Contacts of the helix formed by residues 348 - 362 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E ALA* 2.7 19.1 + - - +
346E THR* 3.0 31.8 + - - +
347E LYS* 1.3 76.8 + - - +
349E ASP* 1.3 60.5 + - - +
350E LYS 3.4 2.5 - - - -
351E VAL* 3.1 29.7 - - + +
352E LEU* 3.2 8.5 + - - +
351G VAL* 3.8 23.9 - - - +
355G LEU* 4.1 17.3 - - + -
2H LEU* 3.6 17.2 - - - +
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Residues in contact with ASP 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E THR* 2.8 36.2 + - - +
19E PHE* 3.6 25.6 - - + -
343E ALA* 3.5 4.1 + - - -
344E LEU* 3.7 31.6 - - + +
347E LYS* 3.6 8.9 - - - +
348E ASN* 1.3 85.3 + - - +
350E LYS* 1.3 67.5 + - - +
352E LEU* 3.2 2.3 + - - +
353E ARG* 2.8 31.0 + - - +
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Residues in contact with LYS 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E ASP* 3.2 31.9 + - - +
16E GLU* 4.7 11.7 - - - +
17E MET 5.0 0.4 - - - -
18E THR* 4.5 6.7 - - - +
348E ASN 3.4 0.6 - - - -
349E ASP* 1.3 90.4 - - - +
351E VAL* 1.3 63.3 + - - +
353E ARG* 3.0 45.6 + - - +
354E ASP* 3.0 15.1 + - - +
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Residues in contact with VAL 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348E ASN* 3.1 30.6 + - + +
350E LYS* 1.3 74.3 - - - +
352E LEU* 1.3 72.7 + - + +
354E ASP* 3.1 7.9 + - - +
355E LEU* 3.1 25.9 + - + +
2F LEU* 4.7 10.3 - - + -
348G ASN* 3.7 34.3 - - + +
351G VAL* 4.3 19.5 - - + -
355G LEU* 5.3 2.0 - - + -
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Residues in contact with LEU 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E PHE* 3.8 17.5 - - + -
339E LEU* 4.2 16.8 - - + -
340E MET* 4.1 14.8 - - + -
343E ALA* 3.7 23.6 - - + -
348E ASN 3.2 9.5 + - - +
349E ASP 3.6 7.6 - - - +
351E VAL* 1.3 83.1 - - + +
353E ARG* 1.3 57.7 + - - +
355E LEU* 3.1 17.1 - - + +
356E MET* 2.9 46.0 + - + +
339G LEU* 4.6 9.2 - - + -
352G LEU* 3.8 27.1 - - + -
355G LEU* 5.0 8.7 - - + -
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Residues in contact with ARG 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ASP* 2.8 46.1 + - - +
17E MET 3.2 17.3 + - - +
18E THR* 4.6 2.7 - - - +
19E PHE* 4.4 2.0 - - + -
305E GLN* 3.3 33.8 - - + +
306E CYS* 4.6 2.2 - - - -
349E ASP 2.8 17.8 + - - +
350E LYS* 3.0 40.7 + - - +
351E VAL 3.2 0.2 - - - -
352E LEU* 1.3 77.7 - - - +
354E ASP* 1.3 102.2 + - - +
356E MET* 3.4 15.2 + - + +
357E MET* 3.0 23.2 + - - +
372E TYR* 3.4 28.3 + - + -
1F MET* 5.2 0.6 - - - +
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Residues in contact with ASP 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E LYS 3.0 9.8 + - - +
351E VAL* 3.1 5.0 + - - +
353E ARG* 1.3 99.7 + - - +
355E LEU* 1.3 53.8 + - - +
357E MET* 3.6 8.2 - - + +
358E LEU* 2.6 38.8 + - - +
372E TYR* 2.5 27.6 + - - -
1F MET* 2.7 30.5 + - - -
2F LEU* 3.1 31.5 + - + +
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Residues in contact with LEU 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351E VAL* 3.1 18.5 + - + +
352E LEU* 3.1 24.7 - - + +
354E ASP* 1.3 74.9 - - - +
356E MET* 1.3 63.9 + - - +
358E LEU 3.2 0.3 + - - -
359E SER* 2.9 24.6 + - - -
2F LEU* 3.5 24.5 - - + -
339G LEU* 4.0 12.6 - - + +
342G THR* 3.6 13.5 - - + +
343G ALA* 4.0 32.5 - - + +
346G THR* 3.7 18.6 - - - +
348G ASN* 4.1 15.3 - - + +
351G VAL* 5.4 1.8 - - + -
352G LEU* 4.6 12.6 - - + -
