Contacts of the helix formed by residues 289 - 305 (chain B) in PDB entry 2X7E
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 289 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B ASN 5.9 1.5 + - - -
166B GLU* 5.3 0.4 + - - -
234B ARG* 3.0 29.6 - - - +
236B HIS* 2.8 29.9 + - - -
267B ALA* 3.5 7.0 - - - +
287B ASN 4.1 1.6 + - - -
288B ILE* 1.3 75.5 - - - +
290B GLN* 1.3 59.0 + - - +
291B SER* 3.3 6.7 - - - +
292B LEU* 2.9 35.0 + - + +
293B LEU* 2.8 35.6 + - + +
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLN* 4.0 30.4 - - - +
313A GLU* 5.2 0.6 + - - +
166B GLU* 3.8 28.9 + - + +
288B ILE* 3.5 11.9 + - + +
289B ASN* 1.3 72.6 - - - +
291B SER* 1.3 55.9 + - - +
293B LEU* 4.2 16.3 - - - +
294B THR* 2.7 44.6 + - - -
297B ARG* 4.5 9.3 + - - +
313B GLU* 2.9 32.2 - - - +
314B SER* 4.0 0.4 - - - -
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Residues in contact with SER 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 4.0 6.3 - - - +
166B GLU* 2.6 24.6 + - - -
236B HIS* 3.4 23.8 - - - -
289B ASN* 3.3 3.3 - - - +
290B GLN* 1.3 77.3 - - - +
292B LEU* 1.3 58.5 + - - +
294B THR* 3.9 0.9 - - - -
295B LEU* 3.0 28.2 + - - +
314B SER* 3.6 8.8 + - - -
316B LEU* 3.2 39.3 + - - +
317B THR* 4.9 0.2 - - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B TYR* 4.5 20.0 - - + +
236B HIS* 3.8 15.7 + - + -
266B LEU* 4.9 3.8 - - + -
267B ALA* 4.0 17.3 - - + +
268B GLY 3.4 25.8 - - - +
269B SER* 3.9 15.0 - - - +
289B ASN* 2.9 30.0 - - + +
291B SER* 1.3 73.8 - - - +
293B LEU* 1.3 68.0 + - + +
295B LEU* 3.2 16.0 + - + +
296B GLY* 3.1 19.1 + - - -
352B TYR* 4.7 1.7 + - - +
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLU* 3.3 29.8 - - - +
288B ILE* 3.0 36.3 - - + -
289B ASN 2.8 22.4 + - - +
290B GLN* 3.9 13.5 - - - +
292B LEU* 1.3 74.3 - - + +
294B THR* 1.3 61.6 + - - +
296B GLY* 3.2 2.1 + - - -
297B ARG* 3.1 44.2 + - - +
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Residues in contact with THR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLN* 2.7 41.0 + - - -
293B LEU* 1.3 73.0 - - - +
295B LEU* 1.3 61.2 + - - +
297B ARG* 3.0 12.3 + - - +
298B VAL* 2.8 32.1 + - + +
310B PRO* 3.4 28.3 - - + +
313B GLU* 3.5 15.0 + - + +
314B SER* 3.6 12.1 - - - +
317B THR* 3.4 17.9 - - - +
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B PHE* 4.8 7.9 - - + -
104B TYR* 4.9 1.6 - - + -
266B LEU* 3.6 40.8 - - + -
291B SER 3.0 18.8 + - - +
292B LEU* 3.2 12.8 + - + +
294B THR* 1.3 76.0 - - - +
296B GLY* 1.3 62.5 - - - +
298B VAL* 3.4 2.5 + - + +
299B ILE* 3.1 32.4 + - + +
316B LEU* 4.2 11.0 - - + -
317B THR* 3.9 10.7 - - + +
324B LEU* 3.7 39.5 - - + -
352B TYR* 3.6 15.5 - - + +
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Residues in contact with GLY 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU 3.1 12.3 + - - -
293B LEU 3.6 4.0 - - - -
295B LEU* 1.3 77.8 - - - +
297B ARG* 1.3 56.9 + - - +
299B ILE* 3.6 3.7 + - - +
300B THR* 3.0 30.6 + - - -
352B TYR* 3.4 27.0 + - - -
355B ARG* 4.0 2.8 + - - -
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A GLN* 5.5 0.2 - - - +
297A ARG* 3.1 55.5 - - - +
310A PRO* 5.5 2.4 - - - +
313A GLU* 2.8 31.7 + - - -
290B GLN* 4.5 13.1 + - - +
293B LEU* 3.1 39.8 + - - +
294B THR* 3.0 11.8 + - - +
