Contacts of the helix formed by residues 388 - 410 (chain I) in PDB entry 2I2X
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 388 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385I ASP* 2.9 9.2 + - + +
387I ASP* 1.3 78.3 - - + +
389I ILE* 1.3 59.3 + - - +
390I TYR* 3.1 11.4 + - - +
391I LEU* 2.7 48.5 + - + +
392I ARG* 2.8 35.8 + - - +
434I ASP 4.8 5.5 + - - -
436I MET* 4.0 21.5 - - - +
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Residues in contact with ILE 389 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I ARG* 3.7 38.1 - - - +
189I GLY 3.8 7.7 - - - +
190I CYS* 4.2 8.5 - - - +
193I SER* 4.0 29.6 + - - +
194I ILE* 4.0 21.3 - - + +
252I PRO* 5.5 0.3 - - - +
387I ASP 3.8 3.7 + - - +
388I ASN* 1.3 72.3 + - - +
390I TYR* 1.3 65.3 + - - +
392I ARG* 3.6 21.7 + - - +
393I ALA* 3.4 22.5 + - - +
436I MET* 3.8 27.5 - - + -
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Residues in contact with TYR 390 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I LEU* 3.8 17.4 - - + +
190I CYS* 4.0 17.5 - - - -
388I ASN* 3.1 6.6 + - - +
389I ILE* 1.3 82.9 - - - +
391I LEU* 1.3 63.0 + - - +
393I ALA* 3.2 4.7 + - - +
394I LYS* 2.9 49.2 + - + +
432I LEU* 3.7 6.2 - - - +
433I PRO 2.6 29.2 + - - -
434I ASP 4.1 11.7 - - - -
435I ASP 4.2 0.2 - - - -
436I MET* 3.6 38.4 - - + -
439I PHE* 3.1 58.6 - + + +
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Residues in contact with LEU 391 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385I ASP* 3.6 32.3 - - + +
388I ASN* 2.7 34.4 + - + +
390I TYR* 1.3 77.5 - - + +
392I ARG* 1.3 60.5 + - - +
394I LYS* 4.0 25.6 - - - +
395I ASN* 2.8 53.6 + - - +
434I ASP* 4.0 31.6 - - + +
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Residues in contact with ARG 392 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I ARG* 4.1 4.0 - - - +
6I TYR 4.5 1.2 + - - +
193I SER* 5.0 1.0 + - - -
252I PRO* 2.9 39.4 + - + +
255I LEU* 4.0 12.4 - - - +
256I VAL* 3.5 10.1 - - - +
259I GLU* 2.4 47.6 + - - -
382I ILE* 3.3 37.1 - - + +
385I ASP 3.7 7.4 + - - +
386I GLY* 3.0 28.5 + - - -
388I ASN 2.8 22.8 + - - +
389I ILE* 3.6 24.1 + - - +
391I LEU* 1.3 71.8 - - - +
393I ALA* 1.3 63.7 + - - +
395I ASN* 3.5 9.8 + - - +
396I ALA* 3.1 22.0 + - - +
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Residues in contact with ALA 393 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I LEU* 3.5 22.9 - - + +
189I GLY* 4.0 17.0 - - - +
249I ILE* 4.1 8.6 - - + +
252I PRO* 3.9 20.2 - - + -
389I ILE 3.4 15.9 + - - +
390I TYR 3.2 1.6 + - - +
392I ARG* 1.3 78.8 - - - +
394I LYS* 1.3 65.4 + - - +
396I ALA* 3.3 3.7 + - - +
397I ALA* 3.1 22.7 + - - +
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Residues in contact with LYS 394 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I LEU* 3.8 23.5 - - + +
390I TYR* 2.9 52.2 + - + +
391I LEU* 3.7 13.9 - - + +
392I ARG 3.3 0.2 - - - -
393I ALA* 1.3 73.8 - - - +
395I ASN* 1.3 66.5 + - - +
397I ALA* 3.3 4.9 + - - +
398I ILE* 3.0 45.0 + - + +
429I LEU* 4.3 8.0 + - + +
430I GLU* 5.5 1.2 + - - +
432I LEU* 4.1 19.1 + - + -
433I PRO 3.5 6.3 - - - -
434I ASP* 2.8 28.9 + - - -
