Contacts of the helix formed by residues 393 - 403 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387D ALA* 4.0 2.7 - - - -
392D LEU* 1.3 75.8 - - - +
394D SER* 1.3 67.0 + - - +
395D ALA* 3.0 25.0 + - - +
396D GLU* 3.8 31.4 - - + +
397D LEU* 3.0 23.6 + - - +
610D LEU* 5.3 0.8 - - - +
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Residues in contact with SER 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D THR* 5.1 7.0 - - - -
383D ALA* 3.6 5.6 - - - +
384D ASP* 2.3 49.8 + - - -
387D ALA* 3.5 14.4 - - - +
393D ASN* 1.3 71.7 + - - +
395D ALA* 1.3 57.8 + - - +
397D LEU* 3.4 4.0 - - - +
398D LEU* 3.0 34.7 + - - +
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Residues in contact with ALA 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380D THR* 6.4 0.4 - - - -
393D ASN* 3.0 10.1 + - - +
394D SER* 1.3 77.1 - - - +
396D GLU* 1.3 70.8 + - + +
397D LEU 2.8 2.0 - - - -
398D LEU* 2.8 19.6 + - - +
399D LYS* 2.9 15.6 + - - +
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Residues in contact with GLU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D ASN* 3.6 32.9 + - + +
395D ALA* 1.3 79.8 - - + +
397D LEU* 1.3 62.8 - - - +
399D LYS* 3.4 6.6 + - - +
400D ALA* 3.1 25.1 + - - +
610D LEU* 3.8 23.6 - - + +
613D MLY 5.8 5.7 - - - -
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Residues in contact with LEU 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D TYR* 4.6 12.8 - - + +
364D LEU* 5.2 5.2 - - + -
383D ALA* 4.6 9.0 - - + +
386D ALA* 5.1 5.4 - - + -
387D ALA* 4.6 16.2 - - + +
392D LEU* 4.2 24.2 - - + -
393D ASN 3.0 18.1 + - - +
394D SER 3.4 3.1 - - - +
395D ALA 2.8 0.8 - - - -
396D GLU* 1.3 78.1 - - - +
398D LEU* 1.3 79.4 + - + +
400D ALA* 3.7 1.0 - - - +
401D LEU* 3.1 37.5 + - + +
607D VAL* 3.9 27.8 - - + -
610D LEU* 3.6 11.2 - - + +
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Residues in contact with LEU 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D LEU* 4.9 6.1 - - + -
366D PHE* 4.8 7.9 - - + -
377D PRO* 4.0 31.2 - - + +
379D GLY 4.3 2.0 - - - +
380D THR* 3.4 33.4 - - + -
383D ALA* 3.6 25.6 - - + -
394D SER 3.0 17.6 + - - +
395D ALA* 2.8 10.4 + - - +
397D LEU* 1.3 86.4 - - + +
399D LYS* 1.3 60.2 + - - +
401D LEU* 3.8 12.5 - - + +
402D CYS* 3.1 29.6 + - - +
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Residues in contact with LYS 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D ALA 2.9 11.4 + - - +
396D GLU* 3.4 12.8 - - - +
398D LEU* 1.3 74.6 - - - +
400D ALA* 1.3 57.5 + - - +
401D LEU 3.0 1.3 - - - -
402D CYS* 2.7 9.2 + - - -
403D TYR* 2.4 67.7 + - + +
414D THR* 6.0 2.4 - - - +
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Residues in contact with ALA 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D GLU 3.1 13.7 + - - +
397D LEU 3.7 4.3 - - - +
399D LYS* 1.3 78.1 - - - +
401D LEU* 1.3 62.1 + - - +
403D TYR 4.4 4.7 - - - -
404D PRO* 3.2 16.6 - - - +
604D ASN* 2.9 17.7 + - - -
606D THR* 3.0 35.4 - - + -
607D VAL* 3.8 12.6 - - + +
610D LEU* 4.2 8.5 - - + -
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Residues in contact with LEU 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D TYR* 6.0 3.8 - - + -
364D LEU* 4.2 19.1 - - + -
366D PHE* 4.3 8.1 - - + -
397D LEU* 3.1 28.1 + - + +
398D LEU* 3.8 8.7 - - + +
399D LYS 3.0 0.2 - - - -
400D ALA* 1.3 83.9 - - - +
402D CYS* 1.4 59.9 + - - +
417D GLU* 3.6 18.9 - - - +
422D VAL* 4.0 27.1 - - + +
425D SER* 4.5 7.6 + - - +
426D VAL* 4.1 18.6 - - + -
429D LEU* 4.0 18.8 - - + -
604D ASN* 3.7 7.5 + - - +
607D VAL* 3.4 26.5 - - + -
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Residues in contact with CYS 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D PHE* 3.9 22.0 - - - -
374D GLN* 2.6 25.1 + - - +
375D ALA* 3.6 28.3 - - - +
377D PRO* 3.9 21.5 - - - -
398D LEU 3.1 17.7 + - - +
399D LYS* 2.7 7.4 + - - +
401D LEU* 1.4 71.7 - - - +
403D TYR* 1.3 70.1 + - + +
404D PRO* 2.9 14.0 - - - +
417D GLU* 3.4 6.4 + - - +
422D VAL* 4.8 6.1 - - - -
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Residues in contact with TYR 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369D MLY 3.9 26.3 + - - +
372D GLU* 5.2 1.0 + - - -
374D GLN* 2.8 46.4 - - + +
375D ALA 4.1 4.0 + - - -
376D GLU* 5.4 3.0 - - + +
399D LYS* 2.4 60.3 + - + +
400D ALA* 3.7 4.1 - - - +
402D CYS* 1.3 78.2 - - + +
404D PRO* 1.3 70.3 - - - +
405D ARG* 3.0 7.6 + - - +
414D THR* 4.1 19.8 + - + +
415D MLY 3.3 5.2 - - - +
416D GLY* 4.3 6.3 - - - -
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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