Contacts of the helix formed by residues 369 - 388 (chain A) in PDB entry 3SRF
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 TYR 369 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A MET* 3.8 16.4 + - + +
335A LYS 4.2 4.0 - - - -
336A LYS* 3.5 26.7 - - - +
337A PRO* 3.5 39.1 - - + +
363A GLU 3.8 5.1 - - - +
367A GLY 3.3 0.2 - - - -
368A ASP* 1.3 101.8 - - + +
370A PRO* 1.3 64.1 - - - +
371A LEU 3.5 1.8 - - - -
372A GLU* 3.4 37.5 - - + +
373A ALA* 3.3 21.3 + - - +
135B LYS* 5.8 6.3 - - - -
199B GLY 5.0 6.6 + - - -
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Residues in contact with PRO 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA* 3.8 24.7 - - + +
59A THR* 5.2 4.9 - - + -
63A MET* 4.7 12.8 - - + -
363A GLU 3.5 10.1 - - - +
364A THR* 3.9 26.1 - - + +
367A GLY 4.0 11.7 - - - +
368A ASP 3.7 5.8 - - - +
369A TYR* 1.3 86.9 - - - +
371A LEU* 1.3 73.1 + - + +
372A GLU* 4.7 1.1 - - - +
373A ALA* 3.3 3.6 + - + +
374A VAL* 3.3 28.0 + - - +
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Residues in contact with LEU 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A THR* 4.4 9.4 - - + +
62A GLU* 3.7 39.3 - - + +
63A MET* 3.8 17.0 - - + -
66A SER* 3.5 17.6 + - - +
370A PRO* 1.3 83.8 - - + +
372A GLU* 1.3 68.8 + - - +
374A VAL* 3.3 5.9 + - - +
375A ARG* 3.1 54.2 + - - +
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Residues in contact with GLU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A MET* 3.5 18.3 - - + +
337A PRO* 4.2 11.6 - - + +
369A TYR* 3.4 41.7 - - + +
370A PRO* 3.4 1.1 - - - +
371A LEU* 1.3 83.2 + - - +
373A ALA* 1.3 56.8 + - - +
375A ARG* 4.0 17.4 + - - +
376A MET* 3.0 31.9 + - - +
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Residues in contact with ALA 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 3.5 12.6 - - + +
333A MET* 3.6 17.2 - - + +
360A LEU* 3.6 22.9 - - + +
363A GLU* 4.0 23.1 - - + +
364A THR* 4.5 0.4 - - + -
369A TYR 3.3 19.8 + - - +
370A PRO 3.5 6.5 - - - +
371A LEU 3.2 0.6 - - - -
372A GLU* 1.3 76.8 - - - +
374A VAL* 1.3 61.1 + - - +
377A GLN* 3.4 16.1 + - - +
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Residues in contact with VAL 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 3.7 12.6 - - + +
48A CYS* 3.7 24.2 - - - -
63A MET* 3.8 14.4 - - + +
66A SER* 3.7 11.7 - - - +
67A GLY* 3.6 31.2 - - - +
68A MET 3.8 10.8 - - - +
360A LEU* 4.0 10.5 - - + -
364A THR* 4.2 0.2 - - + -
370A PRO 3.3 15.8 + - - +
371A LEU* 3.3 6.0 + - - +
373A ALA* 1.3 74.8 - - - +
375A ARG* 1.3 59.2 + - - +
377A GLN* 3.3 5.1 + - - +
378A HIS* 2.9 27.2 + - - +
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Residues in contact with ARG 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLU* 4.6 10.5 + - - -
66A SER* 3.1 36.7 + - - +
371A LEU* 3.1 45.7 + - - +
372A GLU* 4.2 16.5 + - - +
374A VAL* 1.3 75.2 - - - +
376A MET* 1.3 58.4 - - - +
378A HIS* 3.5 9.3 + - - +
379A LEU* 2.9 37.5 + - + +
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Residues in contact with MET 376 (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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330A LEU* 4.3 3.4 - - + -
