Contacts of the helix formed by residues 309 - 329 (chain I) in PDB entry 5U07
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 GLY 309 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I ASP* 1.3 79.3 - - - +
310I TYR* 1.3 64.7 + - - -
311I THR* 3.2 8.3 + - - -
312I LEU* 3.8 20.1 + - - +
313I ARG* 4.1 7.4 + - - +
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Residues in contact with TYR 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ILE* 4.7 12.0 - - + +
194I VAL* 5.7 0.7 - - + -
195I HIS* 3.4 60.9 - + + +
196I GLY 5.0 0.9 + - - -
230I THR* 4.0 23.3 - - + +
304I LEU* 4.1 19.0 + - + +
305I TYR 4.2 3.0 + - - -
306I GLY* 3.1 40.7 - - - -
307I SER 4.3 1.8 + - - -
308I ASP* 3.9 10.3 - - - -
309I GLY* 1.3 71.4 - - - -
311I THR* 1.3 60.2 + - - +
312I LEU 3.4 0.2 - - - -
313I ARG* 3.4 8.1 + - - +
314I ALA* 2.8 33.5 + - + +
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Residues in contact with THR 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ILE* 5.6 2.5 - - + -
11I THR* 3.9 15.3 - - + -
230I THR* 4.8 4.5 - - + -
282I ASP* 3.5 28.7 - - + +
309I GLY* 4.5 4.0 - - - -
310I TYR* 1.3 77.5 - - - +
312I LEU* 1.3 75.9 + - - +
314I ALA* 3.7 4.2 - - - +
315I CYS* 2.9 41.1 + - - -
341I GLU* 5.4 5.8 - - - -
343I LYS* 4.7 0.7 - - - -
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Residues in contact with LEU 312 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I ASP* 6.0 2.7 - - + +
309I GLY* 4.2 14.4 - - - +
310I TYR 3.4 0.2 - - - -
311I THR* 1.3 91.6 + - - +
313I ARG* 1.3 65.4 + - + +
315I CYS* 3.8 1.6 - - - +
316I GLN* 3.0 37.2 + - - +
341I GLU* 6.0 0.9 - - + -
343I LYS* 3.6 39.2 + - + +
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Residues in contact with ARG 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304I LEU* 3.8 30.9 - - + +
305I TYR* 4.0 15.4 - - - +
306I GLY* 3.7 22.8 + - - +
308I ASP* 3.2 42.2 + - - +
309I GLY 4.3 6.5 - - - +
310I TYR* 3.4 9.2 + - - +
311I THR 3.3 0.6 - - - -
312I LEU* 1.3 77.7 - - + +
314I ALA* 1.3 57.7 + - - +
316I GLN* 3.4 12.7 + - - +
317I GLU* 2.9 47.1 + - - +
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Residues in contact with ALA 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ILE* 3.3 34.5 - - + -
194I VAL* 4.4 15.5 - - + -
300I PHE* 4.1 10.9 - - + -
304I LEU* 4.6 1.9 - - + +
310I TYR* 2.8 20.9 + - + +
311I THR 3.7 2.7 - - - +
313I ARG* 1.3 75.3 - - - +
315I CYS* 1.3 66.8 + - - +
317I GLU* 3.2 4.8 + - - +
318I LEU* 2.9 26.3 + - - +
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Residues in contact with CYS 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ILE* 4.7 10.1 - - - -
282I ASP* 5.6 3.4 - - - -
283I LEU* 3.8 31.9 - - + -
311I THR* 2.9 29.6 + - - +
312I LEU 3.8 3.6 - - - +
314I ALA* 1.3 77.3 - - - +
316I GLN* 1.3 64.2 + - + +
318I LEU* 3.9 4.0 - - - +
319I ASN* 2.9 24.3 + - - +
341I GLU* 3.1 30.3 - - - +
343I LYS* 4.2 7.2 - - - +
346I LEU* 3.6 15.0 - - + +
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Residues in contact with GLN 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312I LEU* 3.0 28.4 + - - +
