Contacts of the helix formed by residues 397 - 413 (chain A) in PDB entry 3NIE
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 SER 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.1 3.4 - - - -
396A LEU* 1.3 75.0 - - - +
398A GLU* 1.3 55.5 + - - +
399A THR* 3.3 12.2 + - - -
400A GLN* 2.7 42.3 + - - +
401A LEU* 2.7 34.0 + - - +
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Residues in contact with GLU 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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65A PHE* 3.9 27.4 - - + +
68A LEU* 3.7 21.1 - - + +
397A SER* 1.3 72.7 - - - +
399A THR* 1.3 65.1 + - - +
401A LEU* 3.2 4.4 + - - +
402A ARG* 2.8 65.9 + - - +
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Residues in contact with THR 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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397A SER* 3.3 10.6 + - - +
398A GLU* 1.3 81.8 - - - +
400A GLN* 1.3 69.0 + - + +
402A ARG* 3.2 4.8 + - - +
403A TYR* 3.1 18.9 + - - +
421A LYS 4.4 6.0 + - - +
422A LEU* 3.5 43.7 - - - +
423A ASN 5.0 4.5 - - - -
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Residues in contact with GLN 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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395A VAL 4.2 2.8 + - - +
396A LEU* 3.3 26.2 - - + +
397A SER* 2.7 48.7 + - - +
399A THR* 1.3 80.5 - - + +
401A LEU* 1.3 61.4 + - - +
403A TYR* 3.2 10.3 + - - +
404A ILE* 3.2 29.6 + - + +
422A LEU 5.2 0.2 - - - -
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Residues in contact with LEU 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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65A PHE* 4.3 1.8 - - + -
68A LEU* 3.9 25.8 - - + +
71A CYS* 3.9 31.9 - - + -
72A LYS* 4.4 17.9 - - + -
75A LEU* 3.8 26.4 - - + +
396A LEU* 3.8 40.8 - - + +
397A SER 2.7 18.5 + - - +
398A GLU* 3.8 2.7 - - - +
400A GLN* 1.3 71.1 - - - +
402A ARG* 1.3 63.3 + - - +
404A ILE* 3.5 4.4 + - - +
405A PHE* 3.0 32.1 + - + -
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Residues in contact with ARG 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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65A PHE* 3.4 32.9 - - + +
102A LEU 3.2 25.7 + - - -
103A LYS* 3.9 11.7 + - - +
104A PHE* 3.0 57.9 + - + +
105A ASP* 5.1 1.4 + - - +
398A GLU* 2.8 54.0 + - - +
399A THR* 3.5 5.2 - - - +
401A LEU* 1.3 69.8 - - - +
403A TYR* 1.3 66.3 + - - +
405A PHE* 3.6 4.2 + - - +
406A LEU* 3.1 29.9 + - - +
422A LEU* 4.1 25.1 - - + -
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Residues in contact with TYR 403 (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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399A THR 3.1 7.7 + - - +
400A GLN* 3.2 11.4 + - - +
402A ARG* 1.3 75.9 - - - +
404A ILE* 1.3 74.0 + - + +
406A LEU* 3.1 7.1 + - - +
407A LYS* 3.0 66.1 + - + +
418A ILE* 4.7 17.0 - - + -
422A LEU* 3.9 34.4 - - + +
423A ASN* 4.5 19.3 + - - -
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Residues in contact with ILE 404 (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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75A LEU* 3.5 37.2 - - + -
79A THR* 4.4 2.0 - - + -
389A PRO* 3.8 46.2 - - + +
390A PHE* 4.0 3.8 - - + -
396A LEU* 3.9 23.3 - - + -
400A GLN* 3.2 17.3 + - + +
401A LEU* 3.5 2.4 + - - +
402A ARG 3.4 0.2 - - - -
403A TYR* 1.3 90.2 - - + +
405A PHE* 1.3 63.1 + - - +
407A LYS* 3.4 6.2 + - + +
408A GLU* 3.1 22.4 + - + +
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Residues in contact with PHE 405 (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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64A MET* 4.3 7.6 - - + -
65A PHE* 4.6 9.9 - + - -
71A CYS* 3.8 28.5 - - - -
74A ILE* 3.9 13.5 - - + -
75A LEU* 3.4 49.6 - - + +
78A ILE* 4.8 8.1 - - + -
95A LEU* 6.6 0.2 - - + -
104A PHE* 4.3 17.9 - + + -
107A LEU* 3.5 36.1 - - + -
401A LEU* 3.0 31.5 + - + +
402A ARG 3.8 4.7 - - - +
