Contacts of the helix formed by residues 395 - 416 (chain B) in PDB entry 2N5T
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 395 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LEU* 5.9 0.7 - - - +
478A SER* 6.6 0.2 - - - -
393B ILE* 3.9 2.3 - - - +
394B ILE* 1.3 86.8 - - - +
396B VAL* 1.3 64.3 + - - +
397B GLU* 3.3 20.2 + - - +
398B GLU* 2.9 38.1 + - - +
399B VAL* 3.6 9.4 + - - +
438B ILE* 3.7 12.1 - - - +
442B LEU* 3.7 9.1 - - - +
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Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A PRO* 3.2 27.5 + - + +
557A THR* 4.0 9.4 - - - +
395B SER* 1.3 69.4 - - - +
397B GLU* 1.3 71.4 + - - +
399B VAL* 3.2 4.2 + - - +
400B ARG* 3.1 49.2 + - + +
438B ILE* 3.7 8.2 - - + +
441B HIS* 3.6 32.5 - - + +
442B LEU* 4.0 19.1 - - + -
445B GLU* 4.3 13.2 - - + -
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A PRO* 5.5 2.3 - - - +
556A PRO 4.1 4.5 - - - +
557A THR* 2.7 25.3 + - + +
558A THR* 2.7 41.5 + - - -
559A ASP* 4.0 5.9 + - - +
395B SER* 3.3 20.1 - - - +
396B VAL* 1.3 78.3 + - - +
398B GLU* 1.3 64.1 + - + +
400B ARG* 3.3 7.1 + - - +
401B ALA* 3.0 23.0 + - - +
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Residues in contact with GLU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A LEU* 3.6 34.2 - - + +
360B ILE* 4.5 9.8 - - - +
361B ARG* 4.6 5.9 + - - +
364B MET* 4.4 22.9 - - + +
392B MET 3.8 3.0 - - - +
393B ILE* 3.5 16.0 - - + +
394B ILE* 2.7 37.8 + - - +
395B SER* 2.9 25.7 + - - +
396B VAL 3.3 0.2 - - - -
397B GLU* 1.3 73.1 - - + +
399B VAL* 1.3 64.2 + - - +
401B ALA* 3.1 15.4 + - - +
402B LEU* 3.1 20.9 + - + +
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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
----------------------------------------------------------
390B PHE* 5.5 2.6 - - + -
393B ILE* 3.8 12.3 - - + -
395B SER 3.6 0.4 + - - -
396B VAL* 3.2 8.5 + - + +
398B GLU* 1.3 76.5 - - - +
400B ARG* 1.3 64.3 + - - +
402B LEU* 3.2 9.8 + - + +
403B ARG* 2.9 35.5 + - + +
426B ILE* 6.4 0.2 - - + -
428B VAL* 3.7 24.0 - - + -
442B LEU* 3.6 28.9 - - + -
445B GLU* 4.1 17.3 - - + +
446B VAL* 4.0 20.9 - - + -
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Residues in contact with ARG 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A PRO* 4.6 13.9 - - - +
557A THR* 4.3 13.4 + - - +
560A GLU* 4.9 6.7 + - - -
396B VAL* 3.1 32.3 + - + +
397B GLU* 3.8 8.7 - - - +
399B VAL* 1.3 78.9 - - + +
401B ALA* 1.3 62.3 + - - +
403B ARG* 3.9 6.5 - - - +
404B LYS* 3.1 35.5 + - + +
445B GLU* 3.4 35.0 + - + +
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B MET* 3.9 24.0 - - + -
397B GLU 3.0 17.2 + - - +
398B GLU 3.1 4.9 + - - +
400B ARG* 1.3 77.2 - - - +
402B LEU* 1.3 58.2 + - - +
404B LYS* 3.5 10.2 - - - +
405B GLU* 2.9 37.4 + - - +
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Residues in contact with LEU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ILE* 3.6 21.5 - - + -
364B MET* 3.6 35.0 - - + -
370B LEU* 3.9 22.2 - - + -
374B LEU* 4.8 0.7 - - + +
390B PHE* 3.5 45.4 - - + -
393B ILE* 4.0 12.3 - - + -
398B GLU 3.1 20.9 + - - +
399B VAL* 3.7 4.0 - - - +
400B ARG 3.2 0.2 - - - -
401B ALA* 1.3 77.9 - - - +
403B ARG* 1.3 53.5 + - - +
404B LYS 3.2 1.1 - - - -
405B GLU* 3.2 7.9 + - - +
406B ILE* 2.7 38.8 + - - +
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Residues in contact with ARG 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B PHE* 5.6 1.1 - - + -
399B VAL* 2.9 33.9 + - + +
400B ARG* 3.9 6.5 - - - +
402B LEU* 1.3 73.7 - - + +
404B LYS* 1.3 61.2 + - + +
406B ILE* 3.2 8.2 + - + +
407B GLU* 2.8 49.6 + - + +
410B LYS* 5.6 1.6 - - - +
426B ILE* 3.2 50.0 - - + +
445B GLU* 4.2 17.9 + - + +
446B VAL* 6.2 0.4 - - - +
447B ASP* 5.8 3.8 + - - -
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Residues in contact with LYS 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B ARG* 3.1 25.6 + - + +
401B ALA* 3.5 10.1 - - - +
403B ARG* 1.3 78.9 - - + +
405B GLU* 1.3 64.8 + - - +
407B GLU* 3.3 9.5 + - - +
408B ILE* 3.1 32.5 + - + +
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Residues in contact with GLU 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B MET* 6.0 1.6 - - - +