296B GLY* 1.3 75.3 - - - +
298B VAL* 1.3 58.4 + - - +
300B THR* 3.4 7.8 + - - -
301B ALA* 3.0 28.4 + - - +
310B PRO* 4.2 15.1 - - + +
313B GLU* 4.8 3.2 + - - -
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B THR* 2.8 23.0 + - + +
295B LEU* 3.6 4.5 - - - +
297B ARG* 1.3 68.9 - - - +
299B ILE* 1.3 61.8 + - + +
301B ALA* 3.2 2.9 + - - +
302B LEU* 2.9 43.9 + - + +
309B VAL* 3.7 20.9 - - + -
310B PRO* 3.9 31.0 - - + +
311B TYR* 3.9 16.6 - - + +
317B THR* 3.7 19.3 - - + -
324B LEU* 4.2 14.6 - - + -
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Residues in contact with ILE 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 3.1 28.3 + - + +
296B GLY* 3.9 4.5 - - - +
297B ARG 3.3 0.2 - - - -
298B VAL* 1.3 75.7 - - + +
300B THR* 1.3 63.8 + - - +
302B LEU* 3.9 1.7 - - - -
303B VAL* 3.1 29.8 + - + +
324B LEU* 4.7 10.3 - - + -
332B ILE* 4.9 8.3 - - + -
352B TYR* 3.6 38.6 - - + +
355B ARG* 3.9 17.5 - - + +
356B ALA* 4.4 19.3 - - + +
359B ILE* 3.8 29.6 - - + -
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Residues in contact with THR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B GLY 3.0 14.9 + - - -
297B ARG* 3.6 8.0 - - - +
298B VAL 3.3 0.2 - - - -
299B ILE* 1.3 76.3 - - - +
301B ALA* 1.3 58.1 + - - +
303B VAL* 3.3 2.5 + - - +
304B GLU* 2.9 55.3 + - - +
355B ARG* 2.7 36.1 + - - +
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ARG 3.0 17.1 + - - +
298B VAL 3.2 3.5 + - - +
300B THR* 1.3 78.0 - - - +
302B LEU* 1.3 62.9 - - - +
305B ARG* 3.2 3.6 + - - -
306B THR* 3.2 43.4 + - + +
308B HIS 3.7 23.3 - - - +
309B VAL* 4.1 6.3 - - + -
310B PRO* 4.0 11.4 - - + -
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Residues in contact with LEU 302 (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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298B VAL* 2.9 37.2 + - + +
299B ILE* 4.0 4.9 - - - +
301B ALA* 1.3 77.1 - - - +
303B VAL* 1.3 60.9 + - - +
305B ARG* 2.8 30.3 + - - +
309B VAL* 4.1 16.8 - - + -
311B TYR* 3.8 15.0 - - - +
324B LEU* 3.5 30.7 - - + +
325B GLY* 4.0 14.6 - - - +
359B ILE* 4.2 22.7 - - + -
360B LEU 5.8 0.4 - - - +
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ILE* 3.1 21.9 + - + +
300B THR* 4.0 3.4 - - - +
302B LEU* 1.3 77.9 - - - +
304B GLU* 1.3 65.1 + - + +
305B ARG* 3.3 18.4 + - - +
355B ARG* 3.7 34.3 - - + +
358B ASN* 4.0 24.2 - - + +
359B ILE* 3.4 27.4 - - + +
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Residues in contact with GLU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B THR* 2.9 38.2 + - - +
303B VAL* 1.3 85.1 - - + +
305B ARG* 1.3 69.3 + - - +
306B THR* 3.2 14.1 + - - +
355B ARG* 4.7 7.6 + - - +
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Residues in contact with ARG 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B ALA 3.2 6.0 + - - -
302B LEU* 2.8 28.2 + - - +
303B VAL* 3.3 17.2 + - - +
304B GLU* 1.3 80.0 - - - +
306B THR* 1.3 64.2 + - - +
307B PRO* 3.4 8.7 - - - +
358B ASN* 3.4 34.2 + - - +
359B ILE* 4.8 0.4 - - - +
360B LEU* 4.6 13.9 - - - +
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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
------------------------------------------------------------
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