Contacts of the helix formed by residues 292 - 311 (chain B) in PDB entry 6UZA
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 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B SER* 4.0 2.0 - - - -
291B GLU* 1.3 79.4 - - + +
293B PRO* 1.3 62.5 - - - +
294B VAL* 3.4 5.7 + - - +
295B MET* 3.7 16.0 - - + +
296B THR* 3.1 24.9 + - - -
365B ARG* 3.1 25.8 + - - -
855B TYR* 2.9 31.1 + - + -
859B MET* 3.9 11.8 - - - +
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Residues in contact with PRO 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 3.3 25.9 - - + +
287B SER* 4.9 0.9 - - - +
290B SER* 3.6 10.5 - - - +
291B GLU 3.5 11.0 - - - +
292B ASP* 1.3 83.0 - - - +
294B VAL* 1.3 60.7 + - - +
295B MET 3.4 0.2 - - - -
296B THR* 3.9 3.7 - - - -
297B ALA* 2.9 30.8 + - - +
328B PHE* 3.7 22.6 - - + -
332B LEU* 4.5 3.6 - - + -
859B MET* 3.8 20.0 - - + -
863B ILE* 3.8 26.2 - - + -
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Residues in contact with VAL 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASP* 3.3 3.7 - - - +
293B PRO* 1.3 74.1 - - - +
295B MET* 1.3 59.9 + - - +
297B ALA* 3.4 4.8 + - - +
298B LEU* 3.0 34.3 + - + +
328B PHE* 5.0 0.9 - - + -
329B VAL* 3.7 27.7 - - + +
332B LEU* 3.8 26.5 - - + -
345B ILE* 4.2 23.1 - - + +
365B ARG* 3.8 37.2 - - - +
377B PHE* 5.2 1.1 - - + -
859B MET* 4.2 9.9 - - + -
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Residues in contact with MET 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B ASP* 3.7 27.0 + - + +
293B PRO 3.4 0.2 - - - -
294B VAL* 1.3 77.6 - - - +
296B THR* 1.3 58.0 + - - +
298B LEU* 3.4 8.5 + - + +
299B GLU* 3.0 73.4 + - + +
365B ARG* 4.5 19.2 - - - +
368B LEU* 3.7 22.2 - - + -
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Residues in contact with THR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 5.1 12.3 - - - +
286B LEU* 4.0 19.7 - - + -
289B SER* 6.1 0.4 - - - +
290B SER* 4.0 20.2 + - - +
292B ASP 3.1 17.7 + - - -
293B PRO* 3.9 4.3 - - - -
294B VAL 3.3 0.2 - - - -
295B MET* 1.3 79.2 - - - +
297B ALA* 1.3 56.5 + - - +
299B GLU* 3.5 4.7 + - - +
300B LEU* 2.9 32.6 + - + +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 4.1 15.7 - - + +
293B PRO 2.9 20.3 + - - +
294B VAL 3.9 0.7 - - - +
296B THR* 1.3 75.7 - - - +
298B LEU* 1.3 58.3 + - - +
300B LEU* 3.8 5.5 - - - +
301B SER* 2.9 30.3 + - - -
325B CYS* 3.9 11.3 - - - +
328B PHE* 3.7 14.6 - - + -
329B VAL* 3.7 24.5 - - + -
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B VAL* 3.0 30.2 + - + +
295B MET* 3.8 8.3 - - + +
296B THR 3.3 0.2 - - - -
297B ALA* 1.3 77.2 - - - +
299B GLU* 1.3 61.8 + - + +
301B SER* 2.7 20.5 + - - +
302B ASN 3.0 6.8 + - - -
326B LYS* 6.2 0.7 - - + -
329B VAL* 4.7 16.8 - - + -
365B ARG* 4.0 33.9 - - + +
368B LEU* 4.8 13.7 - - + -
369B ALA* 4.8 11.9 - - + +
372B TYR* 3.5 22.0 - - + -
374B VAL* 3.8 31.9 - - + -
377B PHE* 5.9 2.9 - - + -
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B MET* 3.0 47.1 + - + +
296B THR* 4.0 5.2 - - - +
298B LEU* 1.3 76.1 - - - +
300B LEU* 1.3 57.5 + - - +
302B ASN* 3.4 7.8 + - - +
303B GLU* 2.9 29.9 + - - +
368B LEU* 4.0 2.4 - - - +
372B TYR* 3.0 30.3 + - - -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 3.5 35.2 - - - +
277B TYR* 4.3 17.5 - - + -
280B LEU* 3.4 31.4 - - + +
281B ALA* 3.8 6.1 - - - -
286B LEU* 4.2 12.3 - - + -
296B THR* 2.9 19.7 + - + +
297B ALA 3.9 3.6 - - - +
299B GLU* 1.3 74.4 - - - +
301B SER* 1.3 60.8 + - - +
303B GLU* 3.9 7.4 - - - +
304B LEU* 2.9 43.2 + - + +
325B CYS* 3.8 21.5 - - - -
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA 2.9 15.8 + - - -