313I ARG* 3.8 12.0 - - - +
315I CYS* 1.3 78.9 - - + +
317I GLU* 1.3 58.6 + - + +
319I ASN* 3.4 8.4 + - - +
320I ASN* 2.9 28.9 + - - +
343I LYS* 5.2 4.5 - - - +
344I THR* 4.6 18.8 + - + +
346I LEU* 4.6 4.7 - - + -
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Residues in contact with GLU 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299I ALA* 4.4 13.5 - - - +
300I PHE* 3.8 20.9 - - + -
302I THR* 5.1 4.2 + - - +
304I LEU* 2.9 46.7 - - - +
313I ARG* 2.9 35.3 + - - +
314I ALA* 3.2 3.7 + - - +
316I GLN* 1.3 76.2 - - + +
318I LEU* 1.3 62.2 + - - +
320I ASN* 3.3 5.1 + - - +
321I TYR* 2.9 31.7 + - - +
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Residues in contact with LEU 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I HIS* 4.7 5.8 - - + -
8I ALA 5.7 1.3 - - - +
9I ILE* 5.7 6.1 - - + -
232I TYR* 3.7 30.5 - - + -
283I LEU* 4.6 17.9 - - + -
285I HIS* 4.8 5.6 - - + -
296I PHE* 4.0 24.4 - - + -
299I ALA* 4.9 1.8 - - - -
300I PHE* 4.1 18.5 - - + -
314I ALA 2.9 16.6 + - - +
315I CYS* 4.0 4.9 - - - +
317I GLU* 1.3 75.7 - - - +
319I ASN* 1.3 57.5 + - - +
321I TYR* 4.0 4.6 - - - +
322I ALA* 2.9 31.7 + - - +
349I LEU* 3.8 32.8 - - + -
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Residues in contact with ASN 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315I CYS 2.9 18.4 + - - +
316I GLN* 3.5 6.1 + - - +
318I LEU* 1.3 78.4 - - - +
320I ASN* 1.3 64.6 + - - +
322I ALA* 3.2 6.4 + - - +
323I GLU* 2.9 21.3 + - - +
344I THR* 5.3 3.4 - - - +
346I LEU* 3.4 42.6 - - + +
347I ALA 3.8 4.4 - - - +
348I ALA* 3.1 26.5 + - - +
349I LEU* 4.2 7.3 + - - +
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Residues in contact with ASN 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343E LYS* 4.7 15.1 + - - +
316I GLN 2.9 17.0 + - - +
317I GLU* 3.8 6.1 - - - +
319I ASN* 1.3 76.6 - - - +
321I TYR* 1.3 63.0 + - - +
323I GLU* 2.9 38.6 - - - +
324I ARG* 3.0 15.6 + - - +
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Residues in contact with TYR 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E THR* 5.0 0.7 - - - +
280E LEU 4.6 4.9 + - - -
282E ASP* 4.0 7.6 + - - -
340E VAL* 4.7 20.9 - - + +
295I SER 4.6 1.4 + - - -
296I PHE* 3.9 31.0 - + - -
298I PRO* 3.2 31.1 - - + +
299I ALA* 3.4 35.9 - - + -
317I GLU 2.9 18.7 + - - +
318I LEU* 4.0 2.0 - - - +
320I ASN* 1.3 75.9 - - - +
322I ALA* 1.3 58.6 + - - +
324I ARG* 3.3 6.5 + - + +
325I LEU* 2.9 62.6 + - + +
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Residues in contact with ALA 322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285I HIS* 5.6 0.2 - - - +
289I ARG* 5.9 0.3 + - - -
296I PHE* 4.0 26.2 - - + -
318I LEU 2.9 19.2 + - - +
319I ASN 3.2 2.7 + - - +
321I TYR* 1.3 78.4 - - - +
323I GLU* 1.3 62.0 + - - +
325I LEU* 3.4 2.1 + - - +
326I ARG* 2.9 25.2 + - - +
335I ARG* 4.9 7.0 + - - +
348I ALA* 4.3 6.7 - - + +
349I LEU* 3.5 27.6 - - + -
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Residues in contact with GLU 323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319I ASN* 2.9 11.0 + - - +
