Contacts of the helix formed by residues 399 - 409 (chain A) in PDB entry 2YEM
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 ASP 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A PHE* 3.6 5.4 - - - +
378A LYS 3.4 21.2 - - - +
379A PRO* 3.2 37.4 - - + +
380A VAL* 5.3 0.9 - - + +
397A PRO 5.4 0.3 - - - -
398A MET* 1.3 81.9 - - - +
400A MET* 1.3 63.2 + - - +
401A SER* 3.1 11.3 + - - -
402A THR* 2.6 40.6 + - - -
403A ILE* 3.2 24.8 + - - +
425A MET* 3.7 15.5 - - - -
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Residues in contact with MET 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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361A LEU* 3.8 15.7 - - + +
364A MET* 3.5 46.0 - - + +
365A PHE* 3.6 36.6 - - + +
373A ALA 4.5 1.1 - - - +
376A PHE* 2.9 39.7 + - - +
377A TYR* 4.1 9.0 - - + +
399A ASP* 1.3 73.5 - - - +
401A SER* 1.3 57.3 + - - +
403A ILE* 3.5 7.5 + - + +
404A LYS* 2.9 28.2 + - - +
425A MET* 3.7 17.9 - - + -
446A LEU* 4.0 15.7 - - - -
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Residues in contact with SER 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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365A PHE* 4.0 10.9 - - - -
377A TYR 2.5 23.6 + - - -
378A LYS* 4.2 11.0 - - - +
379A PRO* 4.8 4.3 - - - -
399A ASP* 3.1 7.6 + - - -
400A MET* 1.3 74.5 - - - +
402A THR* 1.3 61.9 + - - +
404A LYS* 3.3 10.3 + - - +
405A SER* 2.9 31.7 + - - -
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Residues in contact with THR 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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379A PRO* 4.3 6.9 - - - +
397A PRO 5.8 0.4 - - - +
398A MET* 3.9 23.1 - - + -
399A ASP* 2.6 33.8 + - - -
401A SER* 1.3 72.3 - - - +
403A ILE* 1.3 60.9 + - - +
405A SER* 3.5 6.8 + - - -
406A LYS* 3.0 41.0 + - + +
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Residues in contact with ILE 403 (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 LEU* 3.9 11.0 - - + -
398A MET* 3.7 16.6 - - + -
399A ASP 3.2 20.5 + - - +
400A MET* 3.7 8.5 - - - +
402A THR* 1.3 74.4 - - - +
404A LYS* 1.3 65.1 + - - +
406A LYS* 3.3 2.4 + - - +
407A LEU* 3.0 22.2 + - - +
412A TYR* 3.7 21.2 - - - +
418A PHE* 3.5 33.0 - - + -
421A ASP* 3.7 6.3 - - + +
422A VAL* 3.6 40.6 - - + +
425A MET* 4.8 7.0 - - + -
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Residues in contact with LYS 404 (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 LEU* 3.5 18.5 - - + +
365A PHE* 4.6 17.9 - - + -
400A MET 2.9 17.7 + - - +
401A SER* 3.3 9.2 + - - +
403A ILE* 1.3 75.9 - - - +
405A SER* 1.3 63.9 + - - +
407A LEU* 3.2 7.2 + - + +
408A GLU* 3.0 54.2 + - + +
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Residues in contact with SER 405 (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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401A SER 2.9 19.0 + - - -
402A THR* 3.7 8.9 - - - -
404A LYS* 1.3 78.6 - - - +
406A LYS* 1.3 59.5 + - - +
408A GLU* 3.5 9.2 + - - +
409A ALA* 2.9 32.6 + - - +
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Residues in contact with LYS 406 (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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398A MET* 4.5 7.9 - - + +
402A THR* 3.0 35.3 + - + +
403A ILE* 3.7 0.4 - - - +
404A LYS 3.2 0.2 - - - -
405A SER* 1.3 76.1 - - - +
407A LEU* 1.3 61.5 + - - +
409A ALA* 3.4 2.0 + - - -
410A ARG 3.1 3.6 + - - -
411A GLU* 2.9 60.1 + - + +
412A TYR* 3.6 34.8 - - + +
421A ASP* 3.0 26.8 + - - +
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Residues in contact with LEU 407 (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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354A LEU* 4.2 33.2 - - + +
357A CYS* 4.2 5.4 - - + +
358A SER* 3.4 41.1 - - - +
361A LEU* 4.6 10.8 - - + -
403A ILE 3.0 12.5 + - - +
404A LYS* 3.4 9.0 - - + +
406A LYS* 1.3 76.7 - - - +
408A GLU* 1.3 59.9 + - + +
410A ARG* 2.8 24.9 + - - +
412A TYR* 3.8 20.5 - - + -
418A PHE* 4.3 14.8 - - + -
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Residues in contact with GLU 408 (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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404A LYS* 3.0 52.6 + - + +
405A SER* 4.0 7.1 + - - +
407A LEU* 1.3 80.0 - - + +
409A ALA* 1.3 57.1 + - - +
410A ARG* 3.1 29.2 + - - +
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Residues in contact with ALA 409 (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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405A SER 2.9 19.5 + - - +
406A LYS 3.9 2.7 - - - +
407A LEU 3.3 0.4 - - - -
408A GLU* 1.3 73.3 - - - +
410A ARG* 1.3 73.8 + - - +
411A GLU* 3.3 26.5 + - + +
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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