Contacts of the strand formed by residues 230 - 238 (chain B) in PDB entry 3M2K
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 GLU 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ILE* 4.8 5.7 - - - +
111A LYS* 4.9 11.8 + - - +
129A TYR* 3.2 38.7 + - - -
215A THR* 5.6 1.4 - - - +
212B LYS* 3.4 31.8 + - - +
228B GLY 3.6 6.9 + - - +
229B TRP* 1.4 72.5 - - - +
231B VAL* 1.3 60.8 + - - +
250B ILE* 3.4 1.2 - - - +
251B TRP* 2.7 56.6 + - + +
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Residues in contact with VAL 231 (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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212B LYS* 3.6 12.2 - - - +
221B ILE* 4.7 8.3 - - + -
222B ARG* 3.1 45.2 + - + +
225B VAL* 3.9 22.4 - - + -
229B TRP 3.5 11.2 + - - +
230B GLU* 1.3 78.3 + - - +
232B ALA* 1.3 72.0 + - - +
233B ASP* 4.0 12.3 - - + -
248B ALA* 4.3 8.1 - - + -
249B ILE 3.3 7.9 - - - +
250B ILE* 4.6 8.3 - - + -
251B TRP* 4.0 2.5 - - - -
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Residues in contact with ALA 232 (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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208B ILE* 4.0 10.3 - - + +
211B MET* 3.3 35.6 - - + +
212B LYS* 3.7 8.7 - - + +
231B VAL* 1.3 69.6 - - - +
233B ASP* 1.4 62.9 + - - +
248B ALA* 3.1 5.5 - - - +
249B ILE* 2.9 38.5 + - + +
251B TRP* 3.5 16.2 - - + -
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Residues in contact with ASP 233 (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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127B LEU 5.0 0.3 - - - +
211B MET* 3.0 29.1 + - - +
214B ASN* 2.6 37.5 + - - +
217B GLY* 3.8 8.2 - - - +
221B ILE* 5.1 1.5 - - + +
222B ARG* 3.3 24.9 + - - +
231B VAL* 4.0 8.3 - - + -
232B ALA* 1.4 76.2 - - - +
234B LYS* 1.3 60.8 + - - +
235B THR* 3.4 7.7 - - - +
246B ASP* 2.8 29.9 - - - +
247B ILE 3.4 5.6 - - - +
248B ALA* 3.8 14.6 - - + -
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Residues in contact with LYS 234 (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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70B SER* 3.6 19.0 - - - +
71B THR* 3.6 10.9 - - - +
73B LYS* 4.0 10.1 - - - -
74B ALA* 4.3 11.9 - - + +
126B SER 3.6 16.4 - - - -
127B LEU* 3.4 34.5 - - + +
130B SER* 2.7 32.0 + - - -
211B MET* 3.6 11.1 - - + +
214B ASN* 4.7 3.4 - - - +
216B THR* 4.8 1.2 + - - -
233B ASP* 1.3 75.3 - - - +
235B THR* 1.3 83.1 + - - +
246B ASP* 3.2 5.4 - - - -
247B ILE* 2.8 49.2 + - + +
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Residues in contact with THR 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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1B CEF 2.6 29.1 + - - +
70B SER* 3.4 10.6 - - - -
71B THR* 4.1 4.0 - - - -
214B ASN* 3.8 5.2 - - - +
216B THR* 2.8 29.5 + - - +
217B GLY* 3.9 11.0 - - - -
220B LEU* 4.6 7.6 - - + -
233B ASP* 3.4 14.8 - - - +
234B LYS* 1.3 91.2 + - - +
236B GLY* 1.3 58.8 + - - +
244B ARG* 4.6 2.2 - - - -
245B ASN 3.5 7.4 - - - -
246B ASP* 3.0 22.7 - - - +
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Residues in contact with GLY 236 (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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1B CEF 3.2 17.9 - - - -
69B ALA* 4.1 6.7 - - - -
70B SER* 3.7 7.9 - - - -
71B THR* 4.1 2.8 - - - +
235B THR* 1.3 75.6 - - - +
237B ALA* 1.3 61.7 + - - +
244B ARG* 3.1 11.7 + - - +
245B ASN 2.9 34.9 + - - -
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Residues in contact with ALA 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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1B CEF 3.2 52.7 + - + +
69B ALA* 3.7 3.7 - - - +
236B GLY* 1.3 77.4 - - - +
238B ALA* 1.3 68.5 + - - +
243B THR 3.0 14.4 - - - +
244B ARG* 3.6 14.6 - - - +
274B TYR* 3.9 22.4 - - + +
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Residues in contact with ALA 238 (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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1B CEF 3.7 36.2 + - - +
67B ALA* 4.9 8.3 - - + -
69B ALA* 4.3 4.9 - - + -
172B VAL* 5.4 3.6 - - + -
237B ALA* 1.3 78.4 - - - +
240B SER* 1.3 74.7 + - - +
241B TYR 3.6 0.2 + - - -
242B GLY* 3.6 3.5 + - - -
243B THR* 2.8 34.9 + - + +
274B TYR* 5.2 3.4 - - - -
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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