Contacts of the helix formed by residues 398 - 410 (chain A) in PDB entry 3NUI
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 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A ASP 4.1 1.0 + - - -
395A GLY 2.9 17.9 + - - -
396A ASN* 4.2 5.3 + - - -
397A LEU* 1.3 79.9 - - - +
399A VAL* 1.3 65.5 + - - +
400A SER* 3.3 3.7 + - - -
401A GLU* 3.3 30.2 + - - -
402A ARG* 3.0 22.2 + - - +
419A GLN* 5.8 2.7 - - - +
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Residues in contact with VAL 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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383A ALA* 4.2 7.0 - - + -
393A PHE* 3.5 45.8 - - + -
394A ASP 5.2 0.4 + - - +
397A LEU* 4.0 17.5 - - + +
398A SER* 1.3 73.5 - - - +
400A SER* 1.3 56.9 + - - +
402A ARG* 3.2 6.5 + - - +
403A ILE* 2.9 32.4 + - + +
419A GLN* 4.5 10.8 + - - +
448A VAL* 4.1 12.6 - - + -
449A PHE* 4.0 27.1 - - + -
452A VAL* 4.3 11.7 - - + -
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Residues in contact with SER 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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383A ALA* 5.5 0.4 - - - +
398A SER 3.3 0.6 - - - -
399A VAL* 1.3 73.3 - - - +
401A GLU* 1.3 62.2 + - - +
403A ILE* 3.3 4.8 + - - +
404A ALA* 2.9 29.5 + - - +
416A PRO* 3.7 11.2 - - - -
418A GLY 3.4 16.8 - - - -
419A GLN* 3.0 27.8 + - - +
420A SER 2.8 26.9 + - - -
421A VAL* 3.5 13.4 - - - +
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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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398A SER* 3.3 30.2 + - - +
400A SER* 1.3 78.0 - - - +
402A ARG* 1.3 61.1 + - + +
404A ALA* 3.7 2.4 - - - +
405A ASN* 2.8 45.4 + - - +
416A PRO* 4.1 21.3 - - + -
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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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396A ASN 5.5 0.4 + - - -
397A LEU* 3.0 39.9 + - - +
398A SER* 3.0 16.7 + - - +
399A VAL* 3.5 9.9 - - - +
401A GLU* 1.3 72.5 - - + +
403A ILE* 1.3 67.5 + - - +
405A ASN* 3.9 7.3 - - - +
406A THR* 3.0 29.3 + - - -
448A VAL* 3.5 14.6 - - + +
451A GLU* 3.5 35.2 + - - +
452A VAL* 3.6 24.2 - - - +
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Residues in contact with ILE 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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383A ALA* 4.6 7.4 - - + -
399A VAL* 2.9 33.2 + - + +
400A SER* 3.3 7.8 + - - +
402A ARG* 1.3 76.5 - - - +
404A ALA* 1.3 58.9 + - - +
406A THR* 3.3 2.6 + - - -
407A CYS* 2.9 41.6 + - - -
421A VAL* 3.8 23.6 - - + -
441A LEU* 4.2 7.0 - - + -
444A ALA* 4.2 3.8 - - + +
445A LEU* 3.5 36.1 - - + -
448A VAL* 3.8 22.7 - - + -
449A PHE* 4.2 11.2 - - + -
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Residues in contact with ALA 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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400A SER 2.9 17.1 + - - +
401A GLU* 3.7 3.8 - - - +
402A ARG 3.2 0.2 - - - -
403A ILE* 1.3 77.5 - - - +
405A ASN* 1.3 63.5 + - - +
407A CYS* 3.2 5.0 + - - +
408A THR* 3.1 24.1 + - - -
414A CYS* 3.6 36.3 + - - +
416A PRO* 4.0 20.2 - - + -
421A VAL* 4.8 0.4 - - + -
85B PHE* 6.0 1.1 - - + -
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Residues in contact with ASN 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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401A GLU* 2.8 33.6 + - - +
402A ARG* 4.0 6.2 - - - +
404A ALA* 1.3 75.6 - - - +
406A THR* 1.3 62.0 + - - +
408A THR* 3.3 11.5 + - - +
409A ASP* 3.2 26.7 + - - +
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Residues in contact with THR 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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402A ARG* 3.0 18.9 + - - +
403A ILE 3.8 3.1 - - - -
405A ASN* 1.3 72.9 - - - +
407A CYS* 1.3 66.2 + - - +
409A ASP* 3.2 14.1 + - + +
410A LEU* 3.1 29.1 + - + +
444A ALA* 3.6 28.3 - - + +
447A LYS* 3.4 40.2 - - + -
448A VAL* 3.5 7.4 - - - +
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Residues in contact with CYS 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 ILE* 2.9 23.2 + - - -
404A ALA 3.2 8.9 + - - +
406A THR* 1.3 75.1 - - - +
408A THR* 1.3 61.6 + - - +
410A LEU* 2.9 8.4 + - - +
411A GLY 2.9 6.6 + - - -
412A LEU* 2.8 61.0 + - + +
414A CYS* 3.8 20.2 - - - +
440A LYS 5.4 0.4 - - - -
441A LEU* 3.9 13.9 - - - -
444A ALA* 3.6 20.2 - - - -
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Residues in contact with THR 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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31A VAL* 5.7 4.3 - - + -
47A ARG* 3.7 1.6 + - - -
49A TYR* 3.5 17.2 - - + -
404A ALA 3.1 9.8 + - - -
405A ASN* 3.4 13.4 - - - +
406A THR 3.3 0.2 - - - -
407A CYS* 1.3 76.0 - - - +
409A ASP* 1.3 62.2 + - - +
411A GLY* 2.8 20.1 + - - -
412A LEU 2.9 15.0 + - - +
413A ILE* 4.6 6.9 - - - +
414A CYS 5.5 0.2 + - - -
85B PHE* 6.0 0.7 - - - -
86B PHE* 3.7 35.5 - - + -
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Residues in contact with ASP 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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47A ARG* 2.8 26.8 + - - +
405A ASN* 3.2 16.6 + - - +
406A THR* 3.2 19.1 + - + +
408A THR* 1.3 79.5 - - - +
410A LEU* 1.3 63.4 + - + +
411A GLY 3.3 0.2 - - - -
447A LYS* 5.6 3.1 - - - -
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Residues in contact with LEU 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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47A ARG* 4.0 7.0 + - - +
406A THR* 3.1 21.1 + - + +
407A CYS* 2.9 10.8 + - - +
409A ASP* 1.3 83.5 - - + +
411A GLY* 1.3 56.5 + - - +
440A LYS* 3.2 45.7 - - + +
443A LYS* 3.9 17.7 - - + -
444A ALA* 3.5 33.2 - - + +
447A LYS* 6.3 0.2 - - + -
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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
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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