298B LEU* 2.7 28.1 + - - +
300B LEU* 1.3 77.5 - - - +
302B ASN* 1.3 56.0 + - - +
304B LEU 3.5 0.2 + - - -
305B ALA* 3.0 26.6 + - - +
322B SER* 3.0 27.5 + - - +
325B CYS* 3.8 19.9 - - - +
326B LYS* 4.2 19.0 - - - +
372B TYR* 4.8 4.4 + - - +
374B VAL* 4.8 3.3 - - - +
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Residues in contact with ASN 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B LEU 3.0 9.2 + - - +
299B GLU* 3.7 11.6 + - - +
301B SER* 1.3 83.7 + - - +
303B GLU* 1.3 58.1 + - - +
305B ALA* 3.3 6.5 + - - +
306B VAL* 2.9 40.8 + - - +
372B TYR* 3.4 52.1 + - + +
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ARG* 2.7 36.0 + - - -
248B PRO 5.4 0.7 - - - +
277B TYR* 2.6 34.8 + - + +
299B GLU 2.9 17.7 + - - +
300B LEU* 3.3 8.4 + - + +
302B ASN* 1.3 78.0 - - - +
304B LEU* 1.3 57.8 + - - +
306B VAL* 3.3 6.3 + - - +
307B LEU* 3.0 39.0 + - + +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B TYR* 3.8 32.8 - - + -
281B ALA* 4.0 15.3 - - + -
300B LEU* 2.9 31.3 + - + +
303B GLU* 1.3 76.8 - - - +
305B ALA* 1.3 57.4 + - - +
307B LEU* 3.7 3.9 - - + -
308B ALA* 2.9 28.9 + - - +
318B TYR* 3.6 36.8 - - + +
321B LEU* 3.7 34.3 - - + +
322B SER* 4.0 15.0 - - - -
325B CYS* 4.0 6.5 - - - -
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B SER 3.0 19.1 + - - +
302B ASN* 3.8 7.9 - - - +
303B GLU 3.3 0.2 - - - -
304B LEU* 1.3 76.2 - - - +
306B VAL* 1.3 60.8 + - + +
308B ALA* 3.7 12.0 + - - +
309B ASN* 3.0 22.9 - - - +
319B LYS* 4.9 10.5 + - + +
322B SER* 4.1 11.8 + - - +
326B LYS* 5.6 4.9 - - - +
372B TYR 6.0 2.0 - - - +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ASN* 2.9 35.0 + - - +
303B GLU* 3.6 7.0 - - - +
305B ALA* 1.3 77.3 - - + +
307B LEU* 1.3 65.6 + - + +
309B ASN* 3.1 8.7 + - - +
310B ILE* 3.0 47.3 + - + +
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B TYR* 5.4 10.5 - - + +
273B ARG* 3.7 17.7 - - - +
277B TYR* 3.7 33.7 - - + +
303B GLU* 3.0 36.9 + - + +
304B LEU* 3.4 6.9 + - + +
306B VAL* 1.3 83.0 - - + +
308B ALA* 1.3 60.2 + - - +
309B ASN 3.2 0.2 - - - -
310B ILE* 3.9 13.0 - - + +
311B GLU* 3.1 35.7 + - + +
318B TYR* 3.7 25.8 - - + +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LEU 2.9 17.2 + - - +
305B ALA* 3.8 9.4 - - - +
306B VAL 3.2 0.6 - - - -
307B LEU* 1.3 78.4 - - - +
309B ASN* 1.3 59.0 + - - +
311B GLU 3.5 10.9 - - - +
312B LYS* 4.8 1.0 - - - -
315B LYS* 3.4 31.6 - - + +
318B TYR* 3.7 21.5 - - + +
319B LYS* 4.0 28.9 - - + +
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Residues in contact with ASN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B ALA 3.0 17.9 - - - +
306B VAL* 3.1 7.8 + - - +
308B ALA* 1.3 81.9 + - - +
310B ILE* 1.3 66.3 + - + +
311B GLU 3.4 2.6 - - - -
312B LYS* 4.6 5.2 + - - +
315B LYS* 5.2 5.1 - - - +
319B LYS* 4.4 16.5 + - - +
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B TYR* 3.6 27.8 - - + -
252B PHE* 3.6 36.7 - - + -
306B VAL* 3.0 38.8 + - + +
307B LEU* 4.3 10.8 - - + -
309B ASN* 1.3 81.2 - - + +
311B GLU* 1.3 58.2 + - + +
312B LYS* 3.6 4.0 + - - +
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B TYR* 3.3 46.1 + - + +
270B SER* 4.1 16.3 + - - -
273B ARG* 3.7 17.1 + - - -
307B LEU* 3.1 21.4 + - + +
308B ALA* 3.5 15.6 - - - +
310B ILE* 1.3 74.7 - - + +
312B LYS* 1.3 61.3 + - - +
313B GLU* 2.9 29.1 - - + +
314B PHE* 3.8 17.2 - - + -
315B LYS* 4.4 2.3 + - - +
318B TYR* 3.9 17.8 + - + -
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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) + - + + + + + -
------------------------------------------------------------
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