Contacts of the helix formed by residues 387 - 403 (chain A) in PDB entry 3NRN
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 ILE 387 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 3.5 26.4 - - + +
59A HIS* 4.1 25.1 + - + +
151A PHE* 4.0 28.3 - - + -
154A TRP* 5.4 4.7 - - + -
155A ALA* 3.9 28.3 - - + +
156A ASP* 4.6 3.4 - - - +
171A GLU* 3.9 28.5 - - + +
174A ALA* 5.4 0.2 - - + -
175A ALA* 6.2 0.7 - - + -
382A ARG* 5.3 0.2 - - - +
385A GLY 3.3 10.9 + - - +
386A GLY* 1.3 70.7 - - - -
388A GLU* 1.3 76.0 + - + +
389A VAL 3.3 0.5 + - - -
390A ASP* 3.0 14.0 + - - +
391A GLY 2.9 12.5 + - - +
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Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA* 3.6 23.0 + - - +
54A LEU 4.9 0.7 + - - -
56A MSE 4.1 6.6 - - - +
58A PRO* 3.6 16.8 - - + +
155A ALA 4.6 8.6 + - - +
379A ASP* 5.3 5.6 - - - +
382A ARG* 3.2 22.6 - - - +
386A GLY 3.8 3.6 + - - -
387A ILE* 1.3 76.8 - - + +
389A VAL* 1.3 93.5 + - + +
391A GLY* 2.8 18.2 + - - -
392A ILE* 2.9 14.8 + - + +
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.8 19.0 - - + +
39A PHE* 3.7 30.7 - - + -
53A ALA* 4.5 1.1 - - + -
56A MSE 4.3 3.8 - - - +
57A ILE* 4.2 6.1 - - - -
58A PRO* 3.4 15.9 - - + -
65A LEU* 3.7 21.8 - - + +
388A GLU* 1.3 103.1 - - + +
390A ASP* 1.3 67.6 + - - +
392A ILE* 3.4 17.2 - - + +
393A ALA* 2.9 22.7 + - - +
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Residues in contact with ASP 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 3.1 16.8 - - - +
58A PRO* 3.2 5.7 - - - +
59A HIS* 2.8 44.5 + - + -
63A GLY* 3.6 4.7 - - - -
64A PRO* 3.2 24.4 - - + +
65A LEU* 3.1 29.6 + - - +
66A ALA 4.4 0.2 + - - -
178A TRP* 5.5 1.1 - - + -
386A GLY* 5.0 1.1 - - - -
387A ILE 3.0 11.6 + - - +
389A VAL* 1.3 79.1 - - - +
391A GLY* 1.3 58.2 + - - +
393A ALA* 3.3 3.6 + - - +
394A LEU* 2.9 28.5 + - - +
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Residues in contact with GLY 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ARG* 3.6 10.7 - - - -
383A PRO* 3.5 9.2 - - - +
386A GLY* 3.5 31.9 - - - -
387A ILE 2.9 7.1 + - - +
388A GLU 2.8 9.2 + - - -
390A ASP* 1.3 76.6 - - - +
392A ILE* 1.3 65.0 + - - +
394A LEU* 3.3 5.2 + - - +
395A GLY 3.0 17.0 + - - -
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Residues in contact with ILE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.4 16.4 - - + -
11A GLY* 3.8 31.4 - - - +
14A LEU* 4.5 2.0 - - + -
378A GLY* 3.8 27.2 + - - +
379A ASP* 3.9 25.8 - - - +
381A TYR 4.6 1.0 - - - +
382A ARG* 4.2 9.0 - - + -
388A GLU* 2.9 16.7 + - + +
389A VAL* 3.1 28.0 + - + +
391A GLY* 1.3 75.9 - - - +
393A ALA* 1.3 63.8 - - - +
395A GLY* 3.0 12.1 + - - -
396A VAL* 3.0 13.3 + - - +
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Residues in contact with ALA 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.3 6.5 - - - +
64A PRO* 3.8 4.5 - - - -
65A LEU* 3.5 43.5 - - + +
68A LEU* 3.8 16.3 - - + +
389A VAL 2.9 11.2 + - - +
390A ASP 3.6 4.7 - - - +
392A ILE* 1.3 76.8 - - - +
394A LEU* 1.3 63.2 + - - +
396A VAL* 3.1 4.1 + - - +
397A MSE 3.0 27.7 + - - +
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PRO* 4.0 9.1 - - + +
178A TRP* 5.4 7.4 - - + -
383A PRO* 3.4 31.6 - - + +
384A PRO 4.4 4.9 - - - +
385A GLY 5.1 0.7 - - - -
386A GLY* 4.0 22.7 - - - +
390A ASP 2.9 16.8 + - - +
391A GLY 3.5 4.9 - - - +
392A ILE 3.2 0.2 - - - -
393A ALA* 1.3 76.2 - - - +
395A GLY* 1.3 60.9 + - - +
397A MSE 3.4 6.7 + - - +
398A LYS* 3.0 30.9 + - + +
412A TYR 3.1 28.3 - - - +
413A LEU* 3.7 29.6 - - + +
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Residues in contact with GLY 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A VAL* 4.9 3.1 - - - -
381A TYR* 3.3 39.7 - - - -
383A PRO* 3.6 9.6 - - - +
391A GLY 3.0 10.1 + - - -
392A ILE 3.0 4.4 + - - -
394A LEU* 1.3 75.5 - - - +
396A VAL* 1.3 59.4 + - - +
