Contacts of the helix formed by residues 301 - 319 (chain B) in PDB entry 2XWU
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 ASP 301 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B ALA* 2.9 23.7 + - + +
299B ASN* 3.3 8.3 - - + -
300B GLY* 1.3 75.4 - - - +
302B MET* 1.3 61.8 + - - +
303B GLU* 3.5 16.7 + - - +
304B THR* 2.8 29.2 + - - +
305B SER* 3.7 10.2 + - - -
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Residues in contact with MET 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.7 26.8 - - + -
300B GLY 3.0 13.6 + - - +
301B ASP* 1.3 70.0 + - - +
303B GLU* 1.3 65.4 + - - +
304B THR 3.1 2.5 - - - -
305B SER* 3.1 21.0 + - - +
306B HIS* 3.1 13.0 + - - +
351B PRO 4.9 3.6 - - - +
352B VAL 4.0 11.2 - - - +
353B ASN 3.4 35.2 - - - +
354B GLU* 4.1 11.2 - - + -
355B THR* 5.1 3.1 + - - +
356B THR* 4.4 1.0 + - - -
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.8 40.9 - - + +
256B PHE* 3.7 11.4 - - + -
257B ASP* 3.4 28.1 - - - +
301B ASP* 3.5 10.2 + - - +
302B MET* 1.3 78.6 - - - +
304B THR* 1.3 62.8 + - - +
306B HIS* 3.6 3.3 - - - +
307B GLY* 3.3 14.4 + - - -
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Residues in contact with THR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B PHE* 3.5 28.7 - - + -
292B GLN* 4.0 15.3 - - + +
296B ALA* 3.9 14.6 - - + -
301B ASP* 2.8 31.5 + - - -
302B MET 3.1 0.6 - - - -
303B GLU* 1.3 76.3 - - - +
305B SER* 1.3 67.1 + - - +
306B HIS 3.0 1.6 - - - -
307B GLY 2.9 11.6 + - - -
308B ILE* 3.0 27.7 + - + +
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Residues in contact with SER 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LEU* 3.8 29.1 - - - +
296B ALA* 4.1 8.9 - - - +
297B VAL* 4.7 7.4 - - - -
301B ASP 3.7 7.3 + - - -
302B MET* 3.1 15.6 + - - -
304B THR* 1.3 77.1 - - - +
306B HIS* 1.3 54.9 + - - +
308B ILE* 3.5 3.0 + - - +
309B CYS* 2.9 35.3 + - - +
346B ILE* 4.3 11.0 - - - +
354B GLU* 5.5 3.3 - - - +
356B THR* 3.0 17.8 + - - +
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Residues in contact with HIS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 2.8 45.8 + - - -
22A PHE* 3.7 31.1 + + + +
23A GLY 5.3 0.4 + - - -
302B MET 3.1 15.9 + - - +
303B GLU 3.6 6.7 - - - +
305B SER* 1.3 81.4 + - - +
307B GLY* 1.3 57.4 + - - +
310B ARG* 3.1 38.3 + - - +
355B THR* 3.4 37.3 + - - -
356B THR* 3.5 10.8 - - - +
359B LEU* 3.6 21.1 - - + +
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Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B PHE* 4.2 2.9 - - - -
260B VAL* 4.0 28.4 - - - +
303B GLU 3.3 7.8 + - - -
304B THR 2.9 9.1 + - - -
306B HIS* 1.3 78.8 - - - +
308B ILE* 1.3 63.1 + - - -
309B CYS 3.1 0.2 - - - -
310B ARG* 3.1 9.8 + - - +
311B ILE* 3.1 25.6 + - - +
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Residues in contact with ILE 308 (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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250B LEU* 5.8 0.2 - - + -
256B PHE* 4.3 11.6 - - + -
289B LEU* 4.1 24.9 - - + +
292B GLN* 3.7 36.1 - - + +
293B LEU* 3.8 35.0 - - + +
304B THR* 3.0 24.5 + - + +
305B SER 4.0 3.1 - - - +
307B GLY* 1.3 75.7 - - - +
309B CYS* 1.3 63.7 + - - +
311B ILE* 3.2 11.1 + - + +
312B ALA* 3.0 20.8 + - - +
339B MET* 3.9 24.2 - - + -
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Residues in contact with CYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B SER 2.9 20.7 + - - +
306B HIS 3.7 3.8 - - - +
308B ILE* 1.3 79.1 - - - +
310B ARG* 1.3 56.8 + - - +
312B ALA* 3.2 4.5 + - - +
313B VAL* 2.8 52.8 + - - +
340B ILE* 6.0 0.2 - - - -
343B CYS* 3.5 17.7 - - - -
356B THR* 3.2 27.6 - - + -
359B LEU* 4.0 11.4 - - + -
360B THR* 3.6 17.7 - - - -
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LYS 4.7 5.5 - - - +
19A ASP* 2.9 29.7 + - - +
20A HIS 3.6 12.2 + - - +
21A PRO* 3.7 16.8 - - - +
22A PHE 4.6 1.8 - - - +
110A LYS* 3.9 11.3 - - - +
260B VAL* 3.8 18.4 - - + +
261B GLU* 2.8 37.2 + - - -
264B VAL* 4.0 15.4 - - + +
306B HIS* 3.1 35.4 + - + +
307B GLY* 3.1 11.7 + - - +
309B CYS* 1.3 78.1 - - - +
311B ILE* 1.3 56.9 + - - +
313B VAL* 3.9 5.1 - - - +
314B ALA* 2.9 30.5 + - - +
359B LEU* 3.8 21.8 - - + -
