Contacts of the helix formed by residues 369 - 387 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C LYS* 5.1 14.0 + - - -
198C ASN* 5.5 1.8 - - + -
199C GLY 4.3 15.4 + - - -
200C GLY* 5.1 2.4 + - - -
333D MET* 3.8 15.3 + - + +
335D LYS 3.7 13.2 + - - -
336D LYS 3.5 22.9 - - - +
337D PRO* 3.5 45.1 - - + +
363D GLU 4.2 3.6 - - - -
367D GLY 3.3 0.8 - - - -
368D ASP* 1.3 96.4 - - + +
370D PRO* 1.3 66.9 - - - +
371D LEU 3.5 2.0 - - - -
372D GLU* 3.4 31.4 + - + +
373D ALA* 3.3 21.3 + - - +
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Residues in contact with PRO 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ALA* 3.8 26.9 - - + +
54D SER* 4.8 0.2 - - - -
59D THR* 5.1 2.7 - - + -
63D MET* 3.6 20.9 - - + -
363D GLU 3.9 11.4 - - - +
364D THR* 3.4 22.1 - - + +
367D GLY 3.9 12.1 - - - +
368D ASP 3.6 5.8 - - - +
369D TYR* 1.3 87.3 - - - +
371D LEU* 1.3 67.9 + - + +
372D GLU* 4.6 1.3 - - - +
373D ALA* 3.2 13.2 + - - +
374D VAL* 3.4 10.7 + - - +
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Residues in contact with LEU 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D THR* 4.0 12.1 - - + +
62D GLU* 3.7 47.1 - - + +
63D MET* 3.9 23.3 - - + -
66D SER* 3.7 6.7 + - - +
369D TYR 3.5 0.2 - - - -
370D PRO* 1.3 76.5 - - + +
372D GLU* 1.3 68.7 + - - +
374D VAL* 3.3 2.1 + - - +
375D ARG* 2.9 64.5 + - - +
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Residues in contact with GLU 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D MET* 3.5 19.5 - - + +
337D PRO* 4.2 10.1 - - + +
369D TYR* 3.4 43.5 - - + +
370D PRO* 4.1 0.9 - - - +
371D LEU* 1.3 85.7 + - - +
373D ALA* 1.3 57.4 + - - +
375D ARG* 4.0 26.3 + - - +
376D MET* 3.1 30.2 + - + +
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Residues in contact with ALA 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D LEU* 3.3 20.0 - - + +
333D MET* 3.9 11.4 - - + +
360D LEU* 3.8 18.6 - - + -
363D GLU* 4.2 20.2 - - + +
364D THR* 4.3 1.8 - - + -
369D TYR 3.3 12.6 + - - +
370D PRO 3.2 11.4 + - - +
371D LEU 3.1 0.4 - - - -
372D GLU* 1.3 76.5 - - - +
374D VAL* 1.3 62.5 + - - +
376D MET 3.5 0.2 + - - -
377D GLN* 3.2 21.5 + - - +
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Residues in contact with VAL 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ILE* 3.7 16.7 - - + +
48D CYS* 3.8 17.5 - - - -
63D MET* 3.6 23.3 - - + +
66D SER* 3.8 30.1 - - - +
67D GLY* 3.9 3.4 - - - -
68D MET* 3.8 20.2 - - - +
360D LEU* 3.9 11.0 - - + -
364D THR* 3.9 0.4 - - + -
370D PRO 3.5 14.4 - - - +
371D LEU 3.3 2.3 + - - +
373D ALA* 1.3 73.0 - - - +
375D ARG* 1.3 61.2 + - - +
377D GLN* 3.3 3.3 + - - +
378D HIS* 3.0 26.3 + - - +
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Residues in contact with ARG 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D GLU* 5.0 7.5 + - - -
66D SER* 3.3 27.8 + - - +
371D LEU* 2.9 51.7 + - - +
372D GLU* 4.0 24.7 + - - +
374D VAL* 1.3 76.6 - - - +
376D MET* 1.3 60.7 - - - +
378D HIS* 3.3 9.4 + - - +
379D LEU* 3.1 33.9 + - + +
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Residues in contact with MET 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C ALA* 5.1 10.1 - - + -
303C GLU* 5.0 7.9 - - - +
330D LEU* 4.0 9.4 - - + -
333D MET* 4.2 7.6 - - + -
337D PRO 5.2 1.3 - - - +
338D ARG* 4.5 17.3 - - - +
339D PRO* 3.8 37.0 - - + -
372D GLU* 3.1 24.0 + - + +
373D ALA 3.7 5.2 - - - +
374D VAL 3.3 0.4 - - - -
375D ARG* 1.3 77.0 - - - +
377D GLN* 1.3 61.6 + - - +
379D LEU* 3.3 17.8 + - + +
380D ILE* 3.1 54.2 + - + +
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Residues in contact with GLN 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D ILE* 3.6 29.5 - - + +
329D MET* 3.3 29.6 - - - +
330D LEU* 3.8 13.5 - - + -
347D VAL* 4.3 14.7 - - + +
358D ILE* 3.4 36.0 + - + +
359D MET 4.0 1.0 + - - -
360D LEU* 3.8 24.0 - - + +
373D ALA 3.2 17.6 + - - +
374D VAL 3.3 8.0 + - - +
376D MET* 1.3 76.0 - - - +
378D HIS* 1.3 58.6 + - - +
380D ILE* 4.6 0.8 - - - +
381D ALA* 3.0 30.7 + - - +
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Residues in contact with HIS 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D THR 4.3 7.2 + - - -
42D ARG* 3.2 54.2 - - + +
46D ILE* 3.7 7.4 - - + +