398A LYS 3.3 0.7 + - - -
399A ALA* 2.9 26.9 + - - +
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY* 3.9 26.9 - - - +
14A LEU* 4.3 10.1 - - + -
15A ALA* 4.2 23.6 - - + +
18A PHE* 5.7 0.2 - - + -
68A LEU* 4.2 14.8 - - + -
377A VAL* 4.1 21.5 - - + -
392A ILE 3.0 15.2 + - - +
393A ALA 3.1 7.8 + - - +
395A GLY* 1.3 76.7 - - - +
397A MSE 1.3 63.7 + - - +
399A ALA* 3.3 1.7 + - - +
400A LEU* 2.9 47.0 + - + +
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Residues in contact with MSE 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PRO* 3.9 28.7 - - + +
67A HIS* 3.7 30.5 - - + -
68A LEU* 4.0 15.0 - - + -
393A ALA 3.0 17.4 + - - +
394A LEU* 3.5 8.1 - - - +
395A GLY 3.2 0.2 - - - -
396A VAL* 1.3 77.4 - - - +
398A LYS* 1.3 56.4 + - - +
400A LEU* 3.3 4.1 + - - +
401A GLU* 3.0 33.8 + - - +
408A PHE* 3.6 38.4 - - + -
412A TYR* 3.8 27.6 - - + +
413A LEU* 3.8 17.3 - - + -
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Residues in contact with LYS 398 (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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381A TYR* 3.3 26.0 - - + +
383A PRO* 3.9 18.4 - - + -
394A LEU* 3.0 19.9 + - + +
395A GLY 3.6 3.8 - - - +
396A VAL 3.2 0.2 - - - -
397A MSE 1.3 73.7 - - - +
399A ALA* 1.3 59.6 + - - +
401A GLU* 3.2 13.0 + - - +
402A LYS* 2.8 30.2 + - - +
413A LEU* 3.8 33.1 + - + +
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Residues in contact with ALA 399 (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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236A ILE* 5.6 2.5 - - + -
375A LEU* 3.7 24.0 - - + +
376A VAL 5.1 0.9 - - - +
377A VAL* 4.0 21.5 - - + -
381A TYR* 4.4 7.3 - - + -
395A GLY 2.9 15.5 + - - +
396A VAL* 3.3 4.9 + - + +
398A LYS* 1.3 75.3 - - - +
400A LEU* 1.3 66.0 + - + +
402A LYS* 3.1 6.2 + - - +
403A LEU* 2.9 30.3 + - + +
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Residues in contact with LEU 400 (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 ALA* 5.1 6.5 - - + +
18A PHE* 3.4 43.7 - - + -
19A LEU* 4.1 25.1 - - + -
68A LEU* 5.1 2.2 - - + -
236A ILE* 6.3 1.3 - - + -
396A VAL* 2.9 41.9 + - + +
397A MSE 3.5 4.7 - - - +
399A ALA* 1.3 78.6 - - + +
401A GLU* 1.3 59.4 + - - +
403A LEU* 3.3 12.6 + - + +
404A ASN 3.2 2.6 + - - -
405A LEU* 2.9 29.4 + - + -
406A GLY* 3.2 9.8 + - - +
408A PHE* 3.7 24.7 - - + -
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Residues in contact with GLU 401 (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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397A MSE 3.0 21.2 + - - +
398A LYS* 3.2 15.0 + - - +
400A LEU* 1.3 73.2 - - - +
402A LYS* 1.3 58.6 + - - +
404A ASN* 2.7 32.4 + - - -
406A GLY 3.4 18.4 - - - +
407A SER* 3.6 6.2 + - - -
408A PHE* 3.0 33.4 + - + +
413A LEU* 3.4 28.2 - - - +
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Residues in contact with LYS 402 (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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368A GLU* 5.8 3.2 + - - -
369A TRP* 4.1 15.6 + - - +
370A PRO 5.0 0.2 - - - -
371A LEU 2.7 28.9 + - - +
372A ASN* 3.2 23.2 + - - +
375A LEU* 3.3 24.9 - - + +
398A LYS 2.8 17.1 + - - +
399A ALA* 3.4 7.6 - - - +
401A GLU* 1.3 77.9 - - - +
403A LEU* 1.3 60.8 + - + +
404A ASN* 3.4 9.0 + - - +
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 5.3 2.9 - - + -
234A VAL* 4.2 31.9 - - + -
236A ILE* 4.3 10.1 - - + -
372A ASN 3.8 18.6 - - - +
375A LEU* 3.6 24.9 - - + -
399A ALA* 2.9 23.0 + - + +
400A LEU* 3.6 15.0 - - + +
401A GLU 3.0 0.2 - - - -
402A LYS* 1.3 78.4 - - + +
404A ASN* 1.3 73.5 + - - +
405A LEU* 3.2 32.6 + - + +
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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
------------------------------------------------------------
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