Contacts of the helix formed by residues 350 - 370 (chain A) in PDB entry 3SF4
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 ASP 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A HIS* 5.7 0.7 + - - -
345A SER* 2.7 24.6 + - - +
346A ARG* 5.8 0.2 - - - -
348A VAL* 3.4 14.5 - - + +
349A GLY* 1.3 71.2 - - - +
351A LYS* 1.3 66.1 + - - +
352A SER* 3.2 11.5 + - - -
353A GLY* 3.1 25.1 + - - -
354A GLU* 3.1 23.4 + - - +
30D ARG* 5.6 4.2 + - - -
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A GLY* 3.5 12.4 + - - +
350A ASP* 1.3 73.5 + - - +
352A SER* 1.3 66.1 + - - +
354A GLU* 3.1 29.1 + - - +
355A LEU* 3.1 15.0 + - - +
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP* 3.2 10.1 + - - -
351A LYS* 1.3 76.7 - - - +
353A GLY* 1.3 60.6 + - - +
355A LEU* 3.3 6.4 + - - +
356A THR* 2.9 37.6 + - - +
30D ARG* 4.5 17.6 + - - -
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Residues in contact with GLY 353 (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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341A HIS* 3.7 8.2 - - - -
345A SER* 3.6 14.8 - - - -
350A ASP* 3.1 16.5 + - - -
352A SER* 1.3 80.1 + - - +
354A GLU* 1.3 60.0 + - - +
356A THR* 3.2 8.9 + - - -
357A ALA* 2.8 34.8 + - - +
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Residues in contact with GLU 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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342A LEU* 3.6 12.3 - - + +
345A SER* 3.6 10.0 - - - -
346A ARG* 3.3 48.1 + - + +
350A ASP 3.1 15.0 + - - +
351A LYS* 3.1 29.2 + - - +
353A GLY* 1.3 74.2 - - - +
355A LEU* 1.3 59.1 + - - +
358A ARG* 2.9 33.8 + - + +
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Residues in contact with LEU 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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351A LYS 3.1 8.6 + - - +
352A SER* 3.7 8.7 - - - +
354A GLU* 1.3 82.0 - - - +
356A THR* 1.3 61.0 + - + +
358A ARG* 3.1 15.2 + - + +
359A LEU* 2.7 49.0 + - + +
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Residues in contact with THR 356 (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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319A TRP* 4.5 11.3 + - + -
341A HIS* 3.7 13.2 - - - -
352A SER* 2.9 21.1 + - - +
353A GLY* 3.2 9.8 + - - -
355A LEU* 1.3 74.3 - - + +
357A ALA* 1.3 64.2 + - - +
359A LEU* 3.2 13.5 + - + +
360A ASN* 2.8 39.8 + - - -
26D ASP* 4.9 9.6 - - - +
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Residues in contact with ALA 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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338A ALA* 3.9 5.8 - - - +
341A HIS* 3.3 24.0 - - + +
342A LEU* 3.4 35.7 - - + +
353A GLY 2.8 21.9 + - - +
354A GLU 3.7 1.3 - - - +
356A THR* 1.3 73.1 + - - +
358A ARG* 1.3 62.0 + - - +
360A ASN* 3.3 8.8 + - - +
361A LEU* 3.0 27.0 + - - +
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Residues in contact with ARG 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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342A LEU* 4.5 18.6 - - - +
346A ARG* 5.4 4.9 - - - +
354A GLU* 2.9 18.7 + - + +
355A LEU* 3.1 20.9 - - + +
357A ALA* 1.3 76.9 - - - +
359A LEU* 1.3 64.4 + - + +
361A LEU* 3.0 29.8 + - - +
362A SER* 3.1 17.9 + - - +
365A GLN* 4.1 16.4 + - - -
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Residues in contact with LEU 359 (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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355A LEU* 2.7 48.1 + - + +
356A THR* 3.7 11.0 - - + +
358A ARG* 1.3 74.1 - - + +
360A ASN* 1.3 62.5 + - - +
362A SER* 3.4 9.4 + - - +
363A ASP* 3.2 25.3 + - - +
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Residues in contact with ASN 360 (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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319A TRP* 4.7 16.2 - - - +
323A ASN* 4.6 15.3 + - - +
338A ALA* 4.3 13.6 - - + +
341A HIS* 5.1 1.6 + - - -
356A THR* 2.8 27.9 + - - +
357A ALA* 3.6 8.8 - - - +
