Contacts of the helix formed by residues 348 - 362 (chain G) 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 348 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351E VAL* 3.7 23.2 - - + +
355E LEU* 4.1 17.3 - - + +
2F LEU* 3.8 15.1 - - - +
343G ALA* 2.7 16.0 + - - +
346G THR* 2.9 32.7 + - - +
347G LYS* 1.3 77.4 + - - +
349G ASP* 1.3 62.1 + - - -
350G LYS 3.4 2.2 - - - -
351G VAL* 3.1 31.7 - - + +
352G LEU* 3.3 7.8 + - - +
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Residues in contact with ASP 349 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G THR* 3.0 29.0 + - - +
19G PHE* 3.7 26.5 - - + -
343G ALA* 3.2 16.8 + - - +
344G LEU* 3.8 24.1 - - + +
347G LYS* 3.5 13.7 - - - +
348G ASN* 1.3 77.0 - - - +
350G LYS* 1.3 71.7 + - - +
352G LEU* 3.1 2.9 + - - +
353G ARG* 2.8 31.5 + - - +
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Residues in contact with LYS 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ASP* 2.8 37.5 + - - +
16G GLU* 3.8 15.7 + - - +
17G MET 4.6 4.3 - - - -
18G THR* 4.8 5.2 - - - +
347G LYS 5.5 0.4 + - - -
348G ASN 3.4 1.0 - - - -
349G ASP* 1.3 90.2 - - - +
351G VAL* 1.3 56.2 + - - +
353G ARG* 3.3 30.9 + - - +
354G ASP* 3.0 35.2 + - - +
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Residues in contact with VAL 351 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348E ASN* 3.8 32.5 - - + +
351E VAL* 4.3 17.3 - - + -
355E LEU* 5.4 1.8 - - + -
348G ASN* 3.1 37.4 + - + +
350G LYS* 1.3 74.8 - - - +
352G LEU* 1.3 62.6 + - + +
354G ASP* 3.3 6.5 + - - +
355G LEU* 2.9 36.8 + - + +
2H LEU* 4.3 13.2 - - + -
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Residues in contact with LEU 352 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339E LEU* 4.5 15.7 - - + -
352E LEU* 3.8 28.7 - - + -
355E LEU* 4.6 7.9 - - + -
19G PHE* 3.8 21.5 - - + -
339G LEU* 4.1 16.8 - - + +
340G MET* 4.1 18.4 - - + -
343G ALA* 3.8 16.6 - - + -
348G ASN 3.3 7.4 + - - +
349G ASP 3.1 6.6 + - - +
351G VAL* 1.3 81.4 - - - +
353G ARG* 1.3 64.1 + - - +
355G LEU* 3.1 13.9 + - + +
356G MET* 2.9 37.6 + - + +
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Residues in contact with ARG 353 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ASP* 2.6 47.5 + - - +
17G MET 3.2 21.1 + - - +
18G THR* 4.5 3.3 - - - +
19G PHE* 3.8 5.1 - - + -
305G GLN* 3.2 28.5 - - + +
306G CYS* 4.6 2.0 - - - -
349G ASP 2.8 21.6 + - - +
350G LYS* 3.3 30.9 + - - +
352G LEU* 1.3 72.5 - - - +
354G ASP* 1.3 105.2 + - - +
356G MET* 3.0 16.6 + - - +
357G MET* 3.1 22.0 + - - +
372G TYR* 2.9 34.4 + - + -
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Residues in contact with ASP 354 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ASP* 5.2 0.2 - - - +
350G LYS 3.0 22.4 + - - +
351G VAL* 3.3 6.7 + - - +
353G ARG* 1.3 89.7 + - - +
355G LEU* 1.3 51.5 - - - +
357G MET* 3.5 8.6 + - + +
358G LEU* 2.8 37.2 + - - +
372G TYR* 2.5 31.0 + - - -
1H MET* 3.3 24.3 - - + +
2H LEU* 3.8 26.0 + - + +
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Residues in contact with LEU 355 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E LEU* 3.8 14.8 - - + -
342E THR* 3.6 25.0 - - + +
343E ALA* 3.9 17.3 - - + +
346E THR* 3.6 23.6 - - - +
348E ASN* 4.1 20.2 - - + +
351E VAL* 5.3 1.6 - - + -
352E LEU* 5.0 8.1 - - + -
351G VAL* 2.9 30.0 + - + +
352G LEU* 3.1 18.8 + - + +
354G ASP* 1.3 73.0 - - - +
356G MET* 1.3 60.7 + - - +
358G LEU* 3.3 0.6 + - + -
359G SER* 2.9 32.4 + - - -
2H LEU* 3.7 14.8 - - + -
