Contacts of the helix formed by residues 288 - 305 (chain A) in PDB entry 4B7B
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 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ILE 5.4 2.9 - - - +
164A TYR* 5.3 1.6 - - + -
165A ASN* 4.1 31.6 + - - +
166A GLU 5.5 1.1 - - - +
234A ARG* 3.2 45.1 - - + +
236A HIS* 4.6 4.3 - - - +
267A ALA* 3.9 18.2 - - + -
268A GLY 5.2 4.7 - - - +
271A ASN* 5.3 11.2 - - - +
287A ASN* 1.3 71.4 - - - +
289A ASN* 1.3 65.4 + - - +
290A GLN 3.2 1.1 - - - -
291A SER* 2.7 30.3 + - - +
292A LEU* 3.1 14.4 + - + +
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Residues in contact with ASN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ASN* 4.9 14.1 - - + +
272A ILE* 3.4 27.9 - - + +
287A ASN* 2.7 14.7 - - + +
288A ILE* 1.3 83.4 - - + +
290A GLN* 1.3 62.9 + - - +
292A LEU* 3.4 6.8 + - - +
293A LEU* 3.2 31.5 + - + +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ASN* 3.3 24.5 + - + +
288A ILE 3.2 0.2 - - - -
289A ASN* 1.3 77.7 - - - +
291A SER* 1.3 59.7 + - - +
293A LEU* 3.3 15.8 + - - +
294A THR* 2.9 36.6 + - - +
297A ARG* 4.5 14.7 + - - -
313A GLU 6.1 0.2 - - - -
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Residues in contact with SER 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A HIS* 2.8 30.6 + - - -
287A ASN 4.1 1.6 + - - -
288A ILE* 2.7 28.4 + - - +
290A GLN* 1.3 78.0 - - - +
292A LEU* 1.3 56.6 + - - +
294A THR* 3.4 2.3 + - - -
295A LEU* 2.9 28.6 + - - +
314A SER* 3.9 26.2 + - - -
316A LEU* 5.0 5.4 - - - +
1387A CO 3.7 19.7 + - - -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A TYR* 4.0 27.6 - - + -
236A HIS* 3.9 19.1 - - + -
266A LEU* 4.1 24.9 - - + -
267A ALA* 3.7 21.8 - - + +
268A GLY 3.8 13.5 - - - +
269A SER* 4.4 10.3 - - - -
272A ILE* 4.4 18.2 - - + -
288A ILE* 3.1 15.6 + - + +
289A ASN* 3.6 8.3 - - - +
290A GLN 3.3 0.2 - - - -
291A SER* 1.3 77.2 + - - +
293A LEU* 1.3 56.4 + - + +
295A LEU* 3.3 4.6 + - + +
296A GLY 3.0 11.1 + - - -
316A LEU* 5.6 0.9 - - + -
352A TYR* 2.8 28.6 + - + +
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A ILE* 4.6 24.7 - - + -
289A ASN* 3.2 25.5 + - + +
290A GLN* 3.6 22.2 - - - +
291A SER 3.2 0.2 - - - -
292A LEU* 1.3 75.7 - - - +
294A THR* 1.3 66.8 + - - +
296A GLY* 3.1 3.3 + - - +
297A ARG* 3.0 41.4 + - + +
352A TYR* 4.6 18.2 - - + -
355A ARG* 4.7 13.0 - - - +
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLN* 2.9 23.0 + - - +
291A SER 3.4 4.9 + - - -
293A LEU* 1.3 76.7 - - - +
295A LEU* 1.3 63.2 + - - +
297A ARG* 3.2 24.6 + - - +
298A VAL* 2.8 26.8 + - + +
310A PRO* 3.4 26.7 - - + +
313A GLU* 3.7 29.7 + - + +
314A SER* 4.0 6.7 - - - +
317A THR* 3.9 14.8 - - + +
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 3.5 38.6 - - + -
266A LEU* 3.8 32.3 - - + -
291A SER 2.9 13.3 + - - +
292A LEU* 3.4 10.3 - - + +
294A THR* 1.3 77.2 - - - +
296A GLY* 1.3 56.6 + - - +
298A VAL* 3.1 3.5 + - + +
299A ILE* 2.9 45.8 + - + +
316A LEU* 4.3 8.7 - - + -
317A THR* 4.0 23.1 - - + +
320A LEU* 5.6 0.2 - - + -
324A LEU* 4.6 6.5 - - + -
332A ILE* 5.9 4.0 - - + -
352A TYR* 3.6 14.8 - - + +
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Residues in contact with GLY 296 (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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292A LEU 3.0 11.6 + - - -
293A LEU* 3.1 6.0 + - - -
295A LEU* 1.3 77.2 - - - +
297A ARG* 1.3 56.2 + - - +