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Residues in contact with ASN 395 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381I SER* 3.1 33.9 + - - +
384I LYS* 3.4 19.3 - - - +
385I ASP* 3.0 34.7 + - - +
391I LEU* 2.8 38.7 + - - +
392I ARG* 3.5 3.3 - - - +
394I LYS* 1.3 76.8 + - - +
396I ALA* 1.3 50.8 + - - +
398I ILE* 3.8 5.7 - - - +
399I GLU* 2.8 37.1 + - - +
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Residues in contact with ALA 396 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248I ALA* 3.6 26.9 - - - +
252I PRO* 4.6 0.7 - - + -
378I VAL* 4.0 8.4 - - + +
381I SER* 3.5 10.7 + - - -
382I ILE* 3.8 22.2 - - + -
392I ARG 3.1 10.6 + - - +
393I ALA* 3.5 10.3 - - - +
394I LYS 3.2 0.4 - - - -
395I ASN* 1.3 77.1 - - - +
397I ALA* 1.3 56.1 + - - +
399I GLU* 3.7 1.2 - - - +
400I CYS* 2.8 35.3 + - - +
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Residues in contact with ALA 397 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185I LEU* 5.3 0.9 - - + -
245I ILE* 4.2 8.0 - - + +
248I ALA* 4.3 10.0 - - - +
249I ILE* 4.0 18.4 - - + -
393I ALA 3.1 13.2 + - - +
394I LYS* 3.3 8.0 + - - +
396I ALA* 1.3 75.8 - - - +
398I ILE* 1.3 62.1 + - - +
400I CYS* 3.3 5.1 + - - +
401I CYS* 3.1 25.3 + - - -
429I LEU* 3.5 30.7 - - + -
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Residues in contact with ILE 398 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394I LYS* 3.0 44.4 + - + +
395I ASN* 4.1 4.9 - - - +
397I ALA* 1.3 71.8 - - - +
399I GLU* 1.3 68.2 + - - +
401I CYS* 3.1 9.9 + - + +
402I ASN* 3.0 37.2 + - - +
426I LYS* 5.0 6.1 - - + +
429I LEU* 3.7 34.8 - - + +
430I GLU* 4.1 26.5 - - + +
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Residues in contact with GLU 399 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377I ARG* 2.7 46.9 + - - +
378I VAL* 4.3 3.6 - - - -
381I SER* 3.5 28.9 - - - +
384I LYS* 4.6 9.5 + - - -
395I ASN 2.8 22.2 + - - +
396I ALA 3.7 3.1 - - - +
398I ILE* 1.3 73.2 - - - +
400I CYS* 1.3 57.1 + - - +
402I ASN* 3.2 13.3 + - - +
403I ILE* 2.9 42.9 + - + +
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Residues in contact with CYS 400 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244I VAL* 3.7 44.2 - - - -
245I ILE* 4.2 7.9 - - + -
248I ALA* 3.6 14.1 - - + -
369I MET* 4.0 18.6 - - + -
378I VAL* 4.8 2.2 - - + +
396I ALA 2.8 14.2 + - - +
397I ALA* 3.3 10.1 - - - +
399I GLU* 1.3 74.9 - - - +
401I CYS* 1.3 64.2 + - - +
403I ILE* 3.0 12.8 + - - +
404I ILE* 2.9 30.9 + - - +
422I LEU* 6.1 0.2 - - - -
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Residues in contact with CYS 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245I ILE* 3.7 27.6 - - - -
397I ALA 3.1 16.4 + - - -
398I ILE* 3.1 8.7 + - - +
400I CYS* 1.3 77.0 - - - +
402I ASN* 1.3 58.5 + - - +
404I ILE* 3.3 1.6 + - - +
405I GLU* 2.9 34.8 + - - +
422I LEU* 4.0 17.5 - - + +
426I LYS* 3.9 43.3 - - + -
429I LEU* 4.2 7.4 - - - -
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Residues in contact with ASN 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377I ARG* 4.1 14.6 - - - +
398I ILE* 3.0 37.0 + - - +
399I GLU* 3.6 14.8 + - - +
401I CYS* 1.3 75.1 - - - +
403I ILE* 1.3 53.9 + - - +
405I GLU* 3.3 9.3 + - - +
406I GLU* 2.8 44.4 + - + +
426I LYS* 2.8 29.7 + - - +
