact with PRO 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B GLU 3.8 18.8 - - - +
220B TYR* 4.5 1.1 - - - +
222B TYR* 3.2 33.9 - - + +
236B LEU* 1.3 86.9 - - + +
238B LYS* 1.3 56.7 + - - +
239B LYS* 3.4 1.8 - - + +
240B VAL* 3.2 14.3 + - + +
241B PHE* 2.7 33.3 + - - +
327B SER* 3.4 10.1 - - - +
328B SER* 6.1 0.7 - - - -
330B GLY* 3.8 11.4 - - - +
331B THR* 3.4 24.5 - - - +
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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