Contacts of the helix formed by residues 384 - 395 (chain A) in PDB entry 1RQG
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 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A GLU* 3.2 14.7 + - - -
370A TYR* 2.9 9.8 + - - -
382A ASP* 4.3 9.6 - - - -
383A PHE* 1.3 80.4 - - - +
385A PHE* 1.3 58.6 + - - +
386A SER* 3.1 21.8 + - - -
387A ASP* 3.5 14.7 + - - +
388A PHE* 2.8 27.0 + - - +
576A TYR* 3.1 9.4 + - - -
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Residues in contact with PHE 385 (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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340A LEU* 4.6 5.6 - - + -
341A GLU* 3.8 17.5 + - + -
353A ILE* 3.6 15.5 - - + -
358A PHE* 4.2 11.7 - + - -
362A PHE* 5.5 3.6 - + - -
383A PHE* 3.8 17.5 - + - -
384A SER* 1.3 70.2 + - - +
386A SER* 1.3 66.1 + - - +
388A PHE* 3.2 10.7 + + - +
389A LYS* 3.1 25.5 + - - +
553A ILE* 3.9 36.9 - - + +
556A PHE* 3.7 25.4 - + + -
557A ILE* 4.2 10.8 - - + -
561A MET* 3.3 35.0 - - + -
572A LEU* 3.9 13.5 - - + -
576A TYR* 4.0 10.8 - + + -
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Residues in contact with SER 386 (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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384A SER* 3.1 11.4 + - - -
385A PHE* 1.3 77.3 - - - +
387A ASP* 1.3 65.9 + - - +
389A LYS* 3.4 12.1 - - - +
390A VAL* 3.1 29.6 + - - +
553A ILE* 5.4 0.2 - - - -
576A TYR* 3.1 32.7 + - - -
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Residues in contact with ASP 387 (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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370A TYR* 2.9 24.8 + - - -
374A ILE* 4.0 4.0 - - - +
382A ASP 4.2 5.9 - - - +
384A SER* 3.2 22.3 + - - +
386A SER* 1.3 80.2 + - - +
388A PHE* 1.3 62.0 + - - +
390A VAL* 4.0 6.6 - - - +
391A ARG* 2.6 63.7 + - - +
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Residues in contact with PHE 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A PHE* 3.7 28.3 - + - -
362A PHE* 3.7 37.0 - + - -
366A TYR* 3.7 36.6 - - + -
367A LEU* 4.9 0.7 - - - -
370A TYR* 3.6 37.9 - + + -
383A PHE* 4.7 3.4 - + + -
384A SER 2.8 14.3 + - - +
385A PHE* 3.2 20.2 + + - +
387A ASP* 1.3 78.7 - - - +
389A LYS* 1.3 74.1 + - + +
391A ARG* 3.9 2.1 - - - +
392A ILE* 3.1 37.6 + - + +
548A VAL* 3.9 15.0 - - + -
553A ILE* 5.2 2.0 - - + -
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Residues in contact with LYS 389 (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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385A PHE 3.1 8.1 + - - +
386A SER* 3.4 16.6 - - - +
388A PHE* 1.3 83.8 - - - +
390A VAL* 1.3 80.6 + - - +
392A ILE* 3.2 0.7 + - - +
393A ASN* 2.9 42.4 + - - +
548A VAL* 3.6 39.9 - - + -
549A THR 4.9 1.1 - - - -
550A ASP* 3.7 27.2 + - - +
553A ILE* 3.4 23.6 - - + -
577A TYR* 4.7 1.1 - - - +
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Residues in contact with VAL 390 (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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386A SER 3.1 16.2 + - - +
387A ASP* 4.0 9.6 - - - +
389A LYS* 1.3 94.6 - - - +
391A ARG* 1.3 66.3 + - + +
393A ASN* 5.0 2.2 - - - -
394A GLU* 2.9 49.4 + - + +
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Residues in contact with ARG 391 (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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369A TYR* 4.4 7.2 - - + -
370A TYR* 4.1 8.2 - - + -
373A THR* 3.0 39.8 + - - +
374A ILE* 3.7 12.5 - - - +
387A ASP* 2.6 53.1 + - - +
388A PHE 3.9 2.9 - - - +
390A VAL* 1.3 81.7 - - + +
392A ILE* 1.3 58.5 + - + +
394A GLU* 4.9 0.2 - - - -
395A GLU* 2.8 65.1 + - - +
457A LYS* 5.9 4.4 - - - +
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Residues in contact with ILE 392 (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 TYR* 3.8 52.7 - - + +
369A TYR* 4.0 14.6 - - + -
370A TYR* 4.7 2.9 - - + +
388A PHE* 3.1 34.0 + - + +
389A LYS 3.7 2.9 - - - +
391A ARG* 1.3 75.5 - - - +
393A ASN* 1.3 59.0 + - - +
396A LEU* 2.7 31.6 + - + +
397A VAL* 2.7 35.2 + - + -
548A VAL* 3.7 24.0 - - + -
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Residues in contact with ASN 393 (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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389A LYS* 2.9 28.7 + - - +
390A VAL* 4.5 1.8 - - - +
392A ILE* 1.3 75.1 - - - +
394A GLU* 1.3 58.4 + - - +
397A VAL* 3.2 9.4 - - - +
398A ASN* 2.8 37.2 + - - -
547A LYS* 3.1 38.2 - - + +
548A VAL* 2.6 52.1 - - - +
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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* 2.9 34.8 + - + +
391A ARG* 4.5 0.4 - - - +
393A ASN* 1.3 79.8 - - - +
395A GLU* 1.3 63.1 + - + +
398A ASN* 2.7 40.6 + - - +
399A ASN* 3.9 4.5 + - - +
547A LYS* 4.9 4.7 + - - -
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Residues in contact with GLU 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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369A TYR* 2.5 42.7 + - + +
373A THR* 4.3 2.4 + - - -
391A ARG* 2.8 53.5 + - - +
394A GLU* 1.3 78.0 - - + +
396A LEU* 1.3 59.0 + - - +
399A ASN* 3.0 34.2 + - - +
400A LEU 3.3 3.5 + - - -
460A MET* 3.7 7.8 - - + +
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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