333A MET* 4.3 9.4 - - + -
337A PRO 5.6 2.7 - - - +
338A ARG* 5.3 8.5 - - - +
339A PRO* 3.7 39.5 - - + -
372A GLU 3.0 20.6 + - - +
373A ALA 4.0 3.6 - - - +
374A VAL 3.2 0.2 - - - -
375A ARG* 1.3 75.4 - - - +
377A GLN* 1.3 59.6 + - - +
379A LEU* 3.2 10.5 + - + +
380A ILE* 2.9 54.9 + - + +
302B ALA* 5.0 12.8 - - + -
303B GLU* 4.4 18.2 - - - +
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Residues in contact with GLN 377 (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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46A ILE* 3.8 19.5 - - + +
329A MET* 3.5 27.5 - - - +
330A LEU* 3.9 18.4 - - + -
347A VAL* 4.2 12.9 - - + +
358A ILE* 3.6 32.3 + - + +
359A MET 4.1 1.4 - - - +
360A LEU* 3.5 36.9 - - - +
373A ALA 3.4 4.0 + - - +
374A VAL 3.3 7.7 + - - +
376A MET* 1.3 76.6 - - - +
378A HIS* 1.3 55.5 + - - +
380A ILE* 3.2 7.4 + - - +
381A ALA* 2.7 38.9 + - - +
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Residues in contact with HIS 378 (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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40A THR 5.0 4.8 + - - -
42A ARG* 3.0 54.3 - - + +
46A ILE* 3.7 13.5 - - + +
66A SER 4.2 12.9 + - - +
67A GLY* 5.2 0.4 - - - -
374A VAL 2.9 17.1 + - - +
375A ARG* 3.5 11.8 + - - +
377A GLN* 1.3 76.8 - - - +
379A LEU* 1.3 64.3 + - + +
382A ARG* 3.1 50.7 + - - +
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Residues in contact with LEU 379 (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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375A ARG* 2.9 28.0 + - + +
376A MET* 3.7 15.5 - - + +
377A GLN 3.2 0.2 - - - -
378A HIS* 1.3 76.8 - - - +
380A ILE* 1.3 64.8 + - - +
382A ARG* 3.5 30.5 + - - +
383A GLU* 3.3 26.9 + - - +
303B GLU* 3.6 37.5 - - + +
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Residues in contact with ILE 380 (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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330A LEU* 4.6 6.7 - - + -
339A PRO* 5.5 0.2 - - + -
344A GLY* 3.7 30.1 - - - +
347A VAL* 3.8 16.4 - - + -
348A ALA* 3.6 37.2 - - + +
376A MET* 2.9 42.7 + - + +
377A GLN* 3.8 3.1 - - - +
379A LEU* 1.3 74.8 - - - +
381A ALA* 1.3 66.9 + - - +
383A GLU* 3.1 13.3 + - - +
384A ALA* 3.1 11.8 + - - +
302B ALA 5.6 0.7 - - - -
303B GLU* 3.9 24.0 - - + +
306B PHE* 4.5 5.3 - - + -
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Residues in contact with ALA 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 4.0 13.2 - - + -
44A THR* 3.9 17.0 - - - -
46A ILE* 5.9 0.2 - - + -
347A VAL* 4.8 1.0 - - - +
351A VAL* 3.9 13.2 - - + +
358A ILE* 4.2 12.6 - - + -
377A GLN 2.7 21.3 + - - +
380A ILE* 1.3 73.9 - - - +
382A ARG* 1.3 58.0 + - - +
384A ALA* 3.0 5.5 + - - +
385A GLU* 2.9 42.7 + - - +
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Residues in contact with ARG 382 (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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38A PRO* 3.4 33.7 + - + +
39A ILE* 3.3 26.7 + - + +
40A THR* 3.8 20.4 + - - +
41A ALA 3.9 7.0 - - - +
42A ARG* 3.7 24.0 - - + -
