Contacts of the helix formed by residues 394 - 402 (chain A) in PDB entry 2MYS
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 SER 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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380A THR* 5.1 7.0 - - - -
383A ALA* 3.6 6.0 - - - +
384A ASP* 2.3 49.5 + - - -
387A ALA* 3.5 14.8 - - - +
392A LEU 4.1 0.2 + - - -
393A ASN* 1.3 71.9 + - - +
395A ALA* 1.3 57.2 + - - +
397A LEU* 3.4 4.0 - - - +
398A LEU* 3.0 34.1 + - - +
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ASN* 3.0 11.2 + - - +
394A SER* 1.3 76.6 - - - +
396A GLU* 1.3 70.4 + - + +
397A LEU 2.8 1.8 - - - -
398A LEU* 2.8 19.5 + - - +
399A LYS* 2.9 15.9 + - - +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A ASN* 3.6 33.0 + - + +
395A ALA* 1.3 80.5 - - + +
397A LEU* 1.3 62.3 + - - +
399A LYS* 3.4 7.4 + - - +
400A ALA* 3.1 25.3 + - - +
610A LEU* 3.8 24.1 - - + +
613A MLY 5.8 5.0 - - - -
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Residues in contact with LEU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A TYR* 4.6 13.0 - - + +
364A LEU* 5.2 4.9 - - + -
383A ALA* 4.6 8.5 - - + +
386A ALA* 5.1 5.8 - - + -
387A ALA* 4.6 16.6 - - + +
392A LEU* 4.2 25.4 - - + -
393A ASN 3.0 18.3 + - - +
394A SER 3.4 3.8 - - - +
395A ALA 2.8 1.0 - - - -
396A GLU* 1.3 76.6 - - - +
398A LEU* 1.3 79.8 + - + +
400A ALA* 3.7 1.2 - - - +
401A LEU* 3.1 37.7 + - + +
607A VAL* 3.9 28.0 - - + -
610A LEU* 3.6 11.6 - - + +
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Residues in contact with LEU 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364A LEU* 4.9 5.6 - - + -
366A PHE* 4.8 8.3 - - + -
377A PRO* 4.0 30.5 - - + +
379A GLY 4.3 2.2 - - - +
380A THR* 3.4 33.2 - - + -
383A ALA* 3.6 25.4 - - + -
394A SER 3.0 16.3 + - - +
395A ALA* 2.8 11.0 + - - +
397A LEU* 1.3 86.4 - - + +
399A LYS* 1.3 60.6 + - - +
401A LEU* 3.8 12.6 - - + +
402A CYS* 3.1 29.1 + - - +
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Residues in contact with LYS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A ALA 2.9 11.3 + - - +
396A GLU* 3.4 12.6 - - - +
398A LEU* 1.3 74.1 - - - +
400A ALA* 1.3 57.9 + - - +
401A LEU 3.0 1.1 - - - -
402A CYS* 2.7 9.2 + - - -
403A TYR* 2.4 66.3 + - + +
414A THR* 6.0 2.6 - - - +
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Residues in contact with ALA 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A GLU 3.1 14.1 + - - +
397A LEU 3.7 4.3 - - - +
399A LYS* 1.3 78.0 - - - +
401A LEU* 1.3 62.0 + - - +
403A TYR 4.4 5.2 - - - -
404A PRO* 3.2 16.8 - - - +
604A ASN* 2.9 17.9 + - - -
606A THR* 3.0 35.0 - - + -
607A VAL* 3.8 12.8 - - + +
610A LEU* 4.2 9.0 - - + -
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A TYR* 6.0 4.0 - - + -
364A LEU* 4.2 19.1 - - + -
366A PHE* 4.3 8.7 - - + -
397A LEU* 3.1 27.2 + - + +
398A LEU* 3.8 9.2 - - + +
399A LYS 3.0 0.4 - - - -
400A ALA* 1.3 83.3 - - - +
402A CYS* 1.4 57.7 + - - +
404A PRO* 3.9 0.3 - - - +
417A GLU* 3.6 18.9 - - - +
422A VAL* 4.0 26.9 - - + +
425A SER* 4.5 7.2 + - - +
426A VAL* 4.1 18.4 - - + -
429A LEU* 4.0 18.6 - - + -
604A ASN* 3.7 7.7 + - - +
607A VAL* 3.4 26.5 - - + -
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Residues in contact with CYS 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366A PHE* 3.9 21.3 - - - -
374A GLN* 2.6 24.5 + - - +
375A ALA* 3.6 28.9 - - - +
377A PRO* 3.9 22.0 - - + -
398A LEU 3.1 17.9 + - - +
399A LYS 2.7 7.5 + - - +
401A LEU* 1.4 71.7 - - - +
403A TYR* 1.3 68.9 + - + +
404A PRO* 2.9 13.7 - - - +
417A GLU* 3.4 6.8 + - - +
422A VAL* 4.7 5.8 - - - -
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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