Contacts of the helix formed by residues 393 - 403 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387P ALA* 3.9 2.2 - - - -
392P LEU* 1.3 77.5 - - - +
394P SER* 1.3 66.8 + - - +
395P ALA* 3.0 24.7 + - - +
396P GLU* 3.6 30.8 + - - +
397P LEU* 3.0 24.7 + - - +
610P LEU* 5.3 1.0 - - - +
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Residues in contact with SER 394 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380P THR* 5.1 6.7 - - - -
383P ALA* 3.6 5.4 - - - +
384P ASP* 2.3 49.1 + - - -
387P ALA* 3.5 15.3 - - - +
392P LEU 4.1 0.2 + - - -
393P ASN* 1.3 73.2 + - - +
395P ALA* 1.3 58.0 + - - +
397P LEU* 3.4 4.0 - - - +
398P LEU* 3.0 34.4 + - - +
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Residues in contact with ALA 395 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380P THR* 6.4 0.7 - - - -
393P ASN* 3.0 10.5 + - - +
394P SER* 1.3 76.3 - - - +
396P GLU* 1.3 70.3 - - + +
397P LEU 2.8 1.6 - - - -
398P LEU* 2.8 19.5 + - - +
399P LYS* 2.9 16.0 + - - +
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Residues in contact with GLU 396 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393P ASN* 3.3 31.2 + - + +
395P ALA* 1.3 80.4 - - + +
397P LEU* 1.3 61.3 - - - +
399P LYS* 3.4 6.9 + - - +
400P ALA* 3.2 25.6 + - - +
610P LEU* 3.8 25.0 - - + +
613P MLY 5.8 5.1 - - - -
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Residues in contact with LEU 397 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361P TYR* 4.6 12.6 - - + +
364P LEU* 5.2 4.9 - - + -
383P ALA* 4.6 9.2 - - + +
386P ALA* 5.1 4.9 - - + -
387P ALA* 4.6 16.2 - - + +
392P LEU* 4.2 24.9 - - + -
393P ASN 3.0 18.8 + - - +
394P SER 3.4 3.1 - - - +
395P ALA 2.8 1.0 - - - -
396P GLU* 1.3 76.4 - - - +
398P LEU* 1.3 80.6 + - + +
400P ALA* 3.5 1.6 + - - +
401P LEU* 3.1 37.3 + - + +
607P VAL* 3.9 27.6 - - + -
610P LEU* 3.6 10.9 - - + +
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Residues in contact with LEU 398 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364P LEU* 4.9 6.5 - - + -
366P PHE* 4.8 7.6 - - + -
377P PRO* 4.0 30.6 - - + +
379P GLY 4.3 2.0 - - - +
380P THR* 3.4 33.0 - - + -
383P ALA* 3.6 25.4 - - + -
394P SER 3.0 16.0 + - - +
395P ALA* 2.8 11.5 + - - +
397P LEU* 1.3 85.6 - - + +
399P LYS* 1.3 61.2 + - - +
401P LEU* 3.8 12.0 - - + +
402P CYS* 3.1 30.0 + - - +
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Residues in contact with LYS 399 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395P ALA 2.9 10.7 + - - +
396P GLU* 3.4 12.3 - - - +
397P LEU 3.1 0.2 - - - -
398P LEU* 1.3 73.8 - - - +
400P ALA* 1.3 57.1 + - - +
401P LEU 3.0 1.1 - - - -
402P CYS* 2.7 8.1 + - - -
403P TYR* 2.4 65.7 + - + +
414P THR* 6.0 2.8 - - - +
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Residues in contact with ALA 400 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396P GLU 3.2 14.3 + - - +
397P LEU 3.7 4.7 - - - +
399P LYS* 1.3 78.9 - - - +
401P LEU* 1.3 61.6 + - - +
403P TYR 4.4 4.3 - - - -
404P PRO* 3.2 16.5 - - - +
604P ASN* 2.9 18.6 + - - -
606P THR* 3.0 34.8 - - + -
607P VAL* 3.8 12.3 - - + +
610P LEU* 4.2 8.3 - - + -
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Residues in contact with LEU 401 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361P TYR* 6.0 4.5 - - + -
364P LEU* 4.2 19.5 - - + -
366P PHE* 4.3 8.5 - - + -
397P LEU* 3.1 26.5 + - + +
398P LEU* 3.8 9.4 - - + +
400P ALA* 1.3 83.1 - - - +
402P CYS* 1.4 58.1 + - - +
404P PRO* 3.9 0.3 - - - +
417P GLU* 3.6 18.7 - - - +
422P VAL* 4.0 27.6 - - + +
425P SER* 4.5 7.8 + - - +
426P VAL* 4.1 18.2 - - + -
429P LEU* 4.0 18.2 - - + -
604P ASN* 3.7 6.9 + - - +
607P VAL* 3.4 25.8 - - + -
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Residues in contact with CYS 402 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366P PHE* 3.9 21.8 - - - -
374P GLN* 2.6 24.9 + - - +
375P ALA* 3.6 27.4 - - - +
377P PRO* 3.9 21.5 - - - -
398P LEU 3.1 18.8 + - - +
399P LYS 2.7 7.4 + - - +
401P LEU* 1.4 71.1 - - - +
403P TYR* 1.3 69.3 + - + +
404P PRO* 2.9 13.5 - - - +
417P GLU* 3.4 6.6 + - - +
422P VAL* 4.8 6.5 - - - -
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Residues in contact with TYR 403 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369P MLY 3.9 26.8 + - - +
372P GLU* 6.0 0.4 - - - -
374P GLN* 2.8 45.1 - - + +
375P ALA 4.1 3.9 + - - -
376P GLU* 5.4 2.8 - - + +
399P LYS* 2.4 63.0 + - + +
400P ALA* 3.7 4.0 - - - +
402P CYS* 1.3 78.3 - - + +
404P PRO* 1.3 68.8 - - - +
405P ARG* 3.0 8.1 + - - +
414P THR* 4.1 18.7 - - + +
415P MLY 3.3 5.2 - - - +
416P GLY* 4.3 6.7 - - - -
606P 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