Contacts of the helix formed by residues 393 - 403 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387J ALA* 3.9 2.5 - - - -
392J LEU* 1.3 76.4 - - - +
394J SER* 1.3 66.8 + - - +
395J ALA* 3.0 24.6 + - - +
396J GLU* 3.8 31.4 + - - +
397J LEU* 3.0 24.1 + - - +
610J LEU* 5.3 0.4 - - - +
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Residues in contact with SER 394 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380J THR* 5.1 6.5 - - - -
383J ALA* 3.6 5.5 + - - +
384J ASP* 2.3 49.8 + - - -
387J ALA* 3.5 14.5 - - - +
392J LEU 4.1 0.2 + - - -
393J ASN* 1.3 73.3 + - - +
395J ALA* 1.3 57.3 + - - +
397J LEU* 3.4 3.9 - - - +
398J LEU* 3.0 34.0 + - - +
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Residues in contact with ALA 395 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393J ASN* 3.0 10.3 + - - +
394J SER* 1.3 76.9 - - - +
396J GLU* 1.3 70.6 + - + +
397J LEU 2.8 2.0 - - - -
398J LEU* 2.8 19.5 + - - +
399J LYS* 2.9 15.4 + - - +
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Residues in contact with GLU 396 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393J ASN* 3.3 31.4 + - + +
395J ALA* 1.3 81.0 - - + +
397J LEU* 1.3 62.7 + - - +
399J LYS* 3.4 7.0 + - - +
400J ALA* 3.2 25.5 + - - +
610J LEU* 3.8 23.1 - - + +
613J MLY 5.8 5.3 - - - -
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Residues in contact with LEU 397 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361J TYR* 4.6 13.2 - - + +
364J LEU* 5.2 4.9 - - + -
383J ALA* 4.6 8.7 - - + +
386J ALA* 5.1 5.2 - - + -
387J ALA* 4.6 15.5 - - + +
392J LEU* 4.2 25.4 - - + -
393J ASN 3.0 17.7 + - - +
394J SER 3.4 3.8 - - - +
395J ALA 2.8 1.0 - - - -
396J GLU* 1.3 78.0 - - - +
398J LEU* 1.3 79.0 + - + +
400J ALA* 3.5 1.4 + - - +
401J LEU* 3.1 37.4 + - + +
607J VAL* 3.9 27.8 - - + -
610J LEU* 3.6 11.0 - - + +
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Residues in contact with LEU 398 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364J LEU* 4.9 6.1 - - + -
366J PHE* 4.8 7.6 - - + -
377J PRO* 4.0 29.5 - - + +
379J GLY 4.3 2.2 - - - +
380J THR* 3.4 33.2 - - + -
383J ALA* 3.6 26.5 - - + -
394J SER 3.0 14.0 + - - +
395J ALA* 2.8 13.1 + - - +
397J LEU* 1.3 86.3 - - + +
399J LYS* 1.3 62.5 + - - +
401J LEU* 3.8 12.5 - - + +
402J CYS* 3.1 28.8 + - - +
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Residues in contact with LYS 399 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395J ALA 2.9 12.0 + - - +
396J GLU* 3.4 12.1 - - - +
398J LEU* 1.3 74.9 - - - +
400J ALA* 1.3 58.2 - - - +
401J LEU 3.0 1.1 - - - -
402J CYS* 2.7 9.3 + - - -
403J TYR* 2.4 66.0 + - + +
414J THR* 6.0 2.8 - - - +
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Residues in contact with ALA 400 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396J GLU 3.2 14.1 + - - +
397J LEU 3.7 4.0 - - - +
399J LYS* 1.3 78.9 - - - +
401J LEU* 1.3 61.1 + - - +
403J TYR 4.4 5.2 - - - -
404J PRO* 3.2 16.8 - - - +
604J ASN* 2.9 19.0 + - - +
606J THR* 3.0 35.4 - - + -
607J VAL* 3.8 12.8 - - + +
610J LEU* 4.2 8.3 - - + -
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Residues in contact with LEU 401 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361J TYR* 6.0 4.0 - - + -
364J LEU* 4.2 18.8 - - + -
366J PHE* 4.3 9.0 - - + -
397J LEU* 3.1 27.4 + - + +
398J LEU* 3.8 8.3 - - + +
399J LYS 3.0 0.2 - - - -
400J ALA* 1.3 82.3 - - - +
402J CYS* 1.4 59.0 + - - +
404J PRO* 3.9 0.3 - - - +
417J GLU* 3.6 18.9 - - - +
422J VAL* 4.0 27.0 - - + +
425J SER* 4.5 7.1 + - - +
426J VAL* 4.1 19.3 - - + -
429J LEU* 4.0 18.4 - - + -
604J ASN* 3.7 8.0 + - - +
607J VAL* 3.4 26.5 - - + -
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Residues in contact with CYS 402 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366J PHE* 3.9 21.3 - - - -
374J GLN* 2.6 25.0 + - - +
375J ALA* 3.6 27.8 - - - +
377J PRO* 3.9 22.7 - - + -
398J LEU 3.1 17.4 + - - +
399J LYS* 2.7 7.9 + - - +
401J LEU* 1.4 72.1 - - - +
403J TYR* 1.3 69.1 + - + +
404J PRO* 2.9 13.6 - - - +
417J GLU* 3.4 6.6 + - - +
422J VAL* 4.8 6.3 - - - -
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Residues in contact with TYR 403 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369J MLY 3.9 25.4 + - - +
372J GLU* 5.2 0.8 + - - -
374J GLN* 2.8 45.0 - - + +
375J ALA 4.1 3.6 + - - -
376J GLU* 5.4 3.0 - - + +
399J LYS* 2.4 61.9 + - + +
400J ALA* 3.7 4.0 - - - +
402J CYS* 1.3 79.2 - - + +
404J PRO* 1.3 68.9 - - - +
405J ARG* 3.0 8.0 + - - +
414J THR* 4.1 18.6 - - + +
415J MLY 3.3 4.9 - - - +
416J GLY* 4.3 7.0 - - - -
606J 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