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Residues in contact with MET 356 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E LEU* 3.6 21.3 - - + +
19G PHE* 3.3 23.1 - - + -
301G ASN* 3.4 19.1 - - - +
302G LEU* 3.5 14.6 + - - -
304G MET* 3.5 37.7 - - + +
305G GLN* 3.8 9.4 - - - +
340G MET* 4.7 4.3 - - - +
352G LEU* 2.9 25.9 + - + +
353G ARG* 3.0 39.9 - - - +
355G LEU* 1.3 77.1 - - - +
357G MET* 1.3 66.6 + - - +
359G SER* 3.3 13.0 + - - -
360G ASP 3.6 0.9 + - - -
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Residues in contact with MET 357 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302G LEU* 3.5 18.8 - - + +
305G GLN* 3.4 23.9 - - - +
353G ARG 3.1 13.9 + - - +
354G ASP* 3.7 11.7 - - + +
356G MET* 1.3 77.2 - - - +
358G LEU* 1.3 67.0 + - + +
360G ASP 3.0 4.7 + - - -
361G ARG* 2.9 61.8 + - - +
371G ALA* 3.5 16.8 - - + -
372G TYR* 4.1 14.1 - - + -
1H MET* 3.8 32.1 - - + -
2H LEU 4.0 11.7 - - - +
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Residues in contact with LEU 358 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E THR* 3.9 6.7 - - + -
346E THR* 3.8 13.9 - - + -
354G ASP 2.8 22.1 + - - +
355G LEU 3.9 2.5 - - - +
357G MET* 1.3 85.4 - - + +
359G SER* 1.3 63.3 + - - +
360G ASP 3.1 0.9 + - - -
361G ARG* 3.4 12.7 + - + +
362G TYR* 3.9 9.8 + - + -
2H LEU* 4.2 8.3 - - + +
3H ASP* 3.6 55.2 - - - +
4H PHE* 3.7 45.2 - - + -
13H LEU* 5.7 0.2 - - - +
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Residues in contact with SER 359 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E ALA* 4.1 10.1 - - - +
339E LEU* 4.3 4.9 - - - -
342E THR* 3.3 24.5 + - - -
301G ASN* 3.3 20.9 + - - -
355G LEU 2.9 13.8 + - - -
356G MET* 3.4 10.8 - - - -
357G MET 3.2 0.2 + - - -
358G LEU* 1.3 76.6 - - - +
360G ASP* 1.3 70.8 + - - +
363G ARG* 3.3 18.5 + - - -
4H PHE* 4.8 1.3 - - - -
12H VAL* 4.4 4.5 - - - +
13H LEU* 3.7 13.5 - - - +
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Residues in contact with ASP 360 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335E TYR* 3.4 7.5 - - - -
298G VAL 4.4 0.7 - - - +
299G MET* 4.0 7.9 - - - -
300G GLY 3.1 8.6 + - - -
301G ASN* 2.7 32.2 + - - -
302G LEU* 3.0 28.4 + - + -
356G MET 3.6 0.4 + - - -
357G MET 3.0 3.4 + - - -
359G SER* 1.3 84.3 + - - +
361G ARG* 1.3 66.8 + - - +
362G TYR 2.9 5.0 + - - -
363G ARG* 2.8 55.0 + - - +
367G ALA* 3.4 8.6 - - + +
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Residues in contact with ARG 361 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302G LEU* 4.0 9.6 - - + -
357G MET* 2.9 42.8 + - - +
358G LEU* 3.4 10.7 + - - +
360G ASP* 1.3 76.6 - - - +
362G TYR* 1.3 91.1 + - + +
363G ARG 3.8 0.2 + - - -
364G ASP 3.9 0.3 - - - +
368G TYR* 3.2 59.8 + - + +
371G ALA* 3.9 2.4 - - + +
373G ASP* 2.5 47.4 + - - -
374G ASN* 3.4 18.2 + - - +
1H MET* 3.6 17.3 - - - -
2H LEU 5.5 0.6 + - - -
3H ASP* 4.3 4.8 + - - -
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Residues in contact with TYR 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358G LEU* 3.9 10.2 + - + -
360G ASP 3.1 0.6 - - - -
361G ARG* 1.3 95.4 + - + +
363G ARG* 1.3 62.7 + - - +
364G ASP 3.2 3.8 + - - -
368G TYR* 3.9 24.9 + + - -
407G GLY 5.5 0.2 - - - -
411G LYS* 3.6 35.3 + - + +
412G LEU* 3.6 34.1 - - + +
413G GLU* 4.9 1.4 + - - +
3H ASP* 2.4 40.1 + - - -
4H PHE* 4.0 15.3 - + - -
9H LEU* 3.8 31.8 - - + +
13H LEU* 4.0 9.4 - - + +
15H ARG* 3.6 15.6 - - - -
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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
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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