404A ILE* 1.3 77.1 - - - +
406A LEU* 1.3 58.0 + - - +
408A GLU* 3.1 7.2 + - + +
409A ILE* 2.9 35.3 + - + +
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Residues in contact with LEU 406 (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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98A PRO* 4.4 9.0 - - + -
101A LEU* 3.5 30.7 - - + +
104A PHE* 4.2 17.9 - - + -
402A ARG 3.1 18.6 + - - +
403A TYR* 3.1 6.7 + - - +
405A PHE* 1.3 76.7 - - - +
407A LYS* 1.3 53.2 + - - +
409A ILE* 3.3 20.7 + - + +
410A GLN* 2.6 35.8 + - - +
416A LEU* 3.8 19.0 - - + +
418A ILE* 5.1 12.8 - - + -
419A PRO* 4.4 13.5 - - + -
422A LEU* 3.7 17.9 - - + -
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Residues in contact with LYS 407 (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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403A TYR* 3.0 63.9 + - + +
404A ILE* 3.7 9.0 - - + +
405A PHE 3.3 0.2 - - - -
406A LEU* 1.3 76.4 - - + +
408A GLU* 1.3 62.0 + - - +
410A GLN* 2.6 42.3 + - - +
411A SER* 2.9 25.5 + - - -
418A ILE* 5.1 6.5 - - + -
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Residues in contact with GLU 408 (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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75A LEU* 4.8 1.1 - - + -
78A ILE* 4.3 8.4 - - + +
79A THR* 3.7 25.5 - - + -
82A ASN* 3.0 20.2 + - - +
83A ARG* 2.7 46.2 + - - -
95A LEU* 3.8 15.5 - - + -
389A PRO* 4.4 3.5 - - - +
404A ILE* 3.1 15.6 + - + +
405A PHE* 3.1 10.9 + - + +
407A LYS* 1.3 80.7 - - - +
409A ILE* 1.3 60.5 + - - +
411A SER* 2.8 28.6 + - - -
412A PHE* 3.6 7.6 - - - -
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Residues in contact with ILE 409 (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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95A LEU* 4.0 35.4 - - + +
96A ILE 4.4 0.9 - - - +
97A ILE* 4.1 23.1 - - + +
98A PRO* 3.8 22.9 - - + -
104A PHE* 5.0 1.8 - - + -
107A LEU* 4.0 21.8 - - + -
405A PHE* 2.9 29.1 + - + +
406A LEU* 3.6 17.5 - - + +
408A GLU* 1.3 75.8 - - - +
410A GLN* 1.3 57.5 + - - +
412A PHE* 3.2 3.3 + - - +
413A HIS* 3.0 26.7 + - - +
416A LEU* 3.7 17.3 - - + -
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Residues in contact with GLN 410 (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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406A LEU 2.6 21.7 + - - +
407A LYS* 2.6 47.4 + - - +
409A ILE* 1.3 72.8 - - - +
411A SER* 1.3 61.9 - - - +
413A HIS 3.0 33.5 - - - +
414A ALA* 3.4 13.2 + - - +
416A LEU* 3.1 32.6 + - + +
417A ILE* 5.1 0.2 - - - +
418A ILE* 4.8 11.5 - - - +
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Residues in contact with SER 411 (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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82A ASN* 3.2 17.6 + - - -
407A LYS 2.9 11.3 + - - -
408A GLU* 2.8 19.8 + - - -
410A GLN* 1.3 77.6 - - - +
412A PHE* 1.3 71.5 + - - +
414A ALA* 5.1 1.0 + - - -
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Residues in contact with PHE 412 (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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82A ASN* 3.4 33.7 - - - -
92A LEU* 3.3 45.1 - - + -
93A HIS 3.6 17.5 - - - -
94A ASP* 3.8 18.6 - - + +
95A LEU* 3.9 21.3 - - + +
408A GLU 3.6 7.9 - - - -
409A ILE 3.2 6.5 + - - +
411A SER* 1.3 97.7 + - - +
413A HIS* 1.3 71.3 + - + +
414A ALA 3.9 1.6 + - - -
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Residues in contact with HIS 413 (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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94A ASP* 3.0 21.7 + - - -
95A LEU 2.9 28.5 + - - -
96A ILE* 4.6 0.8 - - - -
97A ILE* 3.9 39.6 + - + +
409A ILE* 3.0 22.4 + - + +
410A GLN* 3.0 9.7 - - - +
412A PHE* 1.3 87.8 + - + +
414A ALA* 1.3 64.5 + - - +
415A ASP 3.0 4.9 + - - -
416A LEU* 3.1 19.6 + - + +
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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