Contacts of the helix formed by residues 348 - 361 (chain M) 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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343M ALA* 2.6 15.2 + - - +
346M THR* 3.2 29.4 + - - +
347M LYS* 1.3 79.7 + - - +
349M ASP* 1.3 61.2 + - - +
350M LYS 3.3 2.9 - - - -
351M VAL* 3.2 29.2 - - + +
352M LEU* 3.3 8.7 + - - +
351O VAL* 3.6 21.9 - - + +
355O LEU* 4.0 16.7 - - + +
2P LEU* 3.5 19.5 - - - +
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Residues in contact with ASP 349 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M THR* 2.6 34.3 + - - +
19M PHE* 3.5 34.8 - - + -
343M ALA* 3.3 6.5 + - - +
344M LEU* 3.7 22.9 - - + +
347M LYS* 3.9 8.8 - - - +
348M ASN* 1.3 83.3 + - - +
350M LYS* 1.3 62.2 + - - +
352M LEU 3.2 0.5 + - - -
353M ARG* 2.7 37.4 + - - +
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Residues in contact with LYS 350 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M ASP* 3.1 38.4 + - - +
16M GLU* 4.4 13.5 + - - +
17M MET 5.0 1.6 - - - -
18M THR* 4.5 5.6 - - - +
347M LYS 5.4 0.4 + - - -
348M ASN* 3.3 0.8 - - - +
349M ASP* 1.3 93.7 + - - +
351M VAL* 1.3 62.0 + - - +
353M ARG* 3.3 31.1 + - - +
354M ASP* 3.0 29.1 + - - -
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Residues in contact with VAL 351 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348M ASN* 3.2 35.1 + - + +
350M LYS* 1.3 77.0 - - - +
352M LEU* 1.3 58.8 + - + +
354M ASP* 3.2 8.9 + - - +
355M LEU* 2.9 32.5 + - + +
2N LEU* 4.5 9.2 - - + -
348O ASN* 3.5 39.5 - - + +
351O VAL* 4.3 15.5 - - + -
355O LEU* 5.5 1.8 - - + -
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Residues in contact with LEU 352 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M PHE* 3.8 15.9 - - + -
339M LEU* 4.2 23.3 - - + +
340M MET* 4.3 8.1 - - + -
343M ALA* 3.7 23.8 - - + -
348M ASN 3.3 8.9 + - - +
349M ASP 3.2 6.6 + - - +
350M LYS 3.2 0.4 - - - -
351M VAL* 1.3 79.5 - - + +
353M ARG* 1.3 64.8 + - - +
355M LEU* 3.1 12.1 + - + +
356M MET* 2.9 39.2 + - + +
339O LEU* 4.5 15.0 - - + -
352O LEU* 4.0 25.1 - - + -
355O LEU* 4.4 9.6 - - + -
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Residues in contact with ARG 353 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ALA 4.3 0.2 + - - -
15M ASP* 2.6 51.1 + - - +
17M MET 3.2 22.0 + - - +
18M THR* 4.4 3.3 - - - +
19M PHE* 4.1 3.4 - - + -
305M GLN* 3.3 27.4 - - - +
306M CYS* 4.6 0.9 - - - -
349M ASP 2.7 21.3 + - - +
350M LYS* 3.4 30.1 + - - +
352M LEU* 1.3 71.6 - - - +
354M ASP* 1.3 100.2 + - - +
356M MET* 2.8 18.4 + - + +
357M MET* 3.0 28.2 + - - +
372M TYR* 2.9 33.6 + - + -
1N MET* 5.2 0.8 - - - +
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Residues in contact with ASP 354 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350M LYS 3.0 16.0 + - - +
351M VAL* 3.6 9.6 - - - +
353M ARG* 1.3 91.6 + - - +
355M LEU* 1.3 61.3 + - - +
357M MET* 3.6 9.4 - - + +
358M LEU* 2.8 33.6 + - - +
372M TYR* 2.4 30.2 + - - -
1N MET* 3.3 26.8 + - - -
2N LEU* 3.7 24.6 + - + +
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Residues in contact with LEU 355 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351M VAL* 2.9 20.7 + - + +
352M LEU* 3.1 22.9 + - + +
354M ASP* 1.3 78.1 - - - +
356M MET* 1.3 61.2 + - - +