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Residues in contact with ILE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B PHE* 4.0 17.5 - - + -
250B LEU* 3.9 13.5 - - + -
260B VAL* 3.8 26.9 - - + -
263B ILE* 3.6 45.8 - - + -
264B VAL* 4.1 18.4 - - + -
267B ILE* 4.7 3.8 - - + +
286B VAL* 4.1 8.9 - - + +
289B LEU* 4.5 7.4 - - + -
307B GLY 3.1 12.9 + - - +
308B ILE* 3.6 9.0 - - - +
310B ARG* 1.3 76.4 - - - +
312B ALA* 1.3 63.1 + - - +
314B ALA* 3.2 12.2 + - - +
315B LEU* 3.3 13.7 + - - +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B VAL* 3.9 28.5 - - + +
308B ILE 3.0 15.6 + - - +
309B CYS* 3.7 6.5 - - - +
311B ILE* 1.3 78.1 - - - +
313B VAL* 1.3 63.7 + - + +
315B LEU* 3.5 2.1 + - - +
316B GLY 3.1 18.7 + - - -
336B LEU* 4.2 9.8 - - + +
339B MET* 4.1 14.1 - - + -
340B ILE* 3.9 19.3 - - + +
343B CYS* 5.9 2.0 - - - -
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Residues in contact with VAL 313 (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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18A LYS* 3.5 33.9 - - + +
309B CYS* 2.8 44.1 + - - +
310B ARG 4.0 2.7 - - - +
312B ALA* 1.3 71.9 - - + +
314B ALA* 1.3 55.3 + - - +
317B GLU* 2.7 44.7 + - + +
340B ILE* 4.6 14.4 - - + -
359B LEU* 3.5 17.9 - - + +
360B THR* 3.8 19.7 - - + -
362B THR* 5.4 0.4 - - - +
363B PHE* 5.1 5.4 - - + -
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Residues in contact with ALA 314 (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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18A LYS* 5.1 4.9 - - - +
19A ASP* 6.0 3.4 - - + -
264B VAL* 4.4 17.0 - - + -
267B ILE* 3.9 14.5 - - + +
268B SER* 4.2 17.0 - - - +
310B ARG 2.9 19.7 + - - +
311B ILE* 3.2 8.3 + - - +
313B VAL* 1.3 78.3 - - - +
315B LEU* 1.3 56.7 + - - +
317B GLU* 4.9 0.4 - - - -
318B ASN* 3.3 36.3 + - - +
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Residues in contact with LEU 315 (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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267B ILE* 4.0 27.6 - - + +
279B LEU* 4.1 31.0 - - + +
282B LEU* 4.2 6.7 - - + -
283B ILE* 3.8 35.0 - - + +
286B VAL* 3.7 26.2 - - + -
311B ILE 3.3 8.3 + - - +
312B ALA 3.9 6.1 - - - +
313B VAL 3.3 0.2 - - - -
314B ALA* 1.3 80.4 - - - +
316B GLY* 1.3 65.1 + - - +
319B HIS* 3.2 31.1 + - + +
323B LEU* 4.3 8.5 - - + +
336B LEU* 4.2 10.5 - - + -
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Residues in contact with GLY 316 (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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312B ALA 3.1 11.5 + - - -
315B LEU* 1.3 81.7 - - - +
317B GLU* 1.3 56.4 + - - +
320B SER* 3.1 33.8 + - - -
323B LEU* 4.9 0.4 - - - -
333B PHE* 4.4 8.1 - - - -
336B LEU* 3.8 19.4 - - - +
340B ILE* 4.6 2.0 - - - -
363B PHE* 3.5 16.3 - - - -
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Residues in contact with GLU 317 (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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18A LYS* 3.0 35.6 + - + +
313B VAL* 2.7 31.4 + - + +
316B GLY* 1.3 73.9 - - - +
318B ASN* 1.3 63.1 + - - +
320B SER 4.1 1.6 + - - -
362B THR* 3.5 23.0 + - - -
363B PHE* 3.0 34.8 - - + -
366B THR* 3.1 38.5 + - - +
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Residues in contact with ASN 318 (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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18A LYS* 2.7 34.2 + - - +
268B SER* 3.8 32.5 + - - +
273B GLN* 5.6 0.5 - - - +
314B ALA* 3.3 25.3 + - - +
317B GLU* 1.3 81.2 - - - +
319B HIS* 1.3 81.9 + - + +
320B SER 3.7 0.4 - - - -
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Residues in contact with HIS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B ILE* 3.3 31.2 + - + -
269B GLN 5.2 2.7 - - - -
272B ALA* 4.2 2.0 - - + -
273B GLN* 3.9 37.8 - - + +
279B LEU* 3.3 40.3 - - + +
315B LEU* 3.2 19.5 + - + +
316B GLY 4.0 1.8 - - - -
318B ASN* 1.3 99.4 + - + +
320B SER* 1.3 64.2 + - - +
321B ARG* 3.4 3.1 - - - -
322B ALA* 4.0 12.9 - - + +
323B LEU* 2.9 34.2 + - + +
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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