Contacts of the helix formed by residues 354 - 375 (chain A) in PDB entry 4YVF
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 PRO 354 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A GLY 4.2 7.0 - - - +
197A GLU* 3.7 32.3 - - + +
198A SER* 4.1 8.7 - - - +
352A GLY 4.0 3.1 - - - +
353A HIS* 1.3 92.5 - - + +
355A SER* 1.3 65.4 + - - +
356A PHE* 4.4 8.1 - - + +
357A VAL* 3.2 26.1 + - + +
358A MET* 3.3 10.6 + - - +
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Residues in contact with SER 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 4.2 11.9 - - - +
28A GLU* 3.7 25.3 - - - +
29A MET* 3.6 11.0 - - - +
59A GLU* 2.6 37.6 + - - -
353A HIS 3.7 0.6 + - - -
354A PRO* 1.3 71.3 - - - +
356A PHE* 1.3 57.9 + - - +
358A MET* 3.0 5.7 + - - +
359A SER* 2.8 27.5 + - - -
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Residues in contact with PHE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.0 46.4 + - - +
30A PRO* 3.8 22.7 - - + -
189A PHE* 3.7 25.8 - + - -
354A PRO* 3.3 6.0 - - + +
355A SER* 1.3 77.6 - - - +
357A VAL* 1.3 62.8 + - + +
359A SER* 3.2 11.9 - - - -
360A ASN* 3.2 34.2 + - - -
398A HIS* 3.9 19.5 - + + -
401A LYS* 4.3 14.6 - - + -
402A LEU* 4.2 25.4 - - + -
250B LEU* 4.8 0.9 - - + -
254B MET* 4.5 11.2 - - + -
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 3.4 44.9 - - + +
190A ASP* 4.0 2.9 - - - +
193A TYR* 4.4 2.9 - - + -
194A GLY* 3.6 25.4 - - - +
197A GLU* 5.2 2.0 - - + -
353A HIS* 3.7 28.0 - - + -
354A PRO* 3.2 24.0 + - + +
355A SER 3.1 0.6 - - - -
356A PHE* 1.3 76.6 - - + +
358A MET* 1.3 68.2 + - - +
360A ASN* 3.0 15.9 + - - +
361A SER* 3.3 11.2 + - - +
254B MET* 6.2 0.9 - - + -
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Residues in contact with MET 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 3.8 2.5 - - + -
54A LEU* 5.5 0.4 - - + -
59A GLU* 3.6 29.6 - - + -
156A GLU* 5.4 1.3 - - - +
190A ASP* 5.2 2.9 - - - +
353A HIS* 3.8 25.8 - - + -
354A PRO 3.3 12.1 + - - +
355A SER 3.0 8.1 + - - +
357A VAL* 1.3 78.0 - - - +
359A SER* 1.3 56.9 + - - +
361A SER* 3.2 9.8 + - - +
362A PHE* 2.9 68.4 + - + -
502A XFA 3.6 42.6 - - - -
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Residues in contact with SER 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU 4.0 0.7 - - - -
29A MET* 3.3 50.1 + - - +
31A GLY 3.5 3.8 + - - -
32A LEU* 3.9 3.2 + - - -
355A SER 2.8 10.3 + - - -
356A PHE* 3.2 13.0 - - - -
357A VAL 3.1 0.2 - - - -
358A MET* 1.3 77.2 - - - +
360A ASN* 1.3 55.4 + - - +
362A PHE* 4.3 0.2 - - - +
363A THR* 2.5 39.7 + - - -
398A HIS* 2.9 18.8 + - - -
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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
----------------------------------------------------------
185A THR* 3.6 20.6 - - - +
189A PHE* 3.4 44.8 - - + -
356A PHE* 3.2 22.0 + - - -
357A VAL 3.0 8.8 + - - +
359A SER* 1.3 78.9 - - - +
361A SER* 1.3 58.6 + - - +
364A ASN* 2.7 35.2 + - - -
394A VAL* 3.8 11.7 - - - +
398A HIS* 3.5 33.9 + - - -
250B LEU* 4.0 5.0 - - - +
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Residues in contact with SER 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A GLU* 3.7 17.6 - - - +
180A VAL* 4.9 0.2 - - - +
186A LYS* 3.9 36.4 + - - +
190A ASP* 4.1 17.0 + - - +
357A VAL* 3.3 9.0 + - - +
358A MET* 3.2 14.7 + - - +
360A ASN* 1.3 78.5 - - - +
362A PHE* 1.3 65.9 + - - +