320I ASN* 2.9 41.2 - - - +
322I ALA* 1.3 76.3 - - - +
324I ARG* 1.3 88.5 + - - +
326I ARG* 3.1 7.2 + - - +
327I GLU* 2.9 28.8 + - - +
348I ALA* 3.3 23.2 - - + +
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Residues in contact with ARG 324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E THR 3.1 14.5 + - - -
340E VAL* 2.7 34.1 + - + +
342E ASN* 4.7 19.7 - - - +
352E ARG* 3.0 31.0 - - - +
354E ASP* 5.4 2.4 + - - +
320I ASN* 3.0 25.7 + - - +
321I TYR* 3.3 7.8 + - + +
323I GLU* 1.3 92.8 + - - +
325I LEU* 1.3 58.6 + - - +
327I GLU* 2.3 44.2 + - - +
328I VAL* 2.9 36.9 + - - +
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Residues in contact with LEU 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E LEU* 4.1 29.8 - - + +
281E PRO 5.6 0.7 - - - +
340E VAL* 3.8 22.2 - - + -
289I ARG* 5.6 4.3 - - - +
294I ILE* 3.7 23.3 - - + +
295I SER 4.7 0.7 - - - +
296I PHE* 3.6 22.2 - - + -
321I TYR* 2.9 54.7 + - + +
322I ALA* 4.0 4.3 - - - +
324I ARG* 1.3 73.6 - - - +
326I ARG* 1.3 62.2 + - - +
328I VAL* 4.3 4.0 - - + +
329I TRP* 2.9 34.1 + - - +
335I ARG* 5.3 0.2 - - - -
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Residues in contact with ARG 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289I ARG* 5.7 0.2 - - - +
322I ALA 2.9 15.5 + - - +
323I GLU* 3.7 6.1 - - - +
325I LEU* 1.3 76.7 - - - +
327I GLU* 1.3 62.2 + - - +
329I TRP 3.4 17.3 - - - +
330I PRO* 3.7 6.7 - - + +
331I ASP* 3.0 31.1 + - - +
332I ASP* 5.0 3.2 + - - +
333I ALA 4.4 5.3 + - - -
335I ARG* 2.8 58.2 - - - +
348I ALA* 5.3 7.4 - - + +
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Residues in contact with GLU 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354E ASP* 3.9 25.4 - - + +
355E SER* 3.6 14.4 - - - -
323I GLU* 2.9 17.0 + - - +
324I ARG* 2.3 52.4 + - - +
326I ARG* 1.3 79.5 - - - +
328I VAL* 1.3 63.2 + - + +
329I TRP 3.5 0.2 + - - -
330I PRO* 4.1 6.4 - - - +
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Residues in contact with VAL 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E LEU* 5.7 0.4 - - + -
338E ALA* 5.2 0.2 - - + -
339E THR 3.9 17.7 - - - +
340E VAL* 3.7 24.0 - - + -
354E ASP 3.7 14.8 - - - +
355E SER* 3.2 7.7 - - - -
356E TYR* 3.1 74.6 + - + +
357E PRO* 3.8 1.6 - - - +
324I ARG* 2.9 24.6 + - - +
325I LEU* 4.1 6.1 - - + +
327I GLU* 1.3 75.8 - - + +
329I TRP* 1.3 58.7 + - + +
330I PRO* 3.4 2.0 - - - +
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Residues in contact with TRP 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E ARG* 3.4 51.1 - - + -
264E LEU* 5.1 7.6 - - + -
265E SER* 4.3 20.9 - - - -
280E LEU* 3.7 28.5 - - + -
356E TYR* 4.2 30.5 - + + -
357E PRO* 4.6 11.9 - - + -
289I ARG* 5.4 0.2 - - - -
291I ASP* 2.4 33.0 + - + -
292I ARG* 4.8 8.9 - - - +
294I ILE* 4.4 13.2 - - + -
325I LEU 2.9 15.4 + - - +
326I ARG* 3.4 6.7 - - - +
328I VAL* 1.3 76.4 - - + +
330I PRO* 1.3 77.0 + - + +
331I ASP* 2.9 23.9 - - - +
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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