Contacts of the helix formed by residues 309 - 331 (chain I) in PDB entry 1I43
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 THR 309 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266I HIS* 4.6 3.6 - - - -
306I GLY 3.3 12.0 + - - -
307I MET 2.9 0.6 - - - -
308I LYS* 1.3 85.4 - - - +
310I LEU* 1.3 61.7 + - - +
311I HIS* 3.4 9.2 - - - -
312I LEU* 3.4 12.7 + - + -
313I ARG* 3.0 32.6 + - - -
266L HIS* 4.2 9.1 + - - +
309L THR* 4.0 19.1 + - - +
313L ARG* 3.9 25.4 - - + -
392L CYS* 3.8 20.0 - - - -
428L VAL* 5.2 0.2 - - + -
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Residues in contact with LEU 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I ALA* 4.5 4.5 - - + -
126I LEU* 3.8 28.7 - - + -
241I THR* 4.5 8.7 - - + +
242I PRO* 4.6 0.4 - - + -
243I LEU* 3.6 22.2 - - + -
262I PHE* 3.5 20.0 - - + +
263I LEU* 4.0 20.4 - - + -
307I MET* 2.8 23.0 + - + +
308I LYS 3.6 0.2 - - - -
309I THR* 1.3 76.7 - - - +
311I HIS* 1.3 59.7 + - - +
313I ARG* 3.2 24.7 + - - +
314I VAL* 2.9 46.6 + - + +
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Residues in contact with HIS 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57I ASP* 5.1 0.4 - - + -
58I GLY* 3.4 43.5 + - - +
61I ALA* 5.0 1.8 - - + +
62I ILE* 4.0 0.4 - - + -
243I LEU* 3.4 20.1 - - + +
307I MET 4.8 1.0 + - - -
308I LYS 3.4 15.3 - - - -
309I THR* 4.0 0.7 - - - -
310I LEU* 1.3 80.5 + - - +
312I LEU* 1.3 84.7 + - + +
314I VAL* 4.0 0.3 - - - +
315I GLN* 3.0 39.2 + - - +
316L GLN* 5.0 2.7 - - - -
428L VAL* 3.1 46.2 + - + +
430L ASP* 4.9 8.7 - - - +
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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
----------------------------------------------------------
309I THR* 3.7 12.6 - - + +
310I LEU 3.2 0.4 - - - -
311I HIS* 1.3 114.4 + - + +
313I ARG* 1.3 64.5 + - - +
315I GLN* 3.5 12.1 - - - +
316I GLN* 3.3 14.0 + - - +
312L LEU* 3.8 27.2 - - + +
313L ARG* 3.7 28.3 - - + -
316L GLN* 4.1 27.8 - - + +
428L VAL* 3.4 27.6 - - + -
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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
----------------------------------------------------------
262I PHE* 2.7 32.5 + - - +
263I LEU 3.6 7.1 + - - -
264I GLY 4.5 0.2 - - - -
265I GLY* 3.1 20.3 - - - -
266I HIS* 4.4 3.1 - - - -
306I GLY 2.8 23.5 + - - -
309I THR* 3.0 23.3 + - - +
310I LEU* 3.3 25.8 - - - +
312I LEU* 1.3 74.0 - - - +
314I VAL* 1.3 68.0 + - - +
316I GLN* 3.0 6.1 + - - +
317I GLN* 2.9 37.1 + - - +
390I GLY 4.2 6.2 + - - -
392I CYS* 4.0 23.6 - - - +
428I VAL* 4.1 7.9 - - + -
309L THR* 3.9 20.4 - - + -
312L LEU* 3.7 12.6 - - + -
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Residues in contact with VAL 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241I THR* 4.1 14.4 - - + +
243I LEU* 3.7 25.6 - - + -
244I ASN* 4.0 16.8 - - - +
262I PHE* 5.2 9.9 - - + -
310I LEU* 2.9 36.0 + - + +
311I HIS 4.0 2.7 - - - +
313I ARG* 1.3 72.4 - - + +
315I GLN* 1.3 56.1 + - - +
317I GLN* 3.2 8.9 + - + +
318I ASN* 2.7 58.3 + - - +
359I GLY* 6.1 0.2 - - - -
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Residues in contact with GLN 315 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311I HIS* 3.0 34.8 + - - +
312I LEU* 3.5 12.5 - - - +
314I VAL* 1.3 78.7 - - - +
316I GLN* 1.3 62.3 + - - +
318I ASN* 3.5 9.9 - - - +
319I SER* 3.3 22.5 + - - -