364A ASN* 2.9 24.8 + - - +
365A GLN* 3.2 4.3 + - - +
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Residues in contact with PHE 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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29A MET* 3.9 7.2 - - + -
32A LEU* 4.0 10.1 - - + -
54A LEU* 3.4 23.3 - - + -
59A GLU* 3.6 22.7 - - + -
60A THR* 3.4 41.5 - - - -
63A LEU* 3.7 32.8 - - + -
156A GLU* 3.7 17.0 - - - -
358A MET* 2.9 46.3 + - + +
361A SER* 1.3 75.3 - - - +
363A THR* 1.3 62.3 + - - +
364A ASN 2.8 5.4 - - - -
365A GLN* 2.9 17.6 + - + +
366A VAL* 2.9 15.9 + - - +
502A XFA 4.5 0.2 - - - -
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Residues in contact with THR 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY* 3.3 41.2 - - - +
32A LEU* 3.4 12.5 + - - +
35A MET* 4.3 4.9 - - + -
359A SER 2.5 23.0 + - - -
361A SER 3.4 0.2 - - - -
362A PHE* 1.3 76.3 - - - +
364A ASN* 1.3 57.1 + - - +
366A VAL* 3.7 3.1 - - - +
367A MET* 2.9 51.8 + - + +
394A VAL* 4.0 21.1 - - + -
397A ALA* 4.6 1.8 - - + -
398A HIS* 4.0 6.1 - - - -
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Residues in contact with ASN 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A VAL* 3.6 18.4 - - + +
183A SER* 2.8 24.2 + - - -
185A THR* 2.8 24.5 + - - -
186A LYS* 3.6 11.7 - - + +
360A ASN 2.7 21.8 + - - -
361A SER* 2.9 14.6 - - - +
363A THR* 1.3 79.0 - - - +
365A GLN* 1.3 57.5 + - - +
367A MET* 3.2 4.4 + - - +
368A ALA* 2.9 29.5 + - - +
386A LEU* 3.0 24.4 - - - +
394A VAL* 3.7 9.8 - - - +
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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
----------------------------------------------------------
54A LEU* 4.5 1.2 - - - +
63A LEU* 4.5 4.0 - - + -
129A LEU* 3.5 31.7 - - + +
130A ASP 3.1 25.5 + - - -
154A SER* 2.7 35.4 + - - -
156A GLU* 2.8 43.6 + - + +
180A VAL* 4.0 4.9 - - + +
361A SER 3.2 4.4 + - - +
362A PHE* 2.9 15.8 + - + +
364A ASN* 1.3 74.4 - - - +
366A VAL* 1.3 66.0 + - - +
368A ALA* 3.1 4.2 + - - +
369A GLN* 2.8 28.7 + - - +
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Residues in contact with VAL 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.7 17.0 - - + -
35A MET* 3.4 28.9 - - + -
63A LEU* 3.6 21.1 - - + -
66A THR* 4.1 6.1 - - + -
67A LEU* 4.1 13.5 - - + -
70A LEU* 3.6 25.6 - - + -
362A PHE 2.9 16.9 + - - +
363A THR* 3.7 8.1 - - - +
365A GLN* 1.3 76.3 - - - +
367A MET* 1.3 61.8 + - - +
369A GLN* 3.1 8.6 + - - +
370A ILE* 2.9 24.5 + - + +
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Residues in contact with MET 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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35A MET* 3.4 37.9 - - + -
38A ARG* 5.9 1.6 - - - +
363A THR* 2.9 25.9 + - + +
364A ASN* 3.2 8.5 + - - +
366A VAL* 1.3 79.7 - - - +
368A ALA* 1.3 57.4 + - - +
370A ILE* 3.4 6.6 + - - +
371A GLU* 2.9 30.2 + - - +
386A LEU* 4.5 4.3 - - + -
390A LEU* 4.0 31.9 - - + +
393A ALA* 3.7 43.7 - - + +
394A VAL* 3.7 14.4 - - + +
397A ALA* 5.2 0.7 - - + -
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Residues in contact with ALA 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A SER* 3.5 24.0 - - - -
178A ILE* 3.7 19.1 - - + -
180A VAL* 3.7 17.7 - - + -
364A ASN 2.9 13.4 + - - +
365A GLN 3.4 7.9 - - - +
367A MET* 1.3 75.8 - - - +
369A GLN* 1.3 58.0 + - - +
371A GLU* 3.3 2.8 + - - +