299A ILE* 3.3 5.7 + - - +
300A THR* 3.0 34.5 + - - -
352A TYR* 3.3 21.9 + - - -
356A ALA* 4.9 5.3 - - - -
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLN* 4.5 9.5 + - - -
293A LEU* 3.0 33.8 + - + +
294A THR* 3.4 24.4 + - - +
296A GLY* 1.3 73.4 - - - +
298A VAL* 1.3 63.6 + - - +
300A THR* 3.8 6.0 - - - -
301A ALA* 2.9 26.2 + - - +
310A PRO* 3.9 13.4 - - + +
313A GLU* 2.8 30.5 + - - -
1371A CD 4.1 0.8 - - - -
1380A CL 3.3 20.5 - - - +
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A THR 2.8 17.9 + - - +
295A LEU* 3.1 9.2 + - - +
297A ARG* 1.3 77.4 - - - +
299A ILE* 1.3 64.0 + - + +
301A ALA* 3.4 3.1 + - - +
302A LEU* 3.1 31.7 + - + +
309A VAL* 3.7 5.3 - - + +
310A PRO* 3.8 39.0 - - + +
311A TYR* 3.6 30.3 - - + +
317A THR* 3.8 17.0 - - + -
324A LEU* 4.2 13.0 - - + -
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Residues in contact with ILE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 4.1 21.8 - - + -
21A VAL* 5.8 0.2 - - + -
102A PHE* 4.5 3.4 - - + -
295A LEU* 2.9 37.8 + - + +
296A GLY* 3.8 4.7 - - - +
298A VAL* 1.3 75.8 - - - +
300A THR* 1.3 57.4 + - - +
302A LEU* 3.2 13.4 + - + +
303A VAL* 2.8 28.9 + - + +
324A LEU* 4.3 25.8 - - + -
330A THR* 4.4 13.2 - - + -
332A ILE* 4.1 26.5 - - + -
352A TYR* 5.9 0.2 - - - +
356A ALA* 4.2 18.6 - - + +
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLY 3.0 20.6 + - - -
297A ARG* 3.9 7.2 - - - -
299A ILE* 1.3 76.9 - - - +
301A ALA* 1.3 58.9 + - - +
303A VAL* 3.8 1.0 - - + +
304A GLU* 2.8 39.9 + - + +
355A ARG* 2.7 33.0 + - + +
356A ALA* 3.5 12.7 + - - +
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ARG 2.9 18.3 + - - +
298A VAL 3.7 4.3 - - - +
300A THR* 1.3 75.7 - - - +
302A LEU* 1.3 57.6 + - - +
304A GLU* 4.8 0.2 - - - -
305A ARG* 2.7 28.1 + - - -
306A THR* 3.1 34.8 + - - +
308A HIS 3.5 19.5 - - - +
309A VAL* 3.9 13.5 - - + -
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.7 18.9 - - + +
298A VAL* 3.1 25.2 + - + +
299A ILE* 3.2 17.7 + - + +
301A ALA* 1.3 75.2 - - - +
303A VAL* 1.3 65.6 + - - +
305A ARG* 3.3 23.3 + - - +
309A VAL* 3.9 21.3 - - + -
311A TYR* 3.6 23.6 - - - +
324A LEU* 3.8 36.1 - - + +
325A GLY* 5.4 1.3 - - - -
330A THR* 6.0 0.4 - - - +
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Residues in contact with VAL 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY* 4.4 19.8 + - - +
19A ILE* 3.9 28.0 - - + -
299A ILE* 2.8 21.6 + - + +
300A THR* 3.8 3.8 - - + +
302A LEU* 1.3 76.4 - - - +
304A GLU* 1.3 75.2 + - - +
305A ARG* 3.6 13.6 + - - +
356A ALA 3.6 16.6 - - - +
357A LYS* 4.0 32.8 - - + -
358A ASN 5.0 2.2 - - - +
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Residues in contact with GLU 304 (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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300A THR* 2.8 27.2 + - + +
303A VAL* 1.3 90.1 - - - +
305A ARG* 1.3 73.5 + - - +
306A THR* 3.4 20.9 + - + +
358A ASN* 5.4 8.0 + - - +
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Residues in contact with ARG 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY* 5.0 11.1 - - - +
17A LYS 6.0 0.8 - - - +
18A ASN* 5.2 9.7 - - - +
301A ALA 2.7 11.7 + - - -
302A LEU* 3.3 19.4 + - - +
303A VAL* 3.8 10.8 + - - +
304A GLU* 1.3 80.9 - - - +
306A THR* 1.3 63.3 + - - +
307A PRO* 3.6 4.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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