Contacts of the helix formed by residues 348 - 362 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A VAL* 3.5 22.6 - - - +
355A LEU* 4.1 17.0 - - + +
2B LEU* 3.8 16.3 - - - +
343C ALA* 2.8 11.6 + - - +
346C THR* 2.9 32.8 + - - +
347C LYS* 1.3 79.5 + - - +
349C ASP* 1.3 64.0 + - - +
350C LYS 3.3 3.4 - - - +
351C VAL* 3.2 27.1 - - + +
352C LEU* 3.4 8.8 + - - +
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Residues in contact with ASP 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C THR* 2.8 37.3 + - - +
19C PHE* 3.6 29.1 - - + -
343C ALA* 3.2 6.9 + - - +
344C LEU* 3.8 24.7 - - + +
347C LYS* 3.5 18.0 - - - +
348C ASN* 1.3 77.2 - - - +
350C LYS* 1.3 64.4 + - - +
352C LEU 3.2 1.7 + - - -
353C ARG* 2.7 35.3 + - - +
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Residues in contact with LYS 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASP* 2.8 40.8 + - - +
16C GLU* 3.9 15.3 + - - +
17C MET 4.9 1.1 - - - -
18C THR* 4.7 5.2 - - - +
347C LYS 5.5 0.2 + - - -
348C ASN 3.3 1.2 - - - -
349C ASP* 1.3 90.8 - - - +
351C VAL* 1.3 56.8 + - - +
353C ARG* 3.4 31.6 - - - +
354C ASP* 3.0 32.5 + - - -
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Residues in contact with VAL 351 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ASN* 3.6 36.6 - - + +
351A VAL* 4.6 14.1 - - + -
355A LEU* 5.3 2.0 - - + -
348C ASN* 3.2 31.8 + - + +
350C LYS* 1.3 74.4 - - - +
352C LEU* 1.3 66.6 + - + +
354C ASP* 3.0 7.7 + - - +
355C LEU* 2.8 36.0 + - + +
2D LEU* 4.3 9.4 - - + -
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Residues in contact with LEU 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 4.3 21.3 - - + -
352A LEU* 3.9 24.0 - - + -
355A LEU* 4.7 7.6 - - + -
19C PHE* 3.8 13.0 - - + -
339C LEU* 4.2 26.9 - - + +
340C MET* 4.2 7.6 - - + -
343C ALA* 3.7 23.1 - - + -
348C ASN 3.8 8.5 - - - +
349C ASP 3.2 7.9 + - - +
351C VAL* 1.3 80.3 - - + +
353C ARG* 1.3 65.2 + - - +
355C LEU* 3.1 12.1 + - + +
356C MET* 2.9 39.2 + - + +
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Residues in contact with ARG 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA 4.1 0.8 + - - -
15C ASP* 2.7 49.3 + - - +
17C MET 2.8 24.2 + - - +
18C THR* 4.5 3.3 - - - +
19C PHE* 4.1 3.6 - - + -
305C GLN* 3.3 30.7 - - + +
306C CYS* 4.6 1.1 - - - -
349C ASP 2.7 21.3 + - - +
350C LYS* 3.4 31.9 + - - +
352C LEU* 1.3 72.5 - - - +
354C ASP* 1.3 98.3 + - - +
356C MET* 3.2 17.2 + - + +
357C MET* 3.0 21.3 + - - +
372C TYR* 3.1 30.2 + - + -
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Residues in contact with ASP 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350C LYS 3.0 15.7 + - - +
351C VAL* 3.0 9.3 + - - +
353C ARG* 1.3 95.9 + - - +
355C LEU* 1.3 57.3 + - - +
357C MET* 3.3 8.3 + - + +
358C LEU* 2.8 32.7 + - - +
372C TYR* 2.5 27.6 + - - -
1D MET* 3.1 29.9 - - - -
2D LEU* 3.4 25.0 + - + +
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Residues in contact with LEU 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A LEU* 3.9 16.1 - - + +
342A THR* 3.7 16.2 - - + +
343A ALA* 3.9 26.2 - - + +
346A THR* 3.4 18.2 - - - +
348A ASN* 4.2 12.1 - - + +
351A VAL* 5.5 1.3 - - + -
352A LEU* 4.9 11.0 - - + -
351C VAL* 2.8 36.9 + - + +
352C LEU* 3.4 18.2 - - + +
354C ASP* 1.3 72.6 - - - +
356C MET* 1.3 64.1 + - - +
359C SER* 3.0 25.1 + - - -
2D LEU* 3.4 23.6 - - + -
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Residues in contact with MET 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 3.9 21.3 - - + -
19C PHE* 3.4 20.9 - - + -
301C ASN* 3.4 17.7 - - - +
302C LEU* 3.3 18.7 + - - -
304C MET* 3.5 30.1 - - + +
305C GLN* 3.2 25.8 - - - +
340C MET* 4.6 6.1 - - - -
352C LEU* 2.9 25.1 + - + +
353C ARG* 3.2 28.5 - - - +
355C LEU* 1.3 73.0 - - - +
357C MET* 1.3 67.4 + - - +
359C SER* 3.3 12.3 - - - -
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Residues in contact with MET 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C LEU* 3.5 11.5 - - + +
305C GLN* 3.3 28.2 - - - +
353C ARG 3.0 15.2 + - - +
354C ASP* 3.3 12.1 + - + +
356C MET* 1.3 78.5 - - - +
358C LEU* 1.3 69.9 + - + +
360C ASP 3.2 4.0 + - - -
361C ARG* 3.0 53.5 + - - +
371C ALA* 3.5 17.7 - - + -
372C TYR* 4.1 17.5 - - + -
1D MET* 3.7 29.6 - - + -
2D LEU 4.0 13.7 - - - +
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Residues in contact with LEU 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A THR* 3.9 8.5 - - + -
346A THR* 3.8 8.7 - - + -
354C ASP 2.8 17.5 + - - +
357C MET* 1.3 82.5 - - + +
359C SER* 1.3 66.1 + - - +
360C ASP 3.0 3.2 + - - -
361C ARG* 3.4 15.1 + - + +
362C TYR* 3.9 11.0 + - + -
2D LEU* 3.8 18.8 - - + +
3D ASP* 3.6 47.3 - - - +
4D PHE* 3.5 48.5 - - + +
13D LEU* 5.5 0.2 - - - +
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Residues in contact with SER 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ALA* 4.0 12.7 - - - +
339A LEU* 4.7 2.2 - - - -
342A THR* 3.4 20.4 + - - -
301C ASN* 3.0 25.9 + - - +
355C LEU 3.0 13.6 + - - -
356C MET* 3.3 15.3 - - - -
358C LEU* 1.3 75.4 - - - +
360C ASP* 1.3 70.9 + - - -
363C ARG* 3.3 16.6 + - - -
4D PHE* 5.0 0.4 - - - -
12D VAL* 4.4 5.1 - - - +
13D LEU* 3.7 12.3 - - - +
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Residues in contact with ASP 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A TYR* 3.3 11.3 - - - -
298C VAL 4.1 10.5 - - - +
299C MET* 3.2 8.2 - - - -
301C ASN* 2.7 14.9 + - - -
302C LEU* 2.7 41.3 + - + -
357C MET 3.2 2.8 + - - -
358C LEU 3.0 0.4 - - - -
359C SER* 1.3 92.0 + - - +
361C ARG* 1.3 68.8 + - - +
362C TYR 2.7 5.4 + - - -
363C ARG* 2.9 36.9 + - - +
367C ALA* 3.2 16.2 - - + +
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Residues in contact with ARG 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C LEU* 4.3 7.9 - - - -
357C MET* 3.0 33.8 + - - +
358C LEU* 3.4 8.9 + - - +
360C ASP* 1.3 75.8 - - - +
362C TYR* 1.3 91.6 + - + +
363C ARG 3.8 0.3 + - - -
364C ASP 4.1 0.9 - - - +
368C TYR* 3.2 65.9 + - + +
371C ALA* 3.7 7.8 - - + +
373C ASP* 2.6 44.9 + - - -
374C ASN* 3.4 20.6 + - - +
412C LEU* 4.4 0.3 - - - +
1D MET* 3.7 14.5 - - - -
2D LEU 5.6 0.8 + - - -
3D ASP* 4.7 3.6 - - - -
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Residues in contact with TYR 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358C LEU* 3.9 10.5 + - + -
360C ASP 2.7 4.9 + - - -
361C ARG* 1.3 100.4 + - + +
363C ARG* 1.3 60.9 + - - +
364C ASP 3.4 2.5 - - - -
368C TYR* 4.1 14.6 + + - -
407C GLY* 5.5 0.4 - - - -
411C LYS* 3.5 43.0 + - + +
412C LEU* 3.6 34.4 - - + +
413C GLU* 5.0 1.9 + - - +
3D ASP* 2.7 30.7 + - - -
4D PHE* 4.0 20.6 - + - -
9D LEU* 3.8 27.7 - - + +
13D LEU* 3.9 10.4 - - + +
15D ARG* 3.5 15.2 - - - +
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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