66D SER 4.1 14.1 - - - +
67D GLY* 5.3 1.1 - - - -
374D VAL 3.0 14.3 + - - +
375D ARG* 3.4 10.1 + - - +
376D MET 3.2 0.4 - - - -
377D GLN* 1.3 78.9 - - - +
379D LEU* 1.3 68.0 + - + +
382D ARG* 3.5 52.3 + - - +
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Residues in contact with LEU 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C GLU* 4.0 37.2 - - + +
375D ARG* 3.1 28.9 + - + +
376D MET* 3.3 17.9 + - + +
378D HIS* 1.3 80.2 - - - +
380D ILE* 1.3 65.3 + - - +
381D ALA 3.4 0.2 + - - -
382D ARG* 3.3 32.5 + - - +
383D GLU* 3.2 26.3 + - - +
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Residues in contact with ILE 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C ALA* 5.7 1.3 - - + +
303C GLU* 3.7 31.6 - - + +
306C PHE* 4.6 1.1 - - + -
330D LEU* 4.7 6.3 - - + -
339D PRO* 5.4 1.6 - - + -
344D GLY* 3.6 39.0 - - - +
347D VAL* 3.8 17.7 - - + -
348D ALA* 3.7 25.4 - - + +
376D MET* 3.1 39.3 + - + +
379D LEU* 1.3 74.6 - - - +
381D ALA* 1.3 64.7 + - - +
383D GLU* 3.2 4.1 + - - +
384D ALA* 2.9 21.9 + - - +
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Residues in contact with ALA 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ARG* 3.8 14.6 - - + -
44D THR* 4.1 12.6 - - - +
347D VAL* 4.6 1.2 - - - +
351D VAL* 4.0 13.7 - - + +
358D ILE* 4.2 9.4 - - + -
377D GLN 3.0 22.4 + - - +
379D LEU 3.3 0.2 - - - -
380D ILE* 1.3 75.7 - - - +
382D ARG* 1.3 57.7 + - - +
384D ALA* 3.0 6.1 + - - +
385D GLU* 2.8 45.1 + - - +
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Residues in contact with ARG 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D PRO* 3.4 33.4 + - + +
39D ILE 3.5 17.8 + - - +
40D THR* 3.6 25.7 + - - +
41D ALA 3.9 7.0 - - - +
42D ARG* 3.8 17.7 - - + -
378D HIS* 3.5 33.0 + - - +
379D LEU* 3.3 39.0 + - - +
381D ALA* 1.3 76.4 - - - +
383D GLU* 1.3 64.7 + - - +
385D GLU* 3.5 16.1 - - - +
386D ALA* 3.6 12.6 + - - +
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Residues in contact with GLU 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C GLU* 3.6 33.0 - - + +
304C LYS* 3.1 34.7 + - - +
306C PHE* 3.6 7.2 - - + -
307C LEU* 3.3 24.3 - - - +
16D GLN* 4.4 5.7 + - - -
38D PRO* 3.4 26.9 - - + +
379D LEU 3.2 15.7 + - - +
380D ILE 3.4 8.3 - - - +
382D ARG* 1.3 79.8 - - + +
384D ALA* 1.3 61.8 + - - +
386D ALA* 3.7 4.0 + - - +
387D ALA* 3.4 19.2 + - - +
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Residues in contact with ALA 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C PHE* 3.3 21.5 - - + -
348D ALA* 3.7 16.6 - - - +
351D VAL* 3.7 25.8 - - + -
352D LEU* 3.4 13.1 - - + +
380D ILE 2.9 13.8 + - - +
381D ALA 3.5 7.2 - - - +
383D GLU* 1.3 75.4 - - - +
385D GLU* 1.3 64.0 + - - +
386D ALA 3.4 0.2 - - - -
387D ALA* 3.1 8.9 + - - -
388D MET* 3.3 10.7 + - - +
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Residues in contact with GLU 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ALA 3.9 2.4 - - - +
42D ARG* 3.4 8.1 - - - +
43D ASN* 2.6 47.2 + - + +
44D THR* 2.8 36.2 + - - +
351D VAL* 3.9 6.3 - - + -
381D ALA* 2.8 34.7 + - - +
382D ARG* 3.5 13.3 - - - +
383D GLU 3.3 0.2 - - - -
384D ALA* 1.3 77.4 - - - +
386D ALA* 1.3 58.1 + - - +
388D MET* 3.4 14.1 - - - +
390D HIS* 2.8 30.5 + - + -
466D ARG* 5.1 4.5 - - - +
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Residues in contact with ALA 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLN* 3.8 40.8 - - + +
16D GLN* 3.3 24.2 - - + +
28D HIS* 5.4 0.3 - - - -
38D PRO* 4.4 8.1 - - + -
39D ILE* 5.7 1.1 - - + +
382D ARG 3.6 13.4 + - - +
383D GLU 4.1 3.4 - - - +
384D ALA 3.4 0.2 - - - -
385D GLU* 1.3 77.4 - - - +
387D ALA* 1.3 59.8 + - - +
388D MET 3.2 10.7 + - - +
390D HIS* 4.3 7.3 + - - -
446D ARG* 5.5 3.8 + - - +
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Residues in contact with ALA 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C PHE* 3.9 12.8 - - + -
307C LEU* 3.6 24.2 - - + -
16D GLN* 3.9 2.0 - - - +
28D HIS* 2.8 24.3 + - - -
32D LEU* 3.8 18.5 - - + +
352D LEU* 3.7 9.6 - - + +
383D GLU 3.4 13.9 + - - +
384D ALA 3.1 11.9 + - - +
386D ALA* 1.3 75.6 - - - +
388D MET* 1.3 60.2 + - - +
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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