Contacts of the helix formed by residues 399 - 414 (chain B) in PDB entry 6VW1
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 GLY 399 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B TYR* 4.5 0.4 + - - -
397B ASN* 2.7 18.6 + - - -
398B GLU* 1.3 76.0 - - - +
400B PHE* 1.3 58.5 + - - +
401B HIS 3.5 1.1 - - - -
402B GLU* 3.5 2.4 + - - -
403B ALA* 2.9 26.9 + - - +
514B ARG 4.0 8.7 - - - -
517B THR* 4.0 17.9 - - - -
518B ARG* 3.2 11.3 - - - +
521B TYR* 4.2 6.1 - - - -
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Residues in contact with PHE 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B TYR* 3.8 16.8 - + + +
395B GLY* 4.7 0.2 - - - -
396B ALA* 3.7 14.6 - - + +
397B ASN* 3.0 53.1 + - - +
399B GLY* 1.3 76.3 - - - +
401B HIS* 1.3 67.4 + - - +
403B ALA* 3.2 5.8 + - - +
404B VAL* 2.9 29.4 + - + +
521B TYR* 4.0 13.2 - + - -
525B PHE* 4.0 21.8 - + - -
557B MET* 3.3 36.1 - - + -
566B TRP* 3.6 30.1 - + + -
569B ALA* 4.2 6.3 - - + -
570B LEU* 4.2 13.9 - - + -
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Residues in contact with HIS 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B HIS* 3.0 48.1 + + + +
381B TYR* 3.4 36.3 - + + -
382B ASP* 2.9 26.3 + - - -
385B TYR* 3.3 12.3 + + - -
394B ASN* 4.7 3.7 + - - -
395B GLY* 3.4 30.7 - - - -
397B ASN 4.7 2.0 + - - -
398B GLU 4.8 3.3 + - - +
399B GLY 3.5 0.2 - - - -
400B PHE* 1.3 77.2 - - - +
402B GLU* 1.3 64.9 + - + +
404B VAL* 3.2 3.1 + - - +
405B GLY 3.0 19.4 + - - -
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Residues in contact with GLU 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B HIS* 3.2 28.5 + - - -
378B HIS* 3.9 12.0 + - + +
398B GLU 4.4 12.1 - - - +
399B GLY 3.5 2.6 + - - +
400B PHE 3.3 0.6 - - - -
401B HIS* 1.3 77.4 - - + +
403B ALA* 1.3 57.5 + - - +
406B GLU* 2.9 33.1 + - - +
514B ARG* 5.2 8.3 + - + +
515B TYR* 3.6 32.1 + - + -
518B ARG* 3.3 36.7 + - + -
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Residues in contact with ALA 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B GLY 2.9 19.1 + - - +
400B PHE* 3.2 5.6 + - - +
402B GLU* 1.3 77.0 - - - +
404B VAL* 1.3 56.5 + - - +
406B GLU* 3.2 1.8 + - - +
407B ILE* 2.9 35.0 + - - +
518B ARG* 3.7 14.3 - - - +
521B TYR* 3.6 28.7 - - + -
522B GLN* 3.8 4.9 - - - +
525B PHE* 3.8 15.7 - - + -
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Residues in contact with VAL 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLY 4.0 21.5 - - - +
380B GLN* 6.2 0.2 - - + -
381B TYR* 4.2 9.0 - - + -
400B PHE* 2.9 23.2 + - + +
401B HIS* 3.7 5.8 - - - +
403B ALA* 1.3 73.4 - - - +
405B GLY* 1.3 66.4 + - - +
407B ILE* 2.9 29.9 - - + +
408B MET* 3.1 32.5 + - + +
525B PHE* 4.8 9.6 - - + -
554B LEU* 4.5 8.3 - - + -
557B MET* 5.4 2.5 - - - -
558B LEU* 3.9 30.3 - - + -
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Residues in contact with GLY 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B HIS* 3.1 49.7 + - - -
377B GLY* 4.7 0.4 - - - -
378B HIS* 4.5 0.8 + - - -
401B HIS 3.0 12.0 + - - -
404B VAL* 1.3 76.6 - - - +
406B GLU* 1.3 57.3 + - - +
408B MET* 3.3 7.9 + - - +
409B SER* 3.0 24.8 + - - -
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Residues in contact with GLU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374B HIS* 3.0 22.5 + - + +
402B GLU 2.9 21.7 + - - +
403B ALA* 3.6 4.0 - - - +
404B VAL 3.1 0.4 - - - -
405B GLY* 1.3 74.3 - - - +
407B ILE* 1.3 60.0 + - - +
409B SER* 2.8 27.3 + - - -
410B LEU* 2.8 23.5 + - - +
445B THR* 5.9 2.3 - - - +
446B ILE* 5.1 8.1 - - - +
518B ARG* 3.7 28.8 + - - +
522B GLN* 3.2 39.3 + - + +
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Residues in contact with ILE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B ALA 2.9 15.4 + - - +
404B VAL* 2.9 31.0 - - - +
406B GLU* 1.3 72.8 - - - +
408B MET* 1.3 73.2 + - - +
