Contacts of the helix formed by residues 384 - 391 (chain E) in PDB entry 6T8O
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 LEU 384 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377D LYS* 4.8 7.9 - - + +
347E LEU* 4.8 13.2 - - + -
350E PHE* 3.5 51.8 - - + -
352E VAL* 5.5 2.7 - - + -
380E ARG* 3.2 32.8 - - - +
381E ILE* 3.6 13.9 - - + +
382E SER 3.2 0.6 - - - -
383E ASN* 1.3 81.2 - - + +
385E ALA* 1.3 60.5 + - - +
386E LYS* 3.2 4.3 - - - +
387E ASP* 3.3 17.8 + - + +
388E LEU* 2.9 28.4 + - + +
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Residues in contact with ALA 385 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381E ILE 3.9 5.3 + - - -
382E SER* 4.0 12.0 + - - +
383E ASN 3.8 0.8 - - - -
384E LEU* 1.3 75.6 - - - +
386E LYS* 1.3 59.0 + - - +
388E LEU* 4.5 2.9 - - - -
389E ALA* 2.9 26.9 + - - +
397E VAL* 3.3 33.6 - - + +
399E VAL* 4.4 16.4 - - + +
671E GLN* 4.5 13.9 - - - +
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Residues in contact with LYS 386 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D VAL* 5.7 6.1 - - + -
401D GLU* 5.4 14.6 - - + +
402D VAL* 5.6 14.3 - - + +
384E LEU* 3.2 2.1 - - - +
385E ALA* 1.3 78.0 - - - +
387E ASP* 1.3 65.8 + - - +
389E ALA* 3.4 5.1 + - + +
390E ARG* 2.9 27.1 + - + +
395E ILE 5.9 3.7 + - - +
671E GLN* 5.7 4.8 + - - +
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Residues in contact with ASP 387 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D LYS* 3.3 35.2 - - - +
378D VAL* 3.3 35.9 + - - +
379D SER 5.4 0.2 + - - -
350E PHE* 3.9 22.3 - - + -
383E ASN 5.3 0.3 - - - +
384E LEU* 3.3 14.6 + - + +
386E LYS* 1.3 81.6 - - - +
388E LEU* 1.3 61.5 + - - +
390E ARG* 3.2 11.6 + - - +
391E SER* 2.9 30.5 + - - -
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Residues in contact with LEU 388 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E LEU* 5.0 4.3 - - + +
346E LYS* 4.3 16.8 - - + +
347E LEU* 3.8 46.7 - - + -
350E PHE* 4.9 3.3 - - + -
381E ILE* 5.5 6.5 - - + +
384E LEU* 2.9 19.5 + - + +
385E ALA* 4.0 5.8 - - - +
387E ASP* 1.3 76.1 - - - +
389E ALA* 1.3 62.2 + - - +
391E SER* 3.5 4.3 + - - +
392E LEU* 3.3 47.3 + - + +
397E VAL* 4.6 11.2 - - + -
399E VAL* 5.7 2.9 - - + -
411E ILE* 4.5 23.6 - - + -
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Residues in contact with ALA 389 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385E ALA 2.9 19.6 + - - +
386E LYS* 3.8 5.6 - - + +
388E LEU* 1.3 74.6 - - - +
390E ARG* 1.3 63.6 + - - +
392E LEU* 3.7 1.7 + - - -
394E VAL* 3.1 44.2 + - + +
395E ILE 4.3 3.6 - - - +
396E SER* 3.8 13.2 - - - +
397E VAL* 3.6 28.6 - - + +
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Residues in contact with ARG 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371D GLN* 4.2 5.3 - - - +
372D PRO* 3.5 28.0 + - - +
373D ALA 5.4 1.6 + - - -
376D VAL 3.7 21.0 + - - -
378D VAL* 3.3 28.8 - - + +
401D GLU 4.1 10.3 - - - +
402D VAL* 5.2 14.8 - - + +
403D ILE 6.2 0.2 - - - +
406D LYS 4.5 2.8 - - - +
407D THR* 3.1 47.8 + - - +
408D THR 5.1 2.0 - - - +
409D VAL* 3.8 19.7 - - - +
350E PHE* 5.3 3.8 - - - -
386E LYS* 2.9 17.2 + - + +
387E ASP* 3.2 11.5 + - - +
389E ALA* 1.3 78.5 - - - +
391E SER* 1.3 66.8 + - - +
392E LEU 3.1 4.8 + - - -
393E ALA* 3.5 9.9 + - - -
394E VAL 4.9 1.8 - - - -
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Residues in contact with SER 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371D GLN* 6.1 3.1 - - - +
407D THR* 4.8 10.1 - - - -
342E LEU* 5.4 0.2 - - - +
346E LYS* 3.3 53.9 - - - +
349E GLU* 5.4 2.0 - - - -
350E PHE* 4.3 11.8 - - - -
387E ASP 2.9 17.1 + - - -
388E LEU* 3.6 9.2 + - - -
389E ALA 3.4 0.2 - - - -
390E ARG* 1.3 87.2 - - - +
392E LEU* 1.3 57.5 + - - +
393E ALA 3.8 0.9 - - - -
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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