Contacts of the strand formed by residues 243 - 251 (chain A) 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 THR 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A PHE* 5.3 3.1 - - + -
67A ALA* 4.1 22.8 - - + +
69A ALA* 5.3 0.9 - - + -
237A ALA* 3.0 9.2 - - - +
238A ALA* 2.8 43.9 + - + +
240A SER 2.7 17.0 + - - -
241A TYR* 3.2 1.9 + - - +
242A GLY* 1.3 74.3 - - - +
244A ARG* 1.3 60.4 + - - +
245A ASN* 3.6 23.3 - - - +
265A SER 3.0 15.5 - - - +
266A SER* 3.8 12.2 - - - -
274A TYR* 4.2 3.5 - - - -
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Residues in contact with ARG 244 (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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1A CEF 3.4 22.2 + - - +
216A THR 4.6 5.1 + - - -
220A LEU* 3.8 27.0 - - + +
236A GLY 2.9 19.9 + - - +
237A ALA* 3.2 16.6 - - - +
242A GLY 3.5 1.3 + - - +
243A THR* 1.3 74.7 - - - +
245A ASN* 1.3 61.5 + - - +
264A LEU 3.9 0.2 - - - -
265A SER* 2.6 41.5 + - - +
274A TYR* 3.4 44.9 + - + -
275A ASP 5.4 1.3 - - - +
276A ASP* 2.9 29.9 + - - +
279A ILE* 3.2 29.9 - - + +
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Residues in contact with ASN 245 (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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66A PHE* 5.1 0.8 - - - +
67A ALA 3.2 25.5 + - - -
68A PHE 3.8 10.9 + - - -
69A ALA* 4.3 5.1 - - - +
71A THR* 3.8 13.2 - - + -
220A LEU* 4.1 4.0 - - - +
235A THR* 3.4 4.7 - - - -
236A GLY* 2.8 31.8 + - - +
243A THR* 3.6 14.0 - - - +
244A ARG* 1.3 74.8 - - - +
246A ASP* 1.3 64.0 + - - +
263A VAL 3.4 3.1 - - - -
264A LEU* 3.1 44.9 - - + +
265A SER 3.2 9.7 + - - +
279A ILE* 5.2 1.1 - - - -
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Residues in contact with ASP 246 (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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71A THR* 4.9 0.4 - - - -
217A GLY 4.6 0.5 - - - +
220A LEU* 3.4 7.3 - - + +
221A ILE* 2.9 53.4 + - + +
233A ASP* 2.5 32.1 - - - +
234A LYS 3.2 13.0 - - - +
235A THR* 3.4 7.8 + - - -
245A ASN* 1.3 76.1 - - - +
247A ILE* 1.3 70.0 + - - +
263A VAL 3.0 30.4 + - - -
279A ILE* 3.9 13.4 - - + +
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Residues in contact with ILE 247 (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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71A THR* 3.8 31.4 - - + +
74A ALA* 4.8 7.9 - - + -
75A LEU* 5.6 3.8 - - + -
186A LEU* 4.4 29.4 - - + -
187A VAL* 5.9 0.4 - - - -
190A LEU* 4.1 25.8 - - + -
211A MET* 4.4 1.3 - - + +
233A ASP* 3.2 1.4 - - - +
234A LYS* 3.0 44.2 + - + +
246A ASP* 1.3 75.4 + - - +
248A ALA* 1.3 69.2 + - - +
261A LEU 3.3 2.0 - - - +
262A ALA* 3.3 31.4 - - + -
264A LEU* 4.6 5.8 - - + -
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Residues in contact with ALA 248 (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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190A LEU* 3.9 8.3 - - - +
211A MET* 5.1 0.2 - - - -
221A ILE* 3.6 16.6 - - + -
231A VAL* 3.5 17.9 - - + -
232A ALA 3.1 13.2 - - - +
233A ASP* 3.6 5.6 - - + -
247A ILE* 1.3 82.2 - - - +
249A ILE* 1.3 63.6 + - - +
250A ILE* 4.6 2.7 - - + -
260A VAL* 3.5 4.3 - - - +
261A LEU* 2.7 34.7 + - - +
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Residues in contact with ILE 249 (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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190A LEU* 4.1 21.3 - - + +
191A ARG* 6.0 0.2 - - - -
194A ALA* 3.7 29.8 - - + -
195A LEU* 3.4 25.1 - - + -
208A ILE* 5.2 2.2 - - + -
211A MET* 5.2 3.1 - - + -
231A VAL* 3.0 5.9 - - - +
232A ALA* 2.9 37.8 + - + +
248A ALA* 1.3 74.3 - - - +
250A ILE* 1.3 64.4 + - - +
251A TRP* 2.9 54.7 - - + +
258A PRO* 3.9 0.7 - - + -
259A VAL 3.5 13.2 - - - +
260A VAL* 4.4 5.2 - - + +
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Residues in contact with ILE 250 (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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221A ILE* 3.7 14.1 - - + -
225A VAL* 3.7 19.5 - - + -
229A TRP* 4.0 9.2 - - + -
230A GLU 3.0 10.5 - - - +
231A VAL* 3.6 15.5 - - + -
248A ALA* 4.6 0.4 - - + -
249A ILE* 1.3 83.6 - - - +
251A TRP* 1.3 64.4 + - - +
252A PRO* 3.8 2.4 - - + +
258A PRO* 3.3 5.2 - - - +
259A VAL* 3.0 38.7 + - + +
261A LEU* 3.6 39.5 - - + -
283A THR* 5.4 0.2 - - + -
287A MET* 3.7 32.5 - - + -
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Residues in contact with TRP 251 (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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195A LEU* 3.6 18.2 - - + +
208A ILE* 4.0 22.0 - - + -
212A LYS* 4.9 1.6 - - + -
228A GLY 4.4 0.9 - - - +
229A TRP* 3.5 6.1 - - - -
230A GLU* 2.8 75.4 + - + +
232A ALA* 4.0 20.2 - - + -
249A ILE* 2.9 46.7 - - + -
250A ILE* 1.3 70.5 - - - +
252A PRO* 1.4 68.1 - - - +
254A PRO* 3.6 4.1 - - - +
256A GLY 5.2 2.9 - - - +
257A ASP 4.7 0.2 - - - -
258A PRO* 2.3 53.9 - - + +
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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