Contacts of the helix formed by residues 393 - 403 (chain G) in PDB entry 1MVW
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 ASN 393 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387G ALA* 3.9 2.5 - - - -
392G LEU* 1.3 77.5 - - - +
394G SER* 1.3 66.5 + - - +
395G ALA* 3.0 25.0 + - - +
396G GLU* 3.6 31.5 + - + +
397G LEU* 3.0 24.3 + - - +
610G LEU* 6.2 0.4 - - - +
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Residues in contact with SER 394 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380G THR* 5.1 7.0 - - - -
383G ALA* 3.6 5.8 - - - +
384G ASP* 2.3 49.6 + - - -
387G ALA* 3.5 14.4 - - - +
393G ASN* 1.3 73.5 + - - +
395G ALA* 1.3 58.1 + - - +
397G LEU* 3.4 3.8 - - - +
398G LEU* 3.0 34.4 + - - +
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Residues in contact with ALA 395 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393G ASN* 3.0 10.6 + - - +
394G SER* 1.3 76.9 - - - +
396G GLU* 1.3 70.4 - - + +
397G LEU 2.8 1.8 - - - -
398G LEU* 2.8 20.0 + - - +
399G LYS* 2.9 15.5 + - - +
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Residues in contact with GLU 396 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393G ASN* 3.6 32.4 + - + +
395G ALA* 1.3 80.4 - - + +
397G LEU* 1.3 62.4 - - - +
399G LYS* 3.4 6.6 + - - +
400G ALA* 3.2 25.8 + - - +
610G LEU* 3.8 23.3 - - + +
613G MLY 5.8 5.5 - - - -
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Residues in contact with LEU 397 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361G TYR* 4.6 13.2 - - + +
364G LEU* 5.2 5.2 - - + -
383G ALA* 4.6 8.7 - - + +
386G ALA* 5.1 4.7 - - + -
387G ALA* 4.6 17.0 - - + +
392G LEU* 4.2 23.3 - - + -
393G ASN 3.0 18.7 + - - +
394G SER 3.4 3.4 - - - +
395G ALA 2.8 1.2 - - - -
396G GLU* 1.3 77.2 - - - +
398G LEU* 1.3 79.5 + - + +
400G ALA* 3.5 1.0 + - - +
401G LEU* 3.1 37.8 + - + +
607G VAL* 3.9 28.3 - - + -
610G LEU* 3.6 11.0 - - + +
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Residues in contact with LEU 398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364G LEU* 4.9 6.3 - - + -
366G PHE* 4.8 7.9 - - + -
377G PRO* 4.0 29.7 - - + +
379G GLY 4.3 2.2 - - - +
380G THR* 3.4 33.9 - - + -
383G ALA* 3.6 24.7 - - + -
394G SER 3.0 16.2 + - - +
395G ALA* 2.8 10.4 + - - +
397G LEU* 1.3 86.9 - - + +
399G LYS* 1.3 61.4 + - - +
401G LEU* 3.8 12.2 - - + +
402G CYS* 3.1 29.3 + - - +
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Residues in contact with LYS 399 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395G ALA 2.9 10.3 + - - +
396G GLU* 3.4 12.6 - - - +
398G LEU* 1.3 74.4 - - - +
400G ALA* 1.3 57.8 + - - +
401G LEU 3.0 0.9 - - - -
402G CYS* 2.7 9.3 + - - -
403G TYR* 2.4 66.7 + - + +
414G THR* 6.0 3.0 - - - +
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Residues in contact with ALA 400 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396G GLU 3.2 14.0 + - - +
397G LEU 3.7 4.0 - - - +
399G LYS* 1.3 78.6 - - - +
401G LEU* 1.3 62.3 + - - +
403G TYR 4.4 4.7 - - - -
404G PRO* 3.2 16.5 - - - +
604G ASN* 2.9 18.4 + - - +
606G THR* 3.0 35.7 - - + -
607G VAL* 3.8 12.6 - - + +
610G LEU* 4.2 8.3 - - + -
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Residues in contact with LEU 401 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361G TYR* 6.0 4.5 - - + -
364G LEU* 4.2 18.8 - - + -
366G PHE* 4.3 8.7 - - + -
397G LEU* 3.1 27.6 + - + +
398G LEU* 3.8 9.0 - - + +
400G ALA* 1.3 82.7 - - - +
402G CYS* 1.4 60.2 + - - +
404G PRO* 3.9 0.2 - - - +
417G GLU* 3.6 18.7 - - - +
422G VAL* 4.0 26.5 - - + +
425G SER* 4.5 7.2 + - - +
426G VAL* 4.1 18.2 - - + -
429G LEU* 4.0 18.6 - - + -
604G ASN* 3.7 7.4 + - - +
607G VAL* 3.4 26.5 - - + -
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Residues in contact with CYS 402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366G PHE* 3.9 21.8 - - - -
374G GLN* 2.6 25.0 + - - +
375G ALA* 3.6 28.7 - - - +
377G PRO* 3.9 22.0 - - - -
398G LEU 3.1 17.7 + - - +
399G LYS 2.7 7.0 + - - +
401G LEU* 1.4 72.2 - - - +
403G TYR* 1.3 69.7 + - + +
404G PRO* 2.9 13.2 - - - +
417G GLU* 3.4 6.4 + - - +
422G VAL* 4.7 6.3 - - - -
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Residues in contact with TYR 403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369G MLY 3.9 25.7 - - - +
372G GLU* 5.2 0.8 + - - -
374G GLN* 2.8 44.8 - - + +
375G ALA 4.1 3.4 + - - -
376G GLU* 5.4 3.0 - - + +
399G LYS* 2.4 61.5 + - + +
400G ALA* 3.7 4.2 - - - +
402G CYS* 1.3 78.7 - - + +
404G PRO* 1.3 70.2 - - - +
405G ARG* 3.0 7.8 + - - +
414G THR* 4.1 18.4 - - + +
415G MLY 3.3 4.9 - - - +
416G GLY* 4.3 6.5 - - - -
606G THR* 5.4 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