378A HIS* 3.1 35.6 + - - +
379A LEU* 3.5 29.7 - - - +
380A ILE 3.4 0.4 - - - -
381A ALA* 1.3 75.4 - - - +
383A GLU* 1.3 63.8 + - - +
384A ALA 3.4 0.2 - - - -
385A GLU* 3.6 16.7 - - - +
386A ALA* 3.9 10.7 + - - +
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Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN* 4.7 2.9 + - - +
36A SER 4.7 3.8 - - - +
38A PRO* 3.9 24.1 - - + +
379A LEU 3.3 17.0 + - - +
380A ILE 3.1 10.6 + - - +
382A ARG* 1.3 77.6 - - + +
384A ALA* 1.3 61.5 + - - +
386A ALA* 3.8 5.2 + - - +
387A ALA* 3.6 17.5 + - - +
303B GLU* 3.9 26.4 - - + +
304B LYS* 2.9 44.0 + - - +
306B PHE* 3.8 7.9 - - + -
307B LEU* 3.4 22.3 - - - +
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Residues in contact with ALA 384 (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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348A ALA* 3.7 25.1 - - - +
351A VAL* 3.7 16.8 - - + -
352A LEU* 4.0 5.2 - - + +
380A ILE 3.1 7.0 + - - +
381A ALA 3.0 8.5 + - - +
383A GLU* 1.3 75.2 - - - +
385A GLU* 1.3 59.7 + - - +
386A ALA 3.1 2.0 - - - -
387A ALA* 2.9 19.9 + - - +
388A MET* 3.2 15.9 + - - +
306B PHE* 3.6 20.2 - - + -
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Residues in contact with GLU 385 (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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41A ALA 3.8 3.3 - - - +
42A ARG* 3.4 12.0 - - - +
43A ASN* 2.6 48.1 + - + +
44A THR* 2.7 39.5 + - - +
351A VAL* 3.9 9.2 - - + +
381A ALA 2.9 23.4 + - - +
382A ARG* 3.6 12.0 - - - +
384A ALA* 1.3 75.7 - - - +
386A ALA* 1.3 50.8 + - - +
388A MET* 3.9 8.9 - - - +
390A HIS* 2.8 36.6 + - + -
446A ARG* 5.4 0.5 - - - +
466A ARG* 4.7 5.2 - - - +
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Residues in contact with ALA 386 (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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15A GLN* 3.8 40.8 - - + +
16A GLN* 3.4 23.1 - - + +
28A HIS* 5.3 0.9 - - - -
38A PRO* 4.6 7.6 - - + -
39A ILE* 5.7 1.8 - - + +
382A ARG 3.9 9.9 + - - +
383A GLU 3.8 7.7 + - - +
384A ALA 3.1 0.4 - - - -
385A GLU* 1.3 77.1 - - - +
387A ALA* 1.3 59.9 + - - +
388A MET 3.2 12.8 + - - +
390A HIS* 4.2 7.2 + - - -
446A ARG* 5.6 2.7 - - - +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN* 4.2 1.8 - - + -
28A HIS* 2.6 29.4 + - - -
32A LEU* 3.8 28.1 - - + +
352A LEU* 3.7 13.0 - - + +
383A GLU 3.6 12.5 + - - +
384A ALA* 2.9 14.3 + - - +
386A ALA* 1.3 77.0 - - - +
388A MET* 1.3 54.4 + - - +
306B PHE* 4.2 7.9 - - + -
307B LEU* 3.8 14.1 - - + -
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Residues in contact with MET 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA* 5.7 2.4 - - - +
28A HIS* 3.6 5.6 - - - -
351A VAL 3.8 5.6 - - - +
352A LEU* 3.8 31.0 - - + +
354A GLY* 4.5 5.8 - - - -
384A ALA 3.2 13.9 + - - +
385A GLU* 3.9 16.2 - - - +
386A ALA 3.2 3.9 - - - +
387A ALA* 1.3 80.9 - - - +
389A PHE* 1.3 61.1 + - - +
390A HIS* 3.0 40.9 + - + +
393A LEU* 3.7 30.5 - - + -
444A ARG* 5.0 6.5 - - - -
466A ARG* 3.5 35.4 - - - +
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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