359M SER* 3.1 22.2 + - - -
2N LEU* 3.4 27.4 - - + -
339O LEU* 3.9 15.5 - - + +
342O THR* 3.5 16.7 - - + +
343O ALA* 4.0 26.9 - - + +
346O THR* 3.5 17.3 - - - +
348O ASN* 4.1 22.0 - - + +
351O VAL* 5.3 1.6 - - + -
352O LEU* 4.7 9.4 - - + -
355O LEU* 6.6 0.2 - - + -
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Residues in contact with MET 356 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PHE* 3.5 23.6 - - + -
301M ASN* 3.5 18.8 - - + +
302M LEU* 3.2 18.2 + - - +
304M MET* 3.6 36.1 - - + +
305M GLN* 3.6 12.1 - - - +
340M MET* 4.8 5.2 - - - -
352M LEU* 2.9 22.0 + - + +
353M ARG* 2.8 41.5 - - - +
355M LEU* 1.3 72.1 - - - +
357M MET* 1.3 66.8 + - - +
359M SER* 3.3 13.3 - - - -
360M ASP 3.9 0.2 + - - -
339O LEU* 3.8 22.0 - - + -
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Residues in contact with MET 357 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302M LEU* 3.5 14.9 - - - +
305M GLN* 3.4 27.5 - - - +
353M ARG 3.0 14.5 + - - +
354M ASP* 3.6 22.9 - - + +
356M MET* 1.3 79.2 - - - +
358M LEU* 1.3 64.5 - - + +
360M ASP 3.2 1.6 + - - -
361M ARG* 3.0 54.1 + - - +
371M ALA* 3.6 16.4 - - + -
372M TYR* 4.1 14.4 - - + -
373M ASP* 4.9 0.4 - - - +
1N MET* 3.9 25.8 - - - -
2N LEU 3.9 14.8 - - - +
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Residues in contact with LEU 358 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354M ASP 2.8 22.6 + - - +
357M MET* 1.3 78.8 - - + +
359M SER* 1.3 66.7 + - - +
360M ASP 3.2 0.9 + - - -
361M ARG* 3.5 12.5 + - + +
362M TYR* 4.1 10.3 + - + -
2N LEU* 3.8 14.8 - - + +
3N ASP* 3.7 38.1 - - - +
4N PHE* 3.4 39.1 - - + +
13N LEU* 5.7 0.2 - - - +
342O THR* 3.8 9.4 - - + -
346O THR* 3.6 31.0 - - + -
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Residues in contact with SER 359 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301M ASN* 3.1 25.1 + - - -
355M LEU 3.1 13.0 + - - -
356M MET* 3.3 14.1 - - - -
358M LEU* 1.3 76.1 - - - +
360M ASP* 1.3 73.5 + - - +
363M ARG* 3.7 4.2 + - - -
4N PHE* 4.9 0.6 - - - -
12N VAL* 4.3 6.2 - - - +
13N LEU* 3.6 19.2 - - - +
338O ALA* 3.6 14.6 - - - +
339O LEU* 4.6 2.0 - - - -
342O THR* 3.4 20.6 + - - -
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Residues in contact with ASP 360 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298M VAL 4.0 13.2 - - - +
299M MET* 3.2 5.3 - - - -
300M GLY 3.2 5.2 + - - -
301M ASN 2.8 30.3 + - - -
302M LEU* 3.0 21.2 + - + -
356M MET 3.9 0.2 + - - -
357M MET 3.2 3.8 + - - -
358M LEU 3.2 0.2 - - - -
359M SER* 1.3 91.4 + - - +
361M ARG* 1.3 68.5 + - - +
362M TYR 2.8 5.5 + - - -
363M ARG* 2.8 41.5 + - - +
367M ALA* 3.2 14.5 - - + +
335O TYR* 3.3 7.5 - - - -
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Residues in contact with ARG 361 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302M LEU* 4.3 8.5 - - - -
357M MET* 3.0 35.0 + - - +
358M LEU* 3.5 10.1 + - - +
360M ASP* 1.3 75.5 - - - +
362M TYR* 1.3 91.5 + - + +
363M ARG 3.8 0.3 + - - -
364M ASP 3.9 0.5 - - - +
368M TYR* 3.2 70.3 + - + +
371M ALA* 3.9 6.7 - - + +
373M ASP* 2.3 47.3 + - - -
374M ASN* 3.7 12.4 + - - +
1N MET* 4.1 11.1 - - - -
2N LEU 5.7 0.8 + - - -
3N ASP* 4.6 4.3 - - - -
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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