316L GLN* 5.5 5.4 + - - +
430L ASP* 5.4 4.9 + - - -
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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 3.3 8.0 + - - +
313I ARG 3.0 8.5 + - - +
315I GLN* 1.3 75.9 - - - +
317I GLN* 1.3 67.1 + - - +
319I SER* 3.2 7.8 + - - -
320I THR* 3.0 36.0 + - - +
427I GLY 5.0 0.2 - - - +
428I VAL* 3.4 27.6 + - + +
429I GLU 3.2 26.1 + - - -
430I ASP* 4.4 7.3 + - - +
431I PHE* 4.5 4.2 - - - +
311L HIS* 5.0 3.0 + - - -
312L LEU* 4.0 21.8 - - + +
315L GLN* 5.4 5.5 + - - +
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Residues in contact with GLN 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262I PHE* 3.6 34.4 - - + -
313I ARG* 2.9 32.4 + - - +
314I VAL* 3.7 6.0 + - - +
316I GLN* 1.3 74.4 - - - +
318I ASN* 1.3 63.5 + - - +
320I THR* 3.9 4.2 - - - -
321I ALA* 2.9 28.6 + - - +
360I GLY* 3.8 16.1 - - - +
390I GLY* 3.7 11.5 + - - +
391I GLY 4.2 8.8 + - - -
425I SER* 5.3 0.2 + - - -
426I PHE* 2.6 28.6 + - - +
427I GLY* 3.4 22.1 + - - +
428I VAL* 4.2 7.4 - - + -
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Residues in contact with ASN 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I ASN* 3.0 31.7 + - - +
314I VAL* 2.7 32.7 + - - +
315I GLN* 3.5 10.0 - - - +
317I GLN* 1.3 73.5 - - - +
319I SER* 1.3 61.2 + - - +
322I LEU* 3.2 24.8 + - - +
339I TYR* 3.5 5.2 + - - -
357I GLY* 3.9 6.9 - - - -
358I PHE 4.2 6.1 - - - +
359I GLY* 3.0 35.5 + - - +
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Residues in contact with SER 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315I GLN 3.3 11.3 + - - -
316I GLN* 3.2 11.3 + - - -
318I ASN* 1.3 76.0 - - - +
320I THR* 1.3 68.9 + - - +
321I ALA 3.1 0.5 + - - -
322I LEU* 3.1 6.4 + - - +
323I ARG* 2.9 48.7 + - - +
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Residues in contact with THR 320 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316I GLN* 3.0 31.4 + - - +
317I GLN* 3.9 4.5 - - - -
319I SER* 1.3 76.1 - - - +
321I ALA* 1.3 65.1 + - - +
323I ARG* 3.9 5.4 + - - +
324I MET* 2.9 36.6 + - + +
426I PHE* 3.7 31.4 - - + -
427I GLY 5.2 2.2 + - - +
428I VAL* 6.1 0.2 - - - -
429I GLU 4.6 2.6 + - - -
431I PHE* 4.7 20.7 - - + +
434I LEU* 3.8 18.8 - - + +
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Residues in contact with ALA 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317I GLN 2.9 19.3 + - - +
318I ASN 3.7 0.2 - - - +
320I THR* 1.3 76.6 - - - +
322I LEU* 1.3 52.7 + - - +
324I MET* 3.3 2.1 + - - +
325I ALA* 2.8 35.0 + - - +
339I TYR* 3.3 13.2 - - + +
359I GLY 3.3 21.1 - - - +
360I GLY* 3.6 13.2 - - - +
362I VAL* 3.7 11.2 - - + +
426I PHE* 3.8 13.4 - - - -
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Residues in contact with LEU 322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318I ASN 3.2 14.7 + - - +
319I SER* 3.1 6.3 + - - +
321I ALA* 1.3 78.2 - - - +
323I ARG* 1.3 67.6 + - + +
325I ALA* 3.0 17.4 + - - +
326I GLU* 3.2 24.5 + - - +
339I TYR* 3.6 28.1 + - + +
341I GLY* 4.0 22.2 - - - +
342I LEU* 4.6 4.3 - - + +
358I PHE* 4.8 13.9 - - + -
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Residues in contact with ARG 323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319I SER* 2.9 40.2 + - - +
320I THR* 3.9 2.1 + - - +
322I LEU* 1.3 76.1 - - + +
324I MET* 1.3 64.5 + - - +
326I GLU* 3.2 12.5 + - - +
