Contacts of the helix formed by residues 393 - 404 (chain A) in PDB entry 3LLM
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 PHE 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A PRO* 3.7 21.3 - - + -
390A VAL* 2.8 17.4 + - - +
392A LYS* 1.3 90.0 - - + +
394A GLU* 1.3 62.3 + - - -
395A SER 3.4 2.2 - - - -
396A GLU* 3.1 30.0 + - + +
397A ILE* 3.0 28.2 + - + +
561A ILE* 5.1 0.7 - - + -
562A GLU 3.6 20.9 - - - -
563A VAL* 3.7 44.9 - - + -
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Residues in contact with GLU 394 (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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390A VAL 3.7 1.6 + - - -
391A LYS* 2.9 49.6 + - - +
392A LYS 3.3 1.4 - - - +
393A PHE* 1.3 76.3 - - - +
395A SER* 1.3 66.3 + - - +
397A ILE* 3.3 3.4 + - - +
398A LEU* 3.0 44.9 + - + +
424A PHE* 3.6 45.8 - - + +
427A ASP* 5.9 2.1 - - - +
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Residues in contact with SER 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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392A LYS 4.8 2.7 + - - -
393A PHE 3.4 0.4 - - - -
394A GLU* 1.3 81.2 - - - +
396A GLU* 1.3 64.5 + - - +
398A LEU* 3.4 7.1 + - - +
399A GLU* 2.9 27.4 + - - +
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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 PHE* 3.1 37.3 + - + +
395A SER* 1.3 79.8 - - - +
397A ILE* 1.3 57.3 + - + +
399A GLU* 3.5 6.6 + - - +
400A ALA* 2.9 30.4 + - + +
561A ILE* 4.6 22.7 - - + +
562A GLU 5.4 2.5 + - - +
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Residues in contact with ILE 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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390A VAL* 4.1 21.5 - - + -
393A PHE* 3.0 34.1 + - + +
394A GLU* 3.6 8.3 - - - +
396A GLU* 1.3 73.5 - - - +
398A LEU* 1.3 69.3 + - + +
400A ALA* 3.1 6.6 + - + +
401A ILE* 3.0 42.1 + - + +
407A VAL* 5.9 0.7 - - + -
409A ILE* 3.6 26.2 - - + -
421A VAL* 4.5 18.6 - - + -
424A PHE* 4.7 7.2 - - + -
425A ILE* 5.9 0.4 - - + -
561A ILE* 4.0 24.2 - - + -
563A VAL* 4.4 4.7 - - + -
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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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394A GLU* 3.0 40.9 + - + +
395A SER* 3.9 6.3 - - - +
397A ILE* 1.3 77.3 - - + +
399A GLU* 1.3 60.8 + - - +
401A ILE* 4.0 4.9 - - + +
402A SER* 2.7 29.4 + - - -
424A PHE* 3.5 35.0 - - + +
425A ILE* 3.9 16.4 - - + +
428A ASP* 3.8 38.1 - - + +
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Residues in contact with GLU 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 SER 2.9 19.6 + - - +
396A GLU* 3.9 6.2 - - - +
398A LEU* 1.3 76.2 - - - +
400A ALA* 1.3 64.1 + - - +
402A SER* 3.0 17.4 + - - +
403A GLN* 2.8 40.9 + - - +
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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* 2.9 19.9 + - + +
397A ILE 3.5 5.6 - - - +
399A GLU* 1.3 76.6 - - - +
401A ILE* 1.3 61.8 + - - +
404A ASN* 2.8 37.4 + - - +
407A VAL* 3.9 10.8 - - + -
559A PRO* 5.3 2.0 - - + -
561A ILE* 3.8 31.0 - - + -
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Residues in contact with ILE 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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397A ILE* 3.0 39.0 + - + +
398A LEU* 4.0 5.8 - - + +
400A ALA* 1.3 71.7 - - - +
402A SER* 1.3 64.7 + - - +
403A GLN 3.1 1.3 - - - -
404A ASN 2.9 22.8 - - - +
407A VAL* 4.1 20.2 - - + -
409A ILE* 5.0 0.2 - - + -
421A VAL* 4.8 0.4 - - + -
425A ILE* 3.7 31.2 - - + -
507A HIS* 4.1 17.0 - - + +
538A ARG* 2.9 33.0 + - + -
539A ILE 5.6 1.1 - - - +
540A VAL* 3.9 24.7 - - + -
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Residues in contact with SER 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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398A LEU 2.7 24.3 + - - -
399A GLU* 3.0 16.3 + - - +
401A ILE* 1.3 76.9 - - - +
403A GLN* 1.3 63.2 + - - +
428A ASP* 6.1 0.4 - - - -
434A ARG* 6.1 3.4 - - - -
538A ARG* 2.7 21.8 + - - +
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Residues in contact with GLN 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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399A GLU* 2.8 49.8 + - - +
400A ALA* 5.2 0.2 - - - -
401A ILE 3.1 0.8 - - - -
402A SER* 1.3 84.0 - - - +
404A ASN* 1.3 72.8 + - - +
538A ARG* 3.9 4.6 + - - +
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Residues in contact with ASN 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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400A ALA* 2.8 29.1 + - - +
401A ILE* 2.9 18.4 + - - +
402A SER 3.5 0.4 - - - -
403A GLN* 1.3 91.7 + - - +
405A SER* 1.3 63.4 + - - +
406A VAL 3.5 18.5 + - - +
407A VAL* 4.0 2.9 - - + +
538A ARG* 3.0 11.8 + - - +
559A PRO* 3.7 28.3 - - + +
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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