Contacts of the helix formed by residues 388 - 398 (chain I) in PDB entry 6RAR
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 388 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D T 3.7 8.8 + - - -
36D A 3.6 15.9 - - - -
386I GLY 3.8 1.2 + - - -
387I PHE* 1.3 77.5 - - - +
389I ASP* 1.3 64.6 + - - +
390I ILE* 3.4 12.3 + - - +
391I GLN* 2.8 40.9 + - - +
392I ARG* 3.0 21.9 + - - +
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Residues in contact with ASP 389 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D T 4.4 1.4 - - - +
36D A 2.9 36.6 + - - +
37D T 5.1 1.2 + - - -
360I ARG* 2.8 39.6 + - - -
364I ARG* 3.5 22.8 + - - +
387I PHE 3.9 1.1 + - - +
388I SER* 1.3 72.9 - - - +
390I ILE* 1.3 65.8 + - + +
392I ARG* 3.2 15.4 + - - +
393I GLU* 3.2 28.3 + - - +
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Residues in contact with ILE 390 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D A 4.6 10.3 - - - +
388I SER* 3.2 10.7 - - - +
389I ASP* 1.3 80.3 - - + +
391I GLN* 1.3 58.6 + - + +
393I GLU* 3.4 6.7 + - - +
394I GLU* 2.9 34.5 + - + +
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Residues in contact with GLN 391 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386I GLY 3.9 4.7 - - - +
387I PHE* 3.6 11.0 - - + -
388I SER* 2.8 46.8 + - - +
390I ILE* 1.3 76.1 - - + +
392I ARG* 1.3 58.6 + - - +
394I GLU* 4.4 9.4 - - - +
395I TYR* 2.8 67.3 + - + +
430I PHE* 3.8 22.9 - - - -
431I LYS 5.3 2.4 + - - -
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Residues in contact with ARG 392 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B T 4.2 19.0 + - - +
11B G 4.2 0.6 + - - -
360I ARG* 5.6 0.4 - - - +
361I ASN* 3.3 33.4 + - - +
364I ARG* 3.3 10.7 - - - +
365I LEU* 2.6 73.9 + - + +
366I GLY* 2.9 22.8 + - - -
384I GLY 2.8 25.0 + - - -
385I SER* 4.9 0.8 - - - +
386I GLY 5.2 0.2 - - - +
387I PHE* 3.7 28.4 + - + +
388I SER 3.0 16.5 + - - +
389I ASP* 3.2 16.4 + - - +
391I GLN* 1.3 75.6 - - - +
393I GLU* 1.3 58.1 + - - +
396I TRP* 3.2 14.7 + - - +
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Residues in contact with GLU 393 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363I GLY 5.1 2.1 - - - -
364I ARG* 2.7 45.6 + - - +
389I ASP 3.2 16.7 + - - +
390I ILE* 3.8 6.3 - - - +
391I GLN 3.1 0.2 - - - -
392I ARG* 1.3 77.2 - - - +
394I GLU* 1.3 66.0 + - - +
396I TRP* 3.3 3.1 + - - +
397I SER* 2.9 28.6 + - - +
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Residues in contact with GLU 394 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390I ILE* 2.9 24.6 + - + +
391I GLN* 3.9 9.1 - - - +
393I GLU* 1.3 76.2 - - - +
395I TYR* 1.3 89.0 + - + +
397I SER* 3.2 7.5 + - - -
398I LYS* 3.1 41.2 + - + +
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Residues in contact with TYR 395 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365I LEU* 3.8 14.5 - - + +
387I PHE* 4.1 12.6 - + - -
391I GLN* 2.8 53.4 + - + +
394I GLU* 1.3 103.0 + - + +
396I TRP* 1.3 57.8 + - - +
398I LYS* 3.6 3.4 - - + +
399I ARG* 3.1 26.7 + - - +
402I LEU* 3.6 26.8 - - + +
430I PHE* 3.8 14.4 - + - -
432I CYS* 5.9 0.2 - - - -
433I PHE* 3.4 41.4 + + - +
436I PHE* 5.4 5.0 + - - -
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Residues in contact with TRP 396 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354I VAL* 4.0 17.3 - - + -
355I GLU 3.9 4.5 - - - -
356I GLU* 3.6 49.1 - - + -
363I GLY* 3.2 26.9 + - - -
364I ARG* 3.6 17.9 - - + -
365I LEU* 3.7 10.5 - - - +
392I ARG 3.2 22.1 + - - +
393I GLU* 3.3 5.3 + - - +
394I GLU 3.2 1.0 - - - -
395I TYR* 1.3 75.5 - - - +
397I SER* 1.3 61.6 + - - +
398I LYS 3.1 0.2 - - - -
399I ARG* 2.5 84.3 + - - +
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Residues in contact with SER 397 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393I GLU* 2.9 16.1 + - - +
394I GLU* 3.6 9.4 - - - -
396I TRP* 1.3 80.5 - - - +
398I LYS* 1.3 78.0 + - - +
399I ARG* 3.4 7.4 + - - +
400I LYS* 5.2 5.2 - - - +
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Residues in contact with LYS 398 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394I GLU* 3.1 28.4 + - + +
395I TYR* 3.6 2.2 - - + -
396I TRP 3.1 0.2 - - - -
397I SER* 1.3 94.2 - - - +
399I ARG* 1.3 59.0 + - - +
400I LYS* 3.1 3.8 - - - -
401I HIS* 2.8 45.4 + - + +
402I LEU* 2.9 25.6 - - + +
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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