327I ILE* 3.2 26.3 + - + +
431I PHE* 2.9 52.6 - - + +
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Residues in contact with MET 324 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320I THR* 2.9 23.8 + - + +
321I ALA 3.7 0.9 - - - +
323I ARG* 1.3 74.6 - - - +
325I ALA* 1.3 60.2 + - - +
327I ILE* 4.1 17.9 - - + -
328I LEU* 2.9 50.2 + - + +
426I PHE* 3.6 31.2 - - + -
431I PHE* 3.5 29.2 - - + -
434I LEU* 5.5 0.2 - - + -
435I LYS* 3.7 20.4 - - + +
438I ILE* 3.4 32.8 - - + -
439I LEU* 5.8 2.0 - - + -
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Residues in contact with ALA 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321I ALA 2.8 13.9 + - - +
322I LEU* 3.0 14.8 + - - +
324I MET* 1.3 77.2 - - - +
326I GLU* 1.3 57.0 + - - +
328I LEU* 3.2 6.0 + - - +
329I GLU* 2.8 29.6 + - - +
337I VAL* 3.9 10.6 - - + +
339I TYR* 4.1 17.3 - - + -
342I LEU* 3.8 24.9 - - + -
362I VAL* 4.5 8.9 - - + +
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Residues in contact with GLU 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322I LEU* 3.2 23.6 + - - +
323I ARG* 3.2 12.8 + - - +
325I ALA* 1.3 77.8 - - - +
327I ILE* 1.3 66.9 + - + +
329I GLU* 3.2 6.4 + - - +
330I ALA* 2.9 25.0 + - - +
342I LEU* 3.7 21.1 - - + +
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Residues in contact with ILE 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323I ARG* 3.2 11.0 + - + +
324I MET* 3.8 20.0 - - + +
326I GLU* 1.3 76.6 - - + +
328I LEU* 1.3 66.1 + - + +
330I ALA* 3.2 8.0 + - - +
331I HIS* 3.0 22.1 + - + +
431I PHE* 3.9 18.2 - - + -
435I LYS* 3.8 30.1 - - + +
439I LEU* 4.3 26.2 - - + -
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Residues in contact with LEU 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324I MET* 2.9 37.5 + - + +
325I ALA 3.5 3.8 - - - +
327I ILE* 1.3 80.3 - - + +
329I GLU* 1.3 62.7 + - - +
331I HIS* 3.0 12.7 + - + +
334I VAL* 3.1 38.9 - - + +
337I VAL* 3.8 11.2 - - + -
362I VAL* 4.5 11.4 - - + -
364I PHE* 3.6 40.4 - - + -
426I PHE* 5.0 6.5 - - + -
438I ILE* 3.9 25.8 - - + -
439I LEU* 6.1 0.7 - - + -
442I LEU* 4.2 9.2 - - + -
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Residues in contact with GLU 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325I ALA 2.8 20.1 + - - +
326I GLU* 3.6 6.9 - - - +
328I LEU* 1.3 73.6 - - - +
330I ALA* 1.3 61.4 + - - +
331I HIS 3.5 5.4 + - - +
334I VAL* 4.5 5.6 - - - +
336I HIS* 5.7 1.2 - - - -
337I VAL* 3.6 24.6 + - + +
342I LEU* 3.5 21.2 - - + +
343I GLN 5.3 0.7 + - - -
344I SER* 2.9 32.6 + - - -
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Residues in contact with ALA 330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326I GLU 2.9 16.9 + - - +
327I ILE* 3.6 6.3 - - - +
328I LEU 3.2 0.2 - - - -
329I GLU* 1.3 76.2 - - + +
331I HIS* 1.3 65.1 + - - +
332I PRO* 3.5 5.0 - - - +
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Residues in contact with HIS 331 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I ILE* 3.0 13.3 + - + +
328I LEU* 3.0 17.3 + - + +
329I GLU 3.9 2.6 - - - +
330I ALA* 1.3 78.5 - - - +
332I PRO* 1.3 79.0 - - + +
333I LYS* 3.0 51.0 + - + +
334I VAL* 3.3 28.1 + - + +
439I LEU* 3.9 22.6 + - + +
442I LEU* 3.4 37.1 - - + +
443I ASP* 5.4 4.9 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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