Contacts of the strand formed by residues 246 - 259 (chain A) in PDB entry 3A4I
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 ILE 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A VAL* 3.4 6.7 - - - +
243A GLN* 2.9 41.5 + - + +
244A GLY 3.5 0.8 + - - -
245A ASP* 1.3 101.8 - - - +
247A ARG* 1.3 71.1 + - - +
248A ALA* 5.2 3.4 - - + -
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Residues in contact with ARG 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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240A VAL* 4.0 24.7 - - + +
241A GLY 3.3 8.5 - - - +
242A VAL* 4.4 10.3 - - + +
246A ILE* 1.3 85.7 - - - +
248A ALA* 1.3 60.1 + - - +
98B GLU* 5.4 10.3 + - - -
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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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240A VAL* 4.6 3.4 - - - -
241A GLY* 2.8 35.7 + - - +
243A GLN* 4.2 23.1 - - + +
246A ILE* 3.8 5.4 + - + +
247A ARG* 1.3 77.1 - - - +
249A TYR* 1.3 66.0 + - - +
250A LYS* 3.5 6.9 + - + +
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Residues in contact with TYR 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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238A LYS* 3.9 30.7 - - + -
239A THR* 3.4 16.8 - - - -
240A VAL* 3.2 25.2 - - + +
248A ALA* 1.3 75.4 - - - +
250A LYS* 1.3 63.3 + - - +
289A GLU* 6.0 0.2 - - - -
96B ASP* 4.7 2.3 + - - -
97B PRO* 3.9 23.9 - - + +
98B GLU* 3.6 23.2 + - - +
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Residues in contact with LYS 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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238A LYS* 3.2 10.6 - - - -
239A THR* 2.8 35.1 + - + +
241A GLY* 4.1 8.6 - - - +
242A VAL 2.7 41.0 + - - +
243A GLN* 3.6 17.6 - - - +
248A ALA* 3.8 9.9 - - + +
249A TYR* 1.3 78.8 - - - +
251A GLU* 1.3 63.4 + - - +
284A THR 5.4 3.4 + - - -
288A PRO* 3.1 27.7 + - - +
289A GLU* 3.5 7.4 - - - +
290A VAL 4.1 2.6 + - - -
291A GLY* 3.5 29.5 - - - +
302B PRO* 5.4 10.3 + - - +
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Residues in contact with GLU 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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205A LYS* 6.0 2.6 - - - +
208A ILE* 5.0 8.5 - - + -
234A LEU* 3.7 32.7 - - + +
236A GLY* 3.0 41.1 + - - -
237A VAL 3.4 5.1 + - - -
238A LYS* 2.8 31.3 + - - +
239A THR* 4.0 0.9 - - - +
250A LYS* 1.3 75.4 - - - +
252A THR* 1.3 77.5 + - - +
289A GLU 2.8 19.0 + - - +
290A VAL* 3.7 8.3 - - + +
291A GLY* 2.9 23.3 + - - -
292A ARG 3.3 5.4 + - - -
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Residues in contact with THR 252 (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 LEU* 3.9 3.4 - - - +
235A LEU* 2.9 36.7 + - + +
237A VAL* 2.7 39.9 + - + +
239A THR* 4.4 6.9 - - - +
251A GLU* 1.3 84.0 + - - +
253A ILE* 1.3 63.6 + - - +
292A ARG* 3.4 27.8 + - + +
294A LEU* 3.9 32.8 - - + -
235B LEU* 6.0 0.4 - - + -
307B PHE* 5.6 0.7 - - + -
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Residues in contact with ILE 253 (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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208A ILE* 4.5 6.1 - - + -
209A VAL* 4.4 6.1 - - + -
212A ALA* 3.7 22.0 - - + -
232A ALA* 3.9 13.0 - - + -
233A VAL 3.3 13.5 - - - +
234A LEU* 3.8 24.7 - - + +