410B LEU* 3.3 10.0 + - + +
411B SER* 3.0 26.9 + - - -
522B GLN* 3.1 35.0 - - + +
525B PHE* 3.8 25.1 - - + -
526B GLN* 4.0 14.3 - - + +
529B LEU* 4.0 11.2 - - + -
544B ILE* 5.6 2.8 - - + +
554B LEU* 3.8 29.6 - - + -
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Residues in contact with MET 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B PHE* 4.0 20.6 - - + -
315B PHE* 3.5 39.7 - - + -
320B LEU* 5.4 6.1 - - + -
373B HIS* 3.8 22.1 - - + +
377B GLY* 4.1 4.5 - - - -
380B GLN* 6.0 0.9 - - + -
404B VAL* 3.1 30.1 + - + +
405B GLY 3.3 8.1 - - - +
406B GLU 3.2 0.2 - - - -
407B ILE* 1.3 82.4 - - + +
409B SER* 1.3 58.5 + - - +
411B SER* 3.3 3.3 + - - -
412B ALA* 3.0 27.4 + - - +
544B ILE* 5.0 8.5 - - + -
554B LEU* 3.6 30.3 - - + -
558B LEU* 5.7 1.6 - - + -
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Residues in contact with SER 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 3.8 38.0 - - - +
373B HIS* 4.5 1.3 - - - +
374B HIS* 4.9 1.1 - - - -
405B GLY 3.0 8.8 + - - -
406B GLU* 2.8 44.4 + - - -
408B MET* 1.3 72.2 - - - +
410B LEU* 1.3 59.5 + - - +
412B ALA* 3.7 7.2 - - - +
413B ALA* 2.9 33.3 + - - +
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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
----------------------------------------------------------
406B GLU* 2.8 24.3 + - - +
407B ILE* 3.5 14.1 - - - +
409B SER* 1.3 79.0 + - - +
411B SER* 1.3 63.5 + - - +
413B ALA* 3.4 8.1 + - - +
414B THR* 3.5 16.6 + - - +
438B PHE* 5.0 0.3 - - - -
442B GLN* 3.7 28.2 + - - +
446B ILE* 4.0 10.3 - - + -
522B GLN* 3.7 34.8 - - + +
523B PHE* 4.1 14.4 - - + -
526B GLN* 4.2 30.7 - - + +
587B TYR* 3.8 13.8 + - + +
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Residues in contact with SER 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B PHE* 4.1 9.6 - - - -
407B ILE 3.0 12.4 + - - -
408B MET 3.8 6.3 - - - -
410B LEU* 1.3 75.6 - - - +
412B ALA* 1.3 59.4 + - - +
414B THR* 2.9 24.4 + - - -
417B HIS* 3.5 8.1 - - - +
526B GLN* 3.8 13.7 + - - -
542B CYS 4.4 8.3 - - - -
543B ASP* 3.4 19.6 - - - +
544B ILE* 3.3 32.6 + - - +
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Residues in contact with ALA 412 (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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314B PHE* 5.2 1.5 - - + -
369B PHE* 3.9 8.3 - - + -
370B LEU* 4.0 12.8 - - + -
373B HIS* 3.6 34.5 - - + +
408B MET 3.0 18.1 + - - +
409B SER* 3.8 3.8 - - - +
410B LEU 3.2 0.2 - - - -
411B SER* 1.3 77.8 - - - +
413B ALA* 1.3 60.1 + - - +
414B THR 3.5 1.2 + - - +
417B HIS* 3.4 23.9 + - + +
418B LEU* 3.9 14.0 - - - +
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Residues in contact with ALA 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ILE* 4.7 0.7 - - - +
366B MET* 4.2 13.1 - - + +
370B LEU* 3.9 24.4 - - + +
409B SER 2.9 17.5 + - - +
410B LEU 3.4 4.5 + - - +
411B SER 3.3 0.6 - - - -
412B ALA* 1.3 75.8 - - - +
414B THR* 1.3 65.1 + - - +
415B PRO* 3.5 0.5 - - - +
418B LEU* 3.5 13.1 - - - +
438B PHE* 3.3 23.2 - - + -
441B LYS* 5.9 0.2 - - - +
442B GLN* 4.3 14.4 - - - +
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Residues in contact with THR 414 (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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410B LEU 3.5 16.6 - - - +
411B SER 2.9 14.0 + - - +
413B ALA* 1.3 79.7 - - - +
415B PRO* 1.3 67.5 - - - +
416B LYS* 4.3 6.2 - - - +
417B HIS* 3.4 13.5 + - - +
418B LEU* 3.0 24.1 + - - +
438B PHE* 4.0 7.4 - - + -
540B HIS 3.7 20.2 - - - +
541B LYS* 4.8 3.8 - - - -
542B CYS 3.7 23.3 - - - +
543B ASP* 3.8 8.3 - - - +
587B TYR* 5.7 0.9 - - - +
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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
------------------------------------------------------------
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