367B ARG* 4.0 23.5 + - - -
370B LEU* 3.9 17.5 - - + +
374B LEU* 4.9 0.9 - - + -
401B ALA* 2.9 28.0 + - - +
402B LEU* 3.2 13.6 + - - +
404B LYS* 1.3 78.1 - - - +
406B ILE* 1.3 69.2 + - - +
408B ILE* 2.9 29.9 + - - +
409B TYR* 3.0 53.8 + - + +
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Residues in contact with ILE 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B LEU* 4.1 20.6 - - + -
378B LEU* 4.4 13.2 - - + +
388B ILE* 4.4 7.0 - - + -
390B PHE* 3.7 27.6 - - + -
402B LEU 2.7 20.1 + - - +
403B ARG* 3.2 12.5 + - - +
405B GLU* 1.3 71.4 - - - +
407B GLU* 1.3 55.5 + - - +
409B TYR* 2.9 10.5 + - - +
410B LYS* 2.6 61.4 + - + +
426B ILE* 3.5 35.0 - - + -
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Residues in contact with GLU 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ARG* 2.8 36.4 + - + +
404B LYS* 3.6 8.1 - - - +
406B ILE* 1.3 74.9 - - + +
408B ILE* 1.3 61.4 + - + +
410B LYS* 3.1 39.4 + - - +
411B GLN* 3.2 33.0 + - - +
414B ARG* 4.8 6.6 + - - -
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404B LYS* 3.1 20.5 + - + +
405B GLU* 2.9 27.1 + - - +
407B GLU* 1.3 74.8 - - + +
409B TYR* 1.3 75.1 + - + +
411B GLN* 3.1 9.2 + - - +
412B GLU* 3.1 40.9 + - + +
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Residues in contact with TYR 409 (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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367B ARG* 4.5 12.5 - - - +
370B LEU* 4.5 4.5 - - + +
371B ARG* 3.4 51.4 + - + +
374B LEU* 3.9 28.9 - - + -
375B ARG* 4.3 15.0 + - + +
378B LEU* 4.4 12.3 - - + -
405B GLU* 3.0 56.0 + - + +
406B ILE* 2.9 4.9 + - - +
408B ILE* 1.3 85.8 - - + +
410B LYS* 1.3 62.1 + - - +
412B GLU* 3.6 16.6 + - - +
413B LEU* 3.2 27.5 + - - +
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Residues in contact with LYS 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B LEU* 4.0 11.4 - - + +
403B ARG* 5.6 1.4 - - - +
406B ILE* 2.6 38.4 + - + +
407B GLU* 3.1 38.9 + - - +
408B ILE 3.1 0.4 - - - -
409B TYR* 1.3 73.4 - - - +
411B GLN* 1.3 61.8 + - - +
413B LEU* 3.3 1.8 + - - -
414B ARG* 3.0 30.1 + - - +
420B PHE* 3.2 43.3 - - + -
422B GLU* 4.5 13.3 + - - +
424B ILE* 4.2 23.5 + - - +
426B ILE* 5.0 6.2 - - - +
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Residues in contact with GLN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B GLU* 3.2 19.4 + - - +
408B ILE* 3.1 9.5 + - - +
410B LYS* 1.3 77.7 - - - +
412B GLU* 1.3 67.7 + - + +
414B ARG* 2.8 40.9 + - - +
415B ASP* 2.8 37.4 + - - +
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Residues in contact with GLU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ARG* 3.4 25.1 + - - +
375B ARG* 3.3 24.6 + - - +
408B ILE* 3.1 31.0 + - + +
409B TYR* 3.8 12.4 - - - +
411B GLN* 1.3 78.8 - - + +
413B LEU* 1.3 63.7 + - - +
415B ASP* 2.9 22.2 + - - +
416B GLU* 2.9 22.3 + - + +
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B ARG* 3.6 36.6 - - + +
378B LEU* 3.5 35.4 - - + -
379B ARG* 3.5 34.5 - - + +
409B TYR 3.2 14.6 + - - +
410B LYS 3.5 6.3 - - - +
411B GLN 3.2 0.6 - - - -
412B GLU* 1.3 76.4 - - - +
414B ARG* 1.3 62.7 + - - +
416B GLU* 2.9 14.3 + - - +
418B LYS* 3.2 41.6 + - + +
420B PHE* 3.7 14.1 - - + -
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Residues in contact with ARG 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407B GLU* 4.8 3.2 + - - -
410B LYS* 3.0 29.7 + - - +
411B GLN* 2.8 48.2 + - - +
413B LEU* 1.3 74.7 - - - +
415B ASP* 1.3 63.9 + - - +
417B GLY* 3.4 10.9 + - - -
418B LYS 4.7 3.1 - - - +
420B PHE* 3.3 11.2 - - + -
422B GLU* 2.5 53.1 + - - +
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Residues in contact with ASP 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B GLN* 2.8 30.9 + - - +
412B GLU* 2.9 13.7 + - - +
414B ARG* 1.3 75.9 - - - +
416B GLU* 1.3 61.2 + - + +
417B GLY 3.3 1.7 + - - -
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ARG* 4.8 4.5 + - - -
375B ARG* 2.8 28.2 + - - -
412B GLU* 2.9 21.2 + - - +
413B LEU* 2.9 4.6 + - - +
415B ASP* 1.3 79.0 - - + +
417B GLY* 1.3 63.2 + - - +
418B LYS* 2.7 45.2 + - + +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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