372A LEU* 3.0 35.4 + - - +
386A LEU* 4.3 3.8 - - - +
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Residues in contact with GLN 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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45A LEU* 3.9 9.8 - - + +
50A ILE* 3.4 28.5 - - + +
67A LEU* 4.8 1.6 - - + -
127A MET* 3.1 31.7 - - - +
128A ILE 3.2 18.8 + - - -
129A LEU* 3.6 26.5 - - + +
154A SER* 2.9 29.7 + - - +
365A GLN 2.8 18.8 + - - +
366A VAL* 3.4 11.0 - - - +
368A ALA* 1.3 77.0 - - - +
370A ILE* 1.3 57.3 + - - +
373A TRP* 3.0 33.8 + - - +
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Residues in contact with ILE 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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35A MET* 4.0 14.1 - - + -
39A TYR* 4.4 11.9 - - + -
44A PRO* 4.1 24.5 - - + -
45A LEU* 4.0 25.1 - - + -
70A LEU* 3.7 24.9 - - + -
366A VAL* 2.9 26.3 + - + +
367A MET* 3.8 6.1 - - - +
369A GLN* 1.3 75.1 - - - +
371A GLU* 1.3 55.7 + - - +
374A THR* 2.6 48.6 + - + +
375A HIS* 6.3 0.2 - - + -
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Residues in contact with GLU 371 (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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178A ILE* 3.7 10.8 - - + -
367A MET 2.9 18.2 + - - +
368A ALA* 3.3 4.5 + - - +
370A ILE* 1.3 78.2 - - - +
372A LEU* 1.3 55.9 + - - +
374A THR* 4.3 1.8 - - - -
375A HIS* 3.0 48.0 + - - +
378A LYS* 2.7 28.0 + - - -
379A TYR* 2.6 39.3 + - + +
387A PRO* 4.4 3.6 - - + +
390A LEU* 3.7 26.8 - - + +
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Residues in contact with LEU 372 (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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127A MET* 3.9 12.1 - - + -
151A ARG* 3.6 12.9 - - - +
152A GLY* 3.7 7.6 - - - -
153A ILE 3.3 45.8 - - - +
154A SER* 4.5 1.1 - - - +
176A PRO* 4.0 14.6 - - + +
177A ALA 5.2 0.2 - - - -
178A ILE* 3.5 29.2 - - + -
368A ALA 3.0 16.3 + - - +
371A GLU* 1.3 73.0 - - - +
373A TRP* 1.3 68.5 + - - +
376A PRO* 3.3 22.6 - - + +
379A TYR* 3.7 34.3 - - + -
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Residues in contact with TRP 373 (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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44A PRO 3.4 23.8 + - - -
45A LEU* 4.0 14.4 - - + -
46A LYS 3.1 19.4 + - - -
47A GLY* 3.3 20.4 - - - -
48A ALA* 3.8 10.9 - - + +
126A ASN* 3.4 42.4 - - + -
127A MET* 3.5 22.4 - - + +
151A ARG* 3.2 65.4 + - + +
369A GLN 3.0 20.0 + - - +
370A ILE 4.1 1.8 - - - +
372A LEU* 1.3 79.0 - - - +
374A THR* 1.3 61.2 + - + +
376A PRO* 3.8 2.6 - - - +
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Residues in contact with THR 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PRO* 3.3 32.1 - - + +
370A ILE* 2.6 37.2 + - + +
373A TRP* 1.3 79.6 - - + +
375A HIS* 1.3 86.1 + - - +
376A PRO* 3.3 9.4 - - - +
377A ASP* 4.6 2.3 - - - +
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Residues in contact with HIS 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ILE* 6.3 0.4 - - + -
371A GLU* 3.0 34.4 + - - +
372A LEU 3.5 4.0 + - - -
374A THR* 1.3 106.9 + - - +
376A PRO* 1.3 66.2 - - - +
377A ASP* 3.2 10.8 - - - -
378A LYS* 3.0 46.0 + - + -
379A TYR* 3.4 12.8 - - - -
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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