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Residues in contact with MET 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19E PHE* 3.2 39.7 - - + -
301E ASN* 3.7 16.3 - - - +
302E LEU* 3.4 14.9 + - - -
304E MET* 3.5 31.4 - - + +
305E GLN* 3.3 26.2 - - - +
339E LEU* 6.4 0.9 - - - -
340E MET* 4.5 6.7 - - - -
352E LEU* 2.9 29.9 + - + +
353E ARG* 3.6 9.4 - - - +
355E LEU* 1.3 70.0 - - - +
357E MET* 1.3 65.7 + - - +
359E SER* 3.0 18.7 - - - -
360E ASP 3.9 0.2 + - - -
339G LEU* 3.7 21.7 - - + +
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Residues in contact with MET 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E LEU* 3.6 16.5 - - + +
305E GLN* 3.5 22.3 - - - +
353E ARG 3.0 17.7 + - - +
354E ASP* 3.9 10.1 - - + +
356E MET* 1.3 75.7 - - - +
358E LEU* 1.3 74.1 + - - +
359E SER 3.0 1.4 + - - -
360E ASP 3.1 11.8 + - - -
361E ARG* 3.1 40.1 + - - +
371E ALA* 3.5 21.5 - - + -
372E TYR* 4.0 17.7 - - + +
1F MET* 3.7 29.8 - - - -
2F LEU 4.0 12.1 - - - +
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Residues in contact with LEU 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354E ASP 2.6 22.3 + - - +
355E LEU 3.8 2.7 - - - +
357E MET* 1.3 82.5 - - + +
359E SER* 1.3 62.2 + - - +
360E ASP 3.2 1.0 + - - -
361E ARG* 3.6 14.4 + - - +
362E TYR* 4.2 8.7 + - + -
2F LEU* 3.7 29.8 - - + +
3F ASP* 3.7 39.9 - - - +
4F PHE* 3.4 41.2 - - + +
342G THR* 3.8 6.1 - - + -
346G THR* 3.7 19.1 - - + -
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Residues in contact with SER 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301E ASN* 3.1 27.9 + - - -
355E LEU 2.9 12.2 + - - -
356E MET* 3.0 17.7 - - - -
357E MET 3.0 0.2 + - - -
358E LEU* 1.3 77.4 - - - +
360E ASP* 1.3 62.9 + - - +
363E ARG* 3.4 11.3 + - - -
4F PHE* 4.9 0.4 - - - -
12F VAL* 4.4 5.7 - - - +
13F LEU* 3.6 12.0 - - - +
338G ALA* 3.6 19.3 - - - +
339G LEU* 4.8 2.0 - - - -
342G THR* 3.4 18.1 + - - -
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Residues in contact with ASP 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E VAL 4.0 4.3 - - - +
299E MET* 3.1 16.5 - - - -
301E ASN* 2.7 33.2 + - - -
302E LEU* 2.9 23.3 + - + -
357E MET 3.1 3.2 + - - -
359E SER* 1.3 81.6 + - - +
361E ARG* 1.3 67.7 + - - +
362E TYR 3.2 3.1 - - - -
363E ARG* 2.9 46.8 + - - +
367E ALA* 3.1 16.8 - - + +
335G TYR* 3.4 9.7 - - - -
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Residues in contact with ARG 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302E LEU* 4.1 8.5 - - - +
357E MET* 3.1 38.3 + - - +
358E LEU* 3.6 12.4 + - - +
360E ASP* 1.3 77.2 - - - +
362E TYR* 1.3 91.9 + - + +
363E ARG 3.6 0.2 + - - -
364E ASP 4.0 0.5 - - - +
368E TYR* 3.2 63.7 + - + +
371E ALA* 3.5 9.6 - - + +
373E ASP* 2.5 45.4 + - - -
374E ASN* 3.5 19.3 - - - +
412E LEU* 4.1 0.2 - - - +
1F MET* 4.0 6.9 - - - -
3F ASP* 4.0 9.0 + - - -
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Residues in contact with TYR 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358E LEU* 4.2 9.1 + - + -
360E ASP 3.2 0.4 - - - -
361E ARG* 1.3 95.6 + - + +
363E ARG* 1.3 63.6 + - - +
364E ASP 3.3 2.6 + - - -
368E TYR* 3.9 17.2 + + - -
407E GLY 5.3 0.2 - - - -
411E LYS* 3.5 37.3 + - + +
412E LEU* 3.6 36.6 - - + +
413E GLU 5.2 0.7 + - - -
3F ASP* 2.6 39.1 + - - -
4F PHE* 4.0 13.7 - + - -
9F LEU* 3.7 37.2 - - + -
13F LEU* 3.9 8.5 - - + +
15F ARG* 3.6 14.7 - - - -
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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