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Residues in contact with ILE 403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368I TYR* 3.5 17.1 - - + -
369I MET* 4.6 5.4 - - + -
374I ASN* 3.6 42.2 - - + +
377I ARG* 3.5 37.0 - - - +
378I VAL* 3.4 33.2 - - + -
399I GLU* 2.9 23.6 + - + +
400I CYS* 3.5 7.9 - - - +
402I ASN* 1.3 76.1 - - - +
404I ILE* 1.3 65.5 + - + +
406I GLU* 3.3 7.7 + - - +
407I GLY 3.0 17.5 + - - -
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Residues in contact with ILE 404 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241I THR* 4.5 2.7 - - + -
244I VAL* 4.2 8.3 - - + -
365I PRO* 3.5 35.2 - - + +
368I TYR* 3.7 25.1 - - + -
369I MET* 4.0 13.2 - - + -
400I CYS* 2.9 31.3 + - - +
401I CYS 3.9 3.1 - - - +
403I ILE* 1.3 72.7 - - + +
405I GLU* 1.3 56.3 + - - +
407I GLY* 3.0 3.0 + - - +
408I ALA* 2.7 33.6 + - - +
412I LEU* 4.2 8.1 - - + +
414I LEU* 4.1 15.9 - - + -
422I LEU* 3.8 26.2 - - + -
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Residues in contact with GLU 405 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401I CYS 2.9 18.3 + - - +
402I ASN* 3.7 11.4 - - - +
404I ILE* 1.3 75.8 - - - +
406I GLU* 1.3 64.4 + - + +
408I ALA* 3.8 6.5 - - - +
409I ALA* 3.1 23.7 + - - +
422I LEU* 3.8 24.6 - - + +
423I ALA* 4.7 9.5 - - - +
426I LYS* 3.3 42.4 + - - +
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Residues in contact with GLU 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368I TYR* 4.6 2.5 - - - +
377I ARG* 2.5 48.8 + - - -
402I ASN* 2.8 20.4 + - + +
403I ILE* 3.6 5.3 - - - +
404I ILE 3.2 0.2 - - - -
405I GLU* 1.3 80.5 - - + +
407I GLY* 1.3 62.2 + - - +
409I ALA* 3.3 7.5 + - - +
410I GLY* 3.2 15.2 + - - -
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Residues in contact with GLY 407 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362I TYR* 5.9 0.2 - - - -
368I TYR* 3.3 33.1 + - - -
403I ILE 3.0 7.1 + - - -
404I ILE 3.0 6.7 + - - -
406I GLU* 1.3 77.4 - - - +
408I ALA* 1.3 56.1 + - - +
410I GLY* 2.9 17.6 + - - -
411I LYS 3.3 0.7 + - - -
412I LEU* 3.0 27.5 + - - -
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Residues in contact with ALA 408 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404I ILE 2.7 18.3 + - - +
405I GLU* 3.8 7.6 - - - +
407I GLY* 1.3 71.4 - - - +
409I ALA* 1.3 63.1 + - - +
410I GLY 3.2 8.7 + - - +
412I LEU* 3.3 19.9 - - - +
414I LEU* 3.7 28.5 - - + -
419I THR* 5.8 3.1 - - + +
422I LEU* 5.7 0.4 - - + -
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Residues in contact with ALA 409 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405I GLU 3.1 12.7 + - - +
406I GLU* 3.6 11.4 - - - +
408I ALA* 1.3 75.8 - - - +
410I GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 410 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406I GLU 3.2 7.5 + - - -
407I GLY* 2.9 11.7 + - - -
408I ALA 3.4 6.2 - - - +
409I ALA* 1.3 81.4 - - - +
411I LYS* 1.3 64.6 + - - +
412I LEU 4.6 0.3 - - - +
6J GLU* 5.4 1.8 - - - +
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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) + - + + + + + -
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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