359A LEU* 1.3 74.9 - - - +
361A LEU* 1.3 60.1 + - - +
363A ASP* 3.9 5.0 - - - +
364A LEU* 3.1 40.3 + - + +
24D GLN* 5.1 5.9 - - - +
26D ASP* 4.8 4.0 + - - -
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Residues in contact with LEU 361 (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 MET* 3.5 43.3 - - + +
338A ALA* 3.9 12.6 - - + +
339A GLU* 3.8 33.4 - - + -
342A LEU* 4.5 15.3 - - + -
357A ALA 3.0 14.5 + - - +
358A ARG* 3.0 25.2 + - - +
360A ASN* 1.3 74.7 - - - +
362A SER* 1.3 60.5 + - - +
364A LEU* 3.3 4.1 + - - +
365A GLN* 2.9 38.2 + - + +
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Residues in contact with SER 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 ARG* 3.1 25.7 + - - +
359A LEU* 3.4 14.7 + - - +
361A LEU* 1.3 77.7 - - - +
363A ASP* 1.3 59.8 + - - +
365A GLN* 3.2 16.8 + - - +
366A MET* 2.8 37.2 + - - +
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Residues in contact with ASP 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 LEU 3.2 21.9 + - - +
360A ASN* 3.9 6.8 - - - +
362A SER* 1.3 77.4 + - - +
364A LEU* 1.3 60.5 + - - +
366A MET* 3.0 13.3 + - - +
367A VAL* 2.8 42.3 + - - +
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Residues in contact with LEU 364 (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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326A THR* 4.1 17.3 - - + +
331A HIS* 2.8 41.6 + - + +
334A ALA* 3.7 24.9 - - + +
335A MET* 3.6 42.2 - - - +
338A ALA* 4.2 7.0 - - + -
360A ASN* 3.1 32.7 + - + +
361A LEU 3.7 0.2 - - - +
363A ASP* 1.3 79.1 - - + +
365A GLN* 1.3 63.0 + - - +
367A VAL* 3.4 10.2 + - + +
368A LEU 3.1 9.9 + - - -
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Residues in contact with GLN 365 (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 MET* 4.0 25.0 - - + +
358A ARG* 4.1 12.8 + - - -
361A LEU* 2.9 25.2 + - - +
362A SER* 3.5 20.5 - - - +
364A LEU* 1.3 73.2 - - - +
366A MET* 1.3 64.1 + - + +
368A LEU* 3.5 7.0 + - - +
369A GLY* 3.0 26.5 + - - -
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Residues in contact with MET 366 (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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362A SER* 2.8 21.9 + - - +
363A ASP* 3.0 16.8 + - - +
365A GLN* 1.3 78.0 - - + +
367A VAL* 1.3 67.4 + - + +
368A LEU 3.2 0.2 + - - -
369A GLY* 5.2 0.2 - - - -
370A LEU* 2.9 55.7 + - + +
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Residues in contact with VAL 367 (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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331A HIS* 4.3 16.2 - - + +
363A ASP* 2.8 30.9 + - - +
364A LEU* 3.6 15.5 - - + +
366A MET* 1.3 76.8 - - + +
368A LEU* 1.3 55.9 + - - +
370A LEU* 4.2 4.1 - - - +
371A SER* 2.6 36.2 + - - +
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Residues in contact with LEU 368 (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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331A HIS* 3.5 34.8 - - + +
335A MET* 5.9 2.5 - - + -
364A LEU 3.1 9.5 + - - +
365A GLN* 3.8 7.2 - - - +
366A MET 3.1 0.2 - - - -
367A VAL* 1.3 75.6 - - - +
369A GLY* 1.3 68.2 + - - +
371A SER* 3.0 22.2 + - - -
372A TYR* 3.4 31.7 - - + +
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Residues in contact with GLY 369 (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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365A GLN 3.0 16.7 + - - -
366A MET* 3.9 0.7 - - - -
368A LEU* 1.3 79.2 - - - +
370A LEU* 1.3 63.6 + - - +
371A SER 3.2 0.7 + - - -
372A TYR* 3.6 21.1 + - - +
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Residues in contact with LEU 370 (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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366A MET* 2.9 44.9 + - + +
367A VAL* 4.5 3.4 - - - +
369A GLY* 1.3 75.7 - - - +
371A SER* 1.3 57.1 + - - +
372A TYR 3.0 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
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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