Contacts of the helix formed by residues 348 - 364 (chain A) in PDB entry 3C3C
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 ALA 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342A PHE* 3.6 28.0 - - + +
344A TRP 3.0 12.3 + - - +
345A GLU* 3.3 14.8 + - - +
347A PHE* 1.3 76.3 - - - +
349A ARG* 1.3 64.7 + - - +
350A GLY 3.3 3.2 + - - -
351A THR* 3.4 6.2 + - - -
352A LYS* 3.2 44.8 + - - +
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Residues in contact with ARG 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ASP* 3.4 7.8 + - - +
320A SER* 5.4 0.2 - - - -
345A GLU* 3.8 34.3 + - - +
346A ALA* 3.7 25.1 + - - +
348A ALA* 1.3 78.7 - - - +
350A GLY* 1.3 52.5 + - - +
352A LYS* 3.8 7.1 - - + +
353A ALA* 2.8 36.8 + - - +
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Residues in contact with GLY 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A ASP* 3.1 22.8 + - - -
315A CYS* 4.0 20.9 + - - -
320A SER* 4.3 10.4 + - - -
323A TYR* 5.4 1.6 - - - -
339A VAL* 3.6 8.5 - - - +
348A ALA 3.4 0.2 - - - -
349A ARG* 1.3 74.2 - - - +
351A THR* 1.3 58.3 + - - +
353A ALA* 3.7 1.9 + - - +
354A LEU* 3.1 28.9 + - - +
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Residues in contact with THR 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ASP* 4.5 1.1 + - - -
335A TRP* 3.9 22.5 - - + -
338A PRO* 4.4 7.1 - - + +
339A VAL* 3.2 24.9 + - - +
340A GLY* 3.9 7.1 + - - -
342A PHE* 3.8 38.8 - - + +
348A ALA 3.4 4.1 + - - -
349A ARG 3.4 0.2 - - - -
350A GLY* 1.3 73.2 - - - +
352A LYS* 1.3 57.2 + - - +
354A LEU* 3.2 3.8 + - - +
355A MET* 2.8 40.9 + - + +
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Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A PHE* 5.6 1.6 - - + -
345A GLU* 2.4 35.4 + - - +
348A ALA* 3.2 32.5 + - + +
349A ARG* 3.8 6.7 - - + +
351A THR* 1.3 72.2 - - + +
353A ALA* 1.3 66.0 + - - +
354A LEU 3.0 2.0 + - - -
355A MET* 3.3 6.0 + - - +
356A ASP* 3.1 32.9 + - - +
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Residues in contact with ALA 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A SER* 4.2 21.5 - - - +
349A ARG 2.8 23.4 + - - +
350A GLY 3.9 4.3 - - - +
352A LYS* 1.3 73.4 - - - +
354A LEU* 1.3 61.4 + - - +
356A ASP* 3.5 10.0 + - - +
357A GLU* 3.4 25.6 + - - +
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ILE* 4.3 17.7 - - + -
234A ILE* 5.3 0.2 - - + -
320A SER 5.7 0.7 - - - +
323A TYR* 4.0 31.9 - - + -
324A ALA 5.1 0.2 - - - +
327A VAL* 3.9 26.9 - - + -
335A TRP* 3.8 21.8 - - + -
339A VAL* 3.7 30.3 - - + -
350A GLY 3.1 16.9 + - - +
351A THR 3.6 4.3 - - - +
352A LYS 3.0 0.6 - - - -
353A ALA* 1.3 75.3 - - - +
355A MET* 1.3 66.5 + - - +
356A ASP 3.1 1.6 - - - -
357A GLU* 3.1 9.1 + - + +
358A VAL* 3.1 20.7 + - + +
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Residues in contact with MET 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A TRP* 3.9 27.3 - - + -
351A THR* 2.8 25.9 + - + +
352A LYS* 3.7 7.9 - - - +
354A LEU* 1.3 74.2 - - - +
356A ASP* 1.3 60.6 + - - +
358A VAL* 3.3 4.5 + - - +
359A VAL* 2.8 37.0 + - + +
370A ILE* 3.9 33.4 - - + -
388A VAL* 5.0 9.0 - - - -
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Residues in contact with ASP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LYS* 3.2 18.3 - - - +
353A ALA* 3.6 12.3 - - - +
354A LEU 3.1 0.4 - - - -