235A LEU* 4.5 0.9 - - - -
252A THR* 1.3 76.7 - - - +
254A ALA* 1.3 77.1 + - - +
255A VAL* 4.2 4.7 - - + -
283A ILE* 4.1 17.7 - - + -
290A VAL* 3.7 28.2 - - + +
292A ARG 2.9 10.1 + - - +
293A VAL* 3.4 8.4 - - + -
294A LEU* 2.9 26.9 + - - +
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Residues in contact with ALA 254 (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 ALA* 3.3 5.0 - - - -
233A VAL* 2.7 41.3 + - + +
235A LEU* 3.8 25.8 - - + +
253A ILE* 1.3 76.3 - - - +
255A VAL* 1.3 61.6 + - - +
256A ARG 4.0 0.7 + - - -
294A LEU* 3.2 7.9 - - - +
307A PHE* 3.8 28.7 - - + -
294B LEU* 4.2 9.6 - - + -
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Residues in contact with VAL 255 (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 VAL* 4.1 16.2 - - + -
231A PHE 3.6 7.2 - - - +
253A ILE* 4.2 6.5 - - + -
254A ALA* 1.3 74.3 - - - +
256A ARG* 1.3 62.3 + - - +
257A ILE* 3.7 30.3 - - + -
276A LEU* 5.1 1.8 - - + -
279A ILE* 3.8 22.7 - - + -
283A ILE* 4.4 0.7 - - + -
293A VAL* 3.6 28.7 - - + -
294A LEU 2.7 12.4 + - - +
295A TYR* 3.3 16.3 - - + -
296A ASP* 2.9 28.3 + - - +
297B ILE* 5.1 2.0 - - + -
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Residues in contact with ARG 256 (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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229A GLN 3.9 0.4 - - - +
230A ALA* 3.2 3.3 - - - -
231A PHE* 2.8 83.6 + - + -
233A VAL* 5.1 1.1 - - + -
254A ALA 4.0 0.2 + - - -
255A VAL* 1.3 72.9 - - - +
257A ILE* 1.3 62.3 + - - +
258A VAL* 3.5 26.0 - - + +
268A ALA* 4.2 4.2 - - - +
296A ASP* 3.2 40.3 + - - +
298A THR 2.9 31.1 + - - -
299A ASN 4.6 4.6 - - - -
300A LYS* 4.9 1.6 - - - +
303A ALA* 4.2 5.1 - - - +
304A THR 3.0 23.0 + - - -
305A ILE* 3.0 22.8 + - + +
307A PHE* 4.1 10.1 - - + -
292B ARG* 3.7 3.4 - - - +
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Residues in contact with ILE 257 (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 VAL* 4.3 2.5 - - + -
220A VAL* 4.1 19.3 - - + -
227A PRO* 3.7 18.4 - - + -
229A GLN 3.4 4.3 - - - +
230A ALA* 4.0 10.8 - - + -
255A VAL* 3.7 24.5 - - + -
256A ARG* 1.3 82.3 + - - +
258A VAL* 1.3 68.3 + - - +
268A ALA* 3.7 2.4 - - - +
269A MET* 2.9 50.1 + - + -
271A VAL* 4.0 18.6 - - + -
276A LEU* 4.8 0.9 - - + -
279A ILE* 4.1 13.2 - - + -
295A TYR* 3.2 19.0 + - + +
296A ASP 5.1 0.4 + - - +
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Residues in contact with VAL 258 (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 PRO* 3.3 6.8 - - - +
228A TRP* 2.9 47.4 + - + -
229A GLN* 3.0 16.2 + - + +
256A ARG* 3.5 40.4 - - + +
257A ILE* 1.3 81.7 - - - +
259A GLU* 1.3 62.6 + - - +
266A ALA* 4.1 13.9 - - + -
267A ASN 3.2 15.5 - - - +
269A MET* 4.2 0.9 - - - +
299A ASN* 6.4 0.2 - - - -
305A ILE* 4.0 24.5 - - + -
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Residues in contact with GLU 259 (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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226A ARG 5.5 1.1 - - - +
227A PRO* 4.7 5.4 - - + -
228A TRP 4.2 3.4 - - - +
258A VAL* 1.3 75.2 - - - +
260A SER* 1.3 64.6 + - - +
266A ALA* 3.3 2.3 - - - -
267A ASN* 2.8 67.4 + - - +
269A MET* 3.6 44.8 - - + +
270A ASN* 4.6 2.3 + - - +
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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