Contacts of the strand formed by residues 236 - 249 (chain A) in PDB entry 3CMT
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 ASN 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A LYS* 3.2 6.1 - - - +
233A GLU* 2.7 51.4 + - + +
235A GLU* 1.3 86.5 - - - +
237A VAL* 1.3 64.5 + - - +
238A VAL* 4.8 4.3 - - + +
1256A LYS* 6.1 4.2 - - - +
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Residues in contact with VAL 237 (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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227A ARG* 4.0 0.4 - - - +
230A ALA* 4.0 17.5 - - + -
231A VAL 3.7 3.1 - - - +
232A LYS* 4.2 16.8 - - + -
235A GLU 3.9 3.8 + - - +
236A ASN* 1.3 73.8 - - - +
238A VAL* 1.3 61.4 + - - +
239A GLY 3.9 17.0 - - - +
264A TYR* 3.7 12.0 - - + -
1253A ALA* 5.2 3.1 - - - +
1254A PRO 4.1 6.6 - - - +
1255A PHE* 3.6 51.9 + - + +
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Residues in contact with VAL 238 (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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231A VAL* 2.9 31.0 + - + +
232A LYS 4.7 0.7 - - - -
233A GLU* 3.9 30.7 - - + -
236A ASN* 3.6 4.2 + - + -
237A VAL* 1.3 73.9 - - - +
239A GLY* 1.3 57.1 + - - +
263A LEU* 3.8 13.1 - - + +
264A TYR* 3.1 32.0 + - + +
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Residues in contact with GLY 239 (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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230A ALA* 3.7 5.2 - - - -
231A VAL* 2.8 38.8 + - - +
237A VAL* 3.9 3.5 - - - +
238A VAL* 1.3 82.3 - - - +
240A SER* 1.3 56.6 + - - -
262A ILE 3.1 13.0 - - - -
263A LEU* 4.1 2.7 - - - -
264A TYR* 3.5 20.5 + - - -
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Residues in contact with SER 240 (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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69A SER 4.9 1.6 + - - -
70A SER 5.7 1.8 - - - -
227A ARG* 3.0 29.1 + - - +
229A GLY 3.7 4.3 - - - -
231A VAL* 4.0 3.1 - - - +
239A GLY* 1.3 70.8 - - - -
241A GLU* 1.3 62.3 + - - +
242A THR* 3.3 9.8 + - - -
261A GLN* 3.6 0.9 - - - -
262A ILE* 2.8 45.7 + - - -
264A TYR* 2.7 25.6 + - - -
502A ADP 3.5 12.8 + - - -
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Residues in contact with GLU 241 (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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227A ARG* 3.6 4.2 - - - -
228A ILE* 2.8 44.0 + - + -
229A GLY* 2.8 31.9 + - - +
230A ALA 4.4 3.1 - - - +
231A VAL* 3.4 13.6 - - + +
240A SER* 1.3 70.9 - - - +
242A THR* 1.3 59.9 + - - +
259A GLU* 5.6 2.6 - - + +
260A PHE* 3.8 10.3 + - - +
261A GLN* 3.2 39.8 + - - +
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Residues in contact with THR 242 (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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70A SER 4.2 5.7 + - - +
225A ILE* 3.7 28.7 - - + -
226A ARG 3.6 5.9 + - - +
227A ARG* 4.8 1.0 - - - -
228A ILE* 4.4 3.3 - - - +
240A SER* 3.3 18.6 + - - -
241A GLU* 1.3 76.3 + - - +
243A ARG* 1.3 65.7 + - - +
258A ALA 3.9 0.2 - - - +
259A GLU* 3.2 7.3 - - - +
260A PHE* 2.7 72.9 + - + -
262A ILE* 3.7 14.2 - - + +
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Residues in contact with ARG 243 (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 ASP 3.6 2.1 - - - +
225A ILE* 3.5 1.2 - - - -
226A ARG* 2.9 40.2 + - + +
228A ILE* 3.6 39.9 - - + +
242A THR* 1.3 76.0 - - - +
244A VAL* 1.3 66.0 + - - +
245A LYS* 4.1 22.7 - - - +
257A GLN* 3.3 31.1 + - - +
258A ALA 3.3 4.9 - - - +
259A GLU* 2.4 43.3 + - + -
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Residues in contact with VAL 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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47A LEU* 4.3 18.7 - - + +
64A ILE* 6.1 0.2 - - + -
75A LEU* 4.3 7.0 - - + -
223A LEU* 3.7 36.3 - - + -
224A ASP 3.3 7.0 - - - +
225A ILE* 3.8 22.2 - - + -
243A ARG* 1.3 76.6 - - - +
245A LYS* 1.3 66.8 + - - +
246A VAL* 4.1 1.6 + - - +
257A GLN* 3.3 5.0 - - - +
258A ALA* 2.8 37.2 + - + +
260A PHE* 3.7 31.4 - - + -
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Residues in contact with LYS 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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223A LEU* 3.4 5.2 - - - -
224A ASP* 2.8 53.0 + - + +
226A ARG* 5.9 5.5 - - - +
243A ARG* 4.1 19.4 - - - +
244A VAL* 1.3 74.0 - - - +
246A VAL* 1.3 62.7 + - - +
247A VAL* 3.3 12.6 + - + -
255A PHE* 6.0 5.8 - - + +
256A LYS 4.0 3.1 - - - +
257A GLN* 3.5 34.8 - - + +
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Residues in contact with VAL 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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47A LEU* 4.3 9.0 - - + -
50A ALA* 4.1 28.3 - - + +
51A LEU* 4.4 6.5 - - + +
221A VAL* 4.6 0.2 - - + -
222A ARG 3.7 4.9 - - - +
223A LEU* 4.0 18.4 - - + -
244A VAL 5.2 0.9 - - - +
245A LYS* 1.3 72.4 - - - +
247A VAL* 1.3 61.1 + - - +
248A LYS 3.6 20.2 - - - +
249A ASN* 3.9 25.8 - - + +
254A PRO* 4.5 3.1 - - + -
255A PHE* 2.7 36.1 + - - +
256A LYS 3.0 20.5 + - - +
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Residues in contact with VAL 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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65A TYR* 3.5 27.1 - - + +
222A ARG* 2.8 30.9 + - + +
224A ASP* 3.5 24.9 - - + +
245A LYS* 3.9 12.8 - - + +
246A VAL* 1.3 75.0 - - - +
248A LYS* 1.3 60.3 + - + +
254A PRO* 4.5 1.5 - - - +
255A PHE* 3.5 30.9 - - + -
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Residues in contact with LYS 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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216A LYS 2.7 28.9 + - - +
217A PHE* 2.8 26.9 + - - +
219A ALA 3.0 20.5 + - - +
220A SER 4.8 0.4 - - - +
221A VAL* 3.2 5.1 - - - -
222A ARG* 2.9 47.6 + - + +
246A VAL* 3.6 8.6 - - - +
247A VAL* 1.3 82.1 - - + +
249A ASN* 1.3 69.0 + - - +
250A LYS* 4.5 17.9 - - - +
254A PRO* 4.4 1.8 - - - -
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Residues in contact with ASN 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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51A LEU* 3.2 27.9 + - - +
220A SER 3.5 2.0 - - - -
221A VAL* 3.7 9.4 - - - +
246A VAL* 3.9 12.9 - - + +
248A LYS* 1.3 81.3 - - - +
250A LYS* 1.3 60.9 + - - +
251A ILE* 3.0 29.3 + - - +
252A ALA* 3.1 32.2 + - - +
253A ALA 3.3 12.7 + - - -
254A PRO* 3.8 25.1 - - + +
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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