Contacts of the helix formed by residues 365 - 372 (chain D) in PDB entry 5IG3
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 365 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360D ALA* 3.0 23.1 + - - +
363D ASN* 3.4 8.9 - - + +
364D GLY* 1.3 73.1 - - - +
366D PHE* 1.3 60.3 + - - +
367D GLU* 3.4 21.1 + - - +
368D SER* 2.5 32.8 + - - -
369D TYR* 3.2 19.6 + - - +
399D PHE* 4.3 1.1 - - - -
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Residues in contact with PHE 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D GLY 3.3 6.0 + - - +
365D ASP* 1.3 72.1 + - - +
367D GLU* 1.3 56.7 + - - +
369D TYR* 3.9 6.1 - + - -
370D THR* 2.4 60.0 + - + -
392D LEU* 4.0 34.5 - - + -
395D HIS 4.9 0.4 - - - -
396D ARG* 4.0 49.8 - - + -
399D PHE* 3.3 42.8 - + + -
400D GLU* 6.4 1.1 - - + -
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Residues in contact with GLU 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D ASP* 3.2 12.1 + - - +
366D PHE* 1.3 76.8 - - - +
368D SER* 1.3 67.5 + - - +
370D THR* 3.0 8.1 + - - -
371D LYS* 3.0 39.8 + - + +
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Residues in contact with SER 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D ALA* 4.4 10.8 - - - -
365D ASP* 2.5 28.3 + - - -
367D GLU* 1.3 78.4 - - - +
369D TYR* 1.3 61.4 + - - +
371D LYS* 3.2 10.4 + - - +
372D MET* 3.1 35.6 + - - +
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Residues in contact with TYR 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357D LEU* 3.6 30.7 - - + -
360D ALA* 4.3 2.9 - - + +
361D ILE* 3.6 30.8 - - + +
365D ASP 3.2 18.4 + - - +
366D PHE* 3.8 7.4 - + - +
367D GLU 3.2 0.8 - - - -
368D SER* 1.3 79.4 - - - +
370D THR* 1.3 62.0 + - - +
372D MET* 3.3 14.5 + - - +
373D CYS* 3.3 39.5 - - - -
377D MET* 3.6 21.9 - - - +
392D LEU* 3.8 18.8 - - + -
395D HIS* 3.8 27.3 - + + -
399D PHE* 3.4 29.6 - + + -
453D ARG* 4.6 5.8 + - - -
467D PHE* 5.0 0.5 - - - -
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Residues in contact with THR 370 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366D PHE* 2.4 52.1 + - + -
367D GLU* 3.0 6.9 + - - -
369D TYR* 1.3 76.9 - - - +
371D LYS* 1.3 68.3 + - + +
373D CYS 3.1 19.8 - - - +
392D LEU* 3.7 22.2 - - + +
463D GLN* 5.1 0.2 + - - -
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Residues in contact with LYS 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D GLU* 3.0 34.4 + - + +
368D SER* 3.2 10.7 + - - +
370D THR* 1.3 82.0 - - + +
372D MET* 1.3 56.8 + - + +
461D LYS* 3.3 20.7 - - - +
463D GLN* 3.0 26.6 + - - +
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Residues in contact with MET 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D VAL* 3.9 21.3 - - + +
356D GLN* 3.8 14.8 - - - +
357D LEU* 3.6 44.0 - - + -
360D ALA* 3.7 20.6 - - + -
368D SER* 3.1 29.0 + - - +
369D TYR* 3.8 7.9 - - - +
370D THR 3.2 0.4 - - - -
371D LYS* 1.3 77.6 - - + +
373D CYS* 1.3 58.0 + - - +
455D TRP* 3.7 11.0 - - + -
461D LYS* 4.3 15.7 - - - +
462D TRP 4.6 1.8 - - - +
463D GLN* 3.3 10.8 - - - -
464D ILE* 3.0 22.2 + - - +
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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