Contacts of the helix formed by residues 398 - 410 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A GLU 5.5 2.4 + - - -
394B ASP 4.0 0.8 + - - -
395B GLY 2.8 19.4 + - - -
396B ASN* 4.1 6.2 + - - -
397B LEU* 1.3 79.5 - - - +
399B VAL* 1.3 64.6 + - - +
400B SER* 3.3 2.7 - - - -
401B GLU* 3.2 29.7 + - - -
402B ARG* 3.1 20.9 + - - +
419B GLN* 5.9 1.3 - - - -
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Residues in contact with VAL 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ALA* 4.3 5.8 - - + -
393B PHE* 3.5 47.6 - - + -
394B ASP 5.2 0.4 + - - +
397B LEU* 3.8 19.1 - - + +
398B SER* 1.3 76.3 - - - +
400B SER* 1.3 56.6 + - - +
402B ARG* 3.3 6.5 + - - +
403B ILE* 3.0 31.9 + - + +
419B GLN* 4.6 12.7 - - - +
448B VAL* 4.0 17.9 - - + -
449B PHE* 4.2 15.0 - - + -
452B VAL* 4.2 13.7 - - + -
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Residues in contact with SER 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ALA* 5.5 0.9 - - - +
398B SER 3.3 0.2 - - - -
399B VAL* 1.3 75.6 - - - +
401B GLU* 1.3 62.3 + - - +
403B ILE* 3.3 7.1 + - - +
404B ALA* 2.9 30.5 + - - +
416B PRO* 3.5 20.2 - - - +
418B GLY 3.0 25.7 + - - -
419B GLN* 3.1 8.9 + - - +
420B SER 3.1 24.6 + - - -
421B VAL* 3.8 8.7 - - - +
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Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLU* 5.9 2.8 - - - +
317A PHE* 4.5 21.2 + - - -
398B SER* 3.2 28.7 + - - +
400B SER* 1.3 80.2 - - - +
402B ARG* 1.3 59.2 + - + +
404B ALA* 3.3 1.4 + - - +
405B ASN* 2.8 55.0 + - - +
416B PRO* 3.9 15.7 - - + +
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Residues in contact with ARG 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LEU* 3.0 52.5 + - - +
398B SER* 3.1 11.2 + - - +
399B VAL* 3.6 8.3 - - - +
400B SER 3.2 0.2 - - - -
401B GLU* 1.3 74.3 - - + +
403B ILE* 1.3 59.3 + - - +
405B ASN* 3.8 7.3 - - - +
406B THR* 2.8 35.4 + - - +
448B VAL* 3.7 15.2 - - + +
451B GLU* 4.8 22.5 + - - +
452B VAL* 3.9 22.2 - - - +
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Residues in contact with ILE 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B ILE* 5.8 0.4 - - + -
383B ALA* 4.7 7.9 - - + -
399B VAL* 3.0 23.5 + - + +
400B SER* 3.3 7.6 + - - +
402B ARG* 1.3 76.5 - - - +
404B ALA* 1.3 56.7 + - - +
406B THR* 3.2 3.0 + - - -
407B CYS* 2.8 31.1 + - - -
421B VAL* 3.9 24.9 - - + -
441B LEU* 4.1 17.3 - - + -
444B ALA* 4.0 4.7 - - + +
445B LEU* 3.6 34.8 - - + -
448B VAL* 3.7 24.9 - - + -
449B PHE* 4.2 14.4 - - + -
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400B SER 2.9 19.7 + - - +
401B GLU 3.8 2.0 - - - +
403B ILE* 1.3 73.6 - - - +
405B ASN* 1.3 65.8 + - - +
407B CYS* 3.3 3.9 + - - +
408B THR* 3.0 25.6 + - - -
414B CYS* 3.8 33.5 + - - +
416B PRO* 3.6 26.5 - - + -
421B VAL* 5.0 0.4 - - + -
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Residues in contact with ASN 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B GLU* 2.8 49.0 + - - +
402B ARG* 3.9 7.3 - - - +
404B ALA* 1.3 74.6 - - - +
406B THR* 1.3 60.8 + - - +
408B THR* 3.3 10.0 + - - -
409B ASP* 3.2 28.5 + - - +
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Residues in contact with THR 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B ARG* 2.8 18.7 + - - +
403B ILE 3.6 3.4 - - - -
405B ASN* 1.3 72.9 - - - +
407B CYS* 1.3 65.0 + - - +
409B ASP* 3.3 12.7 + - + +
410B LEU* 3.2 26.8 + - + +
444B ALA* 3.7 29.2 - - - +
447B LYS* 4.2 25.9 - - + +
448B VAL* 3.5 11.5 - - - +
451B GLU* 5.1 4.7 + - - -
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Residues in contact with CYS 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B ILE* 2.8 22.2 + - - +
404B ALA 3.4 9.2 - - - +
406B THR* 1.3 71.5 - - - +
408B THR* 1.3 64.4 + - - +
410B LEU* 2.9 13.9 + - - +
411B GLY 3.0 0.3 + - - -
412B LEU* 2.9 54.0 + - + +
414B CYS* 3.8 16.6 - - - +
440B LYS 4.8 0.7 - - - -
441B LEU* 3.7 23.8 - - - -
444B ALA* 3.6 19.5 - - - +
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Residues in contact with THR 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ARG* 4.8 7.9 + - - +
31B VAL* 4.2 19.1 - - + -
47B ARG* 3.1 12.7 + - - +
49B TYR* 3.4 25.6 - - + -
404B ALA 3.0 14.9 + - - -
405B ASN* 3.5 11.3 + - - -
406B THR 3.3 0.4 - - - -
407B CYS* 1.3 73.3 - - - +
409B ASP* 1.3 66.7 + - - +
411B GLY 3.0 11.6 + - - -
412B LEU 3.2 12.0 + - - +
413B ILE* 4.3 12.6 - - + +
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Residues in contact with ASP 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ARG* 3.3 20.6 + - - +
405B ASN* 3.2 14.2 + - - +
406B THR* 3.4 16.1 + - + +
408B THR* 1.3 79.8 - - - +
410B LEU* 1.3 63.5 + - + +
411B GLY 3.3 0.2 - - - -
447B LYS* 6.0 1.1 - - - +
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ARG* 5.7 0.7 - - - -
406B THR* 3.2 18.1 + - + +
407B CYS* 2.9 9.8 + - - +
409B ASP* 1.3 82.2 - - + +
411B GLY* 1.3 57.0 + - - +
412B LEU 3.5 0.2 - - - -
440B LYS* 3.1 57.4 + - + +
443B LYS* 3.7 27.4 - - + +
444B ALA* 3.7 20.4 - - + +
447B LYS* 3.4 26.9 - - - +
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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