Contacts of the helix formed by residues 386 - 396 (chain A) in PDB entry 2O8C
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 386 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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336A PRO* 3.8 29.6 - - + +
337A GLN* 3.7 14.1 + - - +
340A ARG* 3.7 27.0 + - - -
384A PHE 4.0 0.4 + - - -
385A PRO* 1.3 70.5 - - - +
387A LEU* 1.3 63.3 + - - +
388A ASN* 2.9 21.8 + - - +
389A ARG* 3.4 55.0 + - - +
390A LEU* 3.9 10.2 + - - +
596A ASN* 3.8 6.9 - - - +
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Residues in contact with LEU 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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337A GLN* 3.8 7.6 + - - +
384A PHE* 6.2 2.5 - - + -
385A PRO* 3.1 20.2 + - + +
386A ASP* 1.3 73.1 + - - +
388A ASN* 1.3 59.8 + - - +
389A ARG 3.2 0.9 - - - -
390A LEU* 3.3 9.5 + - + -
391A ALA* 2.9 28.6 + - - +
407A LEU* 3.8 28.3 - - + -
592A MET* 3.6 21.0 - - + +
595A LEU* 3.7 26.5 - - + +
596A ASN* 3.5 44.5 + - + +
599A LEU* 4.3 6.7 - - + -
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Residues in contact with ASN 388 (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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169A ILE* 3.0 50.3 + - + +
170A GLN* 4.8 3.6 - - - +
340A ARG* 4.7 5.3 - - - +
386A ASP* 2.9 12.8 + - - +
387A LEU* 1.3 76.7 - - - +
389A ARG* 1.3 63.4 + - - +
391A ALA* 4.0 5.6 - - - -
392A LYS* 3.5 32.1 + - + +
593A GLN* 3.9 19.6 - - - +
596A ASN* 3.0 36.9 + - - +
597A ASP* 5.2 0.2 + - - -
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Residues in contact with ARG 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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136A PHE* 5.8 5.6 + - - +
137A GLY 5.3 2.6 + - - -
138A ASN* 4.6 5.9 - - - +
139A ASN* 3.6 37.5 - - + +
336A PRO* 4.2 14.8 - - - +
340A ARG* 5.9 0.7 - - - +
385A PRO* 6.2 1.2 - - - +
386A ASP* 3.5 43.1 + - + +
387A LEU 3.2 0.4 - - - -
388A ASN* 1.3 78.1 - - - +
390A LEU* 1.3 65.3 - - + +
392A LYS* 4.4 2.5 - - - +
393A LYS* 3.4 36.5 + - + +
406A ARG* 5.1 10.3 - - - +
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Residues in contact with LEU 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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385A PRO* 4.9 8.1 - - + -
386A ASP 3.9 9.9 - - - +
387A LEU* 3.3 15.4 + - + +
389A ARG* 1.3 80.5 - - + +
391A ALA* 1.3 55.5 + - - +
393A LYS* 2.9 7.1 + - + +
394A PHE* 2.8 51.1 + - + -
403A ASP* 3.8 36.6 - - + +
406A ARG* 4.2 17.9 - - - -
407A LEU* 3.8 42.6 - - + +
592A MET* 3.8 7.0 - - + -
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Residues in contact with ALA 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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387A LEU 2.9 16.8 + - - +
388A ASN* 4.1 9.6 - - + +
389A ARG 3.6 0.2 - - - -
390A LEU* 1.3 76.0 - - - +
392A LYS* 1.3 61.9 + - + +
394A PHE* 3.6 6.1 + - - +
395A GLN* 3.2 26.8 + - - +
589A VAL* 4.7 10.1 - - + +
592A MET* 4.2 23.7 - - + +
593A GLN* 4.2 25.6 - - + +
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Residues in contact with LYS 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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168A SER* 3.4 37.8 + - - -
169A ILE* 3.5 30.0 - - - +
388A ASN* 3.5 22.4 + - + +
389A ARG* 4.4 3.1 - - - +
390A LEU 3.2 0.8 - - - -
391A ALA* 1.3 77.8 - - + +
393A LYS* 1.3 60.8 + - + +
395A GLN* 3.5 9.7 + - - +
396A ARG* 3.0 30.0 + - - +
593A GLN* 6.2 1.1 - - - +
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Residues in contact with LYS 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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132A GLU* 5.9 7.1 + - - -
136A PHE* 5.5 9.3 - - - +
389A ARG* 3.4 24.4 + - - +
390A LEU* 2.9 6.7 + - + +
392A LYS* 1.3 76.9 - - + +
394A PHE* 1.3 63.5 + - + +
396A ARG* 4.0 5.6 - - + -
397A GLN* 3.4 1.4 + - - -
398A ALA* 3.3 34.8 + - + +
399A ALA* 3.6 12.7 + - + -
403A ASP* 4.1 22.6 + - - +
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Residues in contact with PHE 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 LEU* 2.8 52.6 + - + +
391A ALA* 4.1 5.2 - - - +
393A LYS* 1.3 72.8 - - + +
395A GLN* 1.3 64.2 + - - +
396A ARG 3.3 0.2 - - - -
397A GLN* 3.5 11.8 + - - +
399A ALA* 3.9 21.1 - - + -
403A ASP* 3.9 29.4 - - + -
404A CYS* 4.4 13.5 - - - -
407A LEU* 4.2 20.2 - - + -
450A PHE* 5.9 0.2 - + - -
582A VAL* 4.1 13.0 - - + +
583A ASN* 5.7 0.2 - - - +
585A SER* 3.3 34.3 - - - +
586A SER* 3.4 29.9 - - - -
589A VAL* 4.6 6.5 - - + -
592A MET* 4.9 7.0 - - + -
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Residues in contact with GLN 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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171A ARG* 4.6 9.3 - - - +
284A SER 4.6 4.4 + - - +
285A ASN* 3.2 44.2 + - - +
286A PHE* 4.0 8.3 + - - +
288A GLN* 3.3 41.6 + - - +
391A ALA 3.2 19.2 + - - +
392A LYS* 3.9 8.7 - - - +
394A PHE* 1.3 76.5 - - - +
396A ARG* 1.3 60.6 + - - +
397A GLN* 3.2 5.2 + - - +
586A SER* 5.3 1.1 - - - -
589A VAL* 4.7 18.0 - - + +
593A GLN* 5.1 2.4 + - - -
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Residues in contact with ARG 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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285A ASN* 4.2 27.3 + - + +
392A LYS 3.0 18.9 + - - +
393A LYS* 3.7 8.3 + - - +
394A PHE 3.3 0.4 - - - -
395A GLN* 1.3 75.1 - - - +
397A GLN* 1.3 68.5 + - - +
398A ALA* 3.2 11.8 + - + +
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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