355A MET* 1.3 82.0 - - - +
357A GLU* 1.3 57.7 + - + +
359A VAL* 3.2 8.0 + - - +
360A LYS* 2.9 45.5 + - + +
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Residues in contact with GLU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A SER 5.7 0.7 - - - +
324A ALA* 3.7 31.6 - - + +
327A VAL* 3.3 25.2 - - + +
328A THR* 5.4 2.4 + - - -
353A ALA 3.4 17.3 - - - +
354A LEU* 3.1 10.2 + - + +
356A ASP* 1.3 76.3 - - - +
358A VAL* 1.3 57.5 + - - +
360A LYS* 3.5 25.2 + - - +
361A ALA* 2.9 29.1 + - - +
364A ARG* 4.6 5.5 + - - -
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Residues in contact with VAL 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ILE* 4.3 9.0 - - + -
327A VAL* 4.2 16.8 - - + -
333A ILE* 4.3 20.0 - - + -
335A TRP* 4.3 17.0 - - + -
354A LEU* 3.1 15.7 + - + +
355A MET* 3.7 8.1 - - - +
357A GLU* 1.3 75.4 - - - +
359A VAL* 1.3 59.6 + - - +
361A ALA* 3.3 4.5 + - - +
362A THR* 2.9 29.8 + - - -
368A THR* 3.5 26.2 - - + +
370A ILE* 4.5 13.0 - - + -
388A VAL* 4.2 13.0 - - + -
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A MET* 2.8 26.9 + - + +
356A ASP* 3.6 9.4 - - - +
358A VAL* 1.3 74.3 - - - +
360A LYS* 1.3 67.6 - - + +
362A THR* 2.9 29.0 + - - -
363A SER* 3.3 10.4 + - - +
387A LYS* 3.6 52.1 - - + +
388A VAL* 4.3 9.0 - - + -
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Residues in contact with LYS 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ASP* 2.9 27.1 + - + +
357A GLU* 3.8 29.8 + - - +
359A VAL* 1.3 82.4 - - + +
361A ALA* 1.3 61.4 + - - +
363A SER* 3.3 22.8 + - - -
364A ARG* 3.5 25.2 + - - +
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Residues in contact with ALA 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A VAL* 4.0 12.8 - - + +
330A ALA 5.6 0.4 - - - +
333A ILE* 4.7 0.7 - - + -
357A GLU 2.9 18.3 + - - +
358A VAL* 3.5 7.6 - - - +
359A VAL 3.2 0.2 - - - -
360A LYS* 1.3 75.2 - - - +
362A THR* 1.3 65.1 + - - +
364A ARG* 3.2 34.4 + - - +
365A GLY 3.5 0.2 + - - -
366A CYS* 3.2 41.9 + - + +
368A THR* 4.7 1.3 - - + -
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Residues in contact with THR 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A VAL 2.9 14.3 + - - -
359A VAL 2.9 11.6 + - - -
361A ALA* 1.3 77.2 - - - +
363A SER* 1.3 58.9 + - - +
365A GLY* 3.2 13.0 + - - -
366A CYS* 3.7 14.9 - - - +
368A THR* 2.8 27.9 + - - +
387A LYS 3.5 20.4 + - - +
388A VAL* 3.8 8.5 - - - -
389A SER* 4.0 8.5 - - - +
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Residues in contact with SER 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A VAL* 3.3 10.3 + - - +
360A LYS* 3.3 15.5 + - - -
361A ALA 3.2 0.4 - - - -
362A THR* 1.3 77.8 - - - +
364A ARG* 1.3 61.7 + - - +
365A GLY 3.3 0.4 + - - -
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Residues in contact with ARG 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A VAL* 4.2 2.8 + - - +
328A THR* 3.9 36.4 + - - +
330A ALA 5.9 0.4 + - - -
357A GLU* 4.6 6.1 + - - -
360A LYS* 3.5 29.3 + - - +
361A ALA* 3.2 33.5 + - - +
363A SER* 1.3 78.5 - - - +
365A GLY* 1.3 57.7 + - - +
366A CYS* 3.7